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Sample records for mercury-alkali molecules orbital-driven

  1. Orbital driven impurity spin effect on the magnetic order of quasi-3D cupric oxide

    NASA Astrophysics Data System (ADS)

    Ganga, B. G.; Santhosh, P. N.; Nanda, B. R. K.

    2017-04-01

    Density functional calculations are performed to study the magnetic order of the severely distorted square planar cupric oxide (CuO) and local spin disorder in it in the presence of the transition metal impurities M (=Cr, Mn, Fe, Co and Ni). The distortion in the crystal structure, arisen to reduce the band energy by minimizing the covalent interaction, creates two crisscrossing zigzag spin-1/2 chains. From the spin dimer analysis we find that while the spin chain along ≤ft[1 0 \\bar{1}\\right] has strong Heisenberg type antiferromagnetic coupling (J ~ 127 meV), along ≤ft[1 0 1\\right] it exhibits weak, but robust, ferromagnetic coupling (J ~ 9 meV) mediated by reminiscent p-d covalent interactions. The impurity effect on the magnetic ordering is independent of M and purely orbital driven. If the given spin-state of M is such that the {{d}{{x2}-{{y}2}}} orbital is spin-polarized, then the original long-range ordering is maintained. However, if {{d}{{x2}-{{y}2}}} orbital is unoccupied, the absence of corresponding covalent interaction breaks the weak ferromagnetic coupling and a spin-flip takes place at the impurity site leading to breakdown of the long range magnetic ordering.

  2. Orbital driven impurity spin effect on the magnetic order of quasi-3D cupric oxide.

    PubMed

    Ganga, B G; Santhosh, P N; Nanda, B R K

    2017-04-20

    Density functional calculations are performed to study the magnetic order of the severely distorted square planar cupric oxide (CuO) and local spin disorder in it in the presence of the transition metal impurities M (=Cr, Mn, Fe, Co and Ni). The distortion in the crystal structure, arisen to reduce the band energy by minimizing the covalent interaction, creates two crisscrossing zigzag spin-1/2 chains. From the spin dimer analysis we find that while the spin chain along [Formula: see text] has strong Heisenberg type antiferromagnetic coupling (J ~ 127 meV), along [Formula: see text] it exhibits weak, but robust, ferromagnetic coupling (J ~ 9 meV) mediated by reminiscent p-d covalent interactions. The impurity effect on the magnetic ordering is independent of M and purely orbital driven. If the given spin-state of M is such that the [Formula: see text] orbital is spin-polarized, then the original long-range ordering is maintained. However, if [Formula: see text] orbital is unoccupied, the absence of corresponding covalent interaction breaks the weak ferromagnetic coupling and a spin-flip takes place at the impurity site leading to breakdown of the long range magnetic ordering.

  3. Orbitally driven low thermal conductivity of monolayer gallium nitride (GaN) with planar honeycomb structure: a comparative study.

    PubMed

    Qin, Zhenzhen; Qin, Guangzhao; Zuo, Xu; Xiong, Zhihua; Hu, Ming

    2017-03-23

    Two-dimensional (2D) materials with graphene as a representative have been intensively studied for a long time. Recently, monolayer gallium nitride (ML GaN) with honeycomb structure was successfully fabricated in experiments, generating enormous research interest for its promising applications in nano- and opto-electronics. Considering all these applications are inevitably involved with thermal transport, systematic investigation of the phonon transport properties of 2D GaN is in demand. In this paper, by solving the Boltzmann transport equation (BTE) based on first-principles calculations, we performed a comprehensive study of the phonon transport properties of ML GaN, with detailed comparison to bulk GaN, 2D graphene, silicene and ML BN with similar honeycomb structure. Considering the similar planar structure of ML GaN to graphene, it is quite intriguing to find that the thermal conductivity (κ) of ML GaN (14.93 W mK(-1)) is more than two orders of magnitude lower than that of graphene and is even lower than that of silicene with a buckled structure. Systematic analysis is performed based on the study of the contribution from phonon branches, comparison among the mode level phonon group velocity and lifetime, the detailed process and channels of phonon-phonon scattering, and phonon anharmonicity with potential energy well. We found that, different from graphene and ML BN, the phonon-phonon scattering selection rule in 2D GaN is slightly broken by the lowered symmetry due to the large difference in the atomic radius and mass between Ga and N atoms. Further deep insight is gained from the electronic structure. Resulting from the special sp orbital hybridization mediated by the Ga-d orbital in ML GaN, the strongly polarized Ga-N bond, localized charge density, and its inhomogeneous distribution induce large phonon anharmonicity and lead to the intrinsic low κ of ML GaN. The orbitally driven low κ of ML GaN unraveled in this work would make 2D GaN prospective for

  4. Molecule nanoweaver

    DOEpatents

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    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.

  5. Interstellar Molecules

    ERIC Educational Resources Information Center

    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)

  6. Modeling Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    The molecule modeling method known as Multibody Order (N) Dynamics, or MBO(N)D, was developed by Moldyn, Inc. at Goddard Space Flight Center through funding provided by the SBIR program. The software can model the dynamics of molecules through technology which stimulates low-frequency molecular motions and properties, such as movements among a molecule's constituent parts. With MBO(N)D, a molecule is substructured into a set of interconnected rigid and flexible bodies. These bodies replace the computation burden of mapping individual atoms. Moldyn's technology cuts computation time while increasing accuracy. The MBO(N)D technology is available as Insight II 97.0 from Molecular Simulations, Inc. Currently the technology is used to account for forces on spacecraft parts and to perform molecular analyses for pharmaceutical purposes. It permits the solution of molecular dynamics problems on a moderate workstation, as opposed to on a supercomputer.

  7. Mobius Molecules

    ERIC Educational Resources Information Center

    Eckert, J. M.

    1973-01-01

    Discusses formation of chemical molecules via Mobius strip intermediates, and concludes that many special physics-chemical properties of the fully closed circular form (1) of polyoma DNA are explainable by this topological feature. (CC)

  8. Enumerating molecules.

    SciTech Connect

    Visco, Donald Patrick, Jr.; Faulon, Jean-Loup Michel; Roe, Diana C.

    2004-04-01

    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  9. Mind Molecules

    PubMed Central

    Snyder, Solomon H.

    2011-01-01

    Scientific styles vary tremendously. For me, research is largely about the unfettered pursuit of novel ideas and experiments that can test multiple ideas in a day, not a year, an approach that I learned from my mentor Julius “Julie” Axelrod. This focus on creative conceptualizations has been my métier since working in the summers during medical school at the National Institutes of Health, during my two years in the Axelrod laboratory, and throughout my forty-five years at Johns Hopkins University School of Medicine. Equally important has been the “high” that emerges from brainstorming with my students. Nothing can compare with the eureka moments when, together, we sense new insights and, better yet, when high-risk, high-payoff experiments succeed. Although I have studied many different questions over the years, a common theme emerges: simple biochemical approaches to understanding molecular messengers, usually small molecules. Equally important has been identifying, purifying, and cloning the messengers' relevant biosynthetic, degradative, or target proteins, at all times seeking potential therapeutic relevance in the form of drugs. In the interests of brevity, this Reflections article is highly selective, and, with a few exceptions, literature citations are only of findings of our laboratory that illustrate notable themes. PMID:21543333

  10. Orbital-driven nematicity in FeSe.

    PubMed

    Baek, S-H; Efremov, D V; Ok, J M; Kim, J S; van den Brink, Jeroen; Büchner, B

    2015-02-01

    A fundamental and unconventional characteristic of superconductivity in iron-based materials is that it occurs in the vicinity of two other instabilities. In addition to a tendency towards magnetic order, these Fe-based systems have a propensity for nematic ordering: a lowering of the rotational symmetry while time-reversal invariance is preserved. Setting the stage for superconductivity, it is heavily debated whether the nematic symmetry breaking is driven by lattice, orbital or spin degrees of freedom. Here, we report a very clear splitting of NMR resonance lines in FeSe at Tnem = 91 K, far above the superconducting Tc of 9.3 K. The splitting occurs for magnetic fields perpendicular to the Fe planes and has the temperature dependence of a Landau-type order parameter. Spin-lattice relaxation rates are not affected at Tnem, which unequivocally establishes orbital degrees of freedom as driving the nematic order. We demonstrate that superconductivity competes with the emerging nematicity.

  11. Orbitally-driven giant phonon anharmonicity in SnSe

    SciTech Connect

    Li, Chen W.; Hong, Jiawang; May, Andrew F.; Bansal, Dipanshu; Chi, Songxue; Hong, Tao; Ehlers, Georg; Delaire, Olivier A.

    2015-10-19

    We understand that elementary excitations and their couplings in condensed matter systems is critical to develop better energy-conversion devices. In thermoelectric materials, the heat-to-electricity conversion efficiency is directly improved by suppressing the propagation of phonon quasiparticles responsible for macroscopic thermal transport. The material with the current record for thermoelectric conversion efficiency, SnSe, achieves an ultra-low thermal conductivity, but the mechanism enabling this strong phonon scattering remains largely unknown. Using inelastic neutron scattering measurements and first-principles simulations, we mapped the four-dimensional phonon dispersion surfaces of SnSe, and revealed the origin of ionic-potential anharmonicity responsible for the unique properties of SnSe. We show that the giant phonon scattering arises from an unstable electronic structure, with orbital interactions leading to a ferroelectric-like lattice instability. Our results provide a microscopic picture connecting electronic structure and phonon anharmonicity in SnSe, and offers precious insights on how electron-phonon and phononphonon interactions may lead to the realization of ultra-low thermal conductivity.

  12. Orbitally-driven giant phonon anharmonicity in SnSe

    DOE PAGES

    Li, Chen W.; Hong, Jiawang; May, Andrew F.; ...

    2015-10-19

    We understand that elementary excitations and their couplings in condensed matter systems is critical to develop better energy-conversion devices. In thermoelectric materials, the heat-to-electricity conversion efficiency is directly improved by suppressing the propagation of phonon quasiparticles responsible for macroscopic thermal transport. The material with the current record for thermoelectric conversion efficiency, SnSe, achieves an ultra-low thermal conductivity, but the mechanism enabling this strong phonon scattering remains largely unknown. Using inelastic neutron scattering measurements and first-principles simulations, we mapped the four-dimensional phonon dispersion surfaces of SnSe, and revealed the origin of ionic-potential anharmonicity responsible for the unique properties of SnSe. Wemore » show that the giant phonon scattering arises from an unstable electronic structure, with orbital interactions leading to a ferroelectric-like lattice instability. Our results provide a microscopic picture connecting electronic structure and phonon anharmonicity in SnSe, and offers precious insights on how electron-phonon and phononphonon interactions may lead to the realization of ultra-low thermal conductivity.« less

  13. Physics of Molecules

    NASA Astrophysics Data System (ADS)

    Williams, D.; Murdin, P.

    2000-11-01

    Many varieties of molecule have been detected in the Milky Way and in other galaxies. The processes by which these molecules are formed and destroyed are now broadly understood (see INTERSTELLAR CHEMISTRY). These molecules are important components of galaxies in two ways. Firstly, radiation emitted by molecules enables us to trace the presence of diffuse gas, to infer its physical properties and ...

  14. Formation of Ultracold Molecules

    SciTech Connect

    Cote, Robin

    2016-01-28

    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  15. [Endothelial cell adhesion molecules].

    PubMed

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  16. Enzymatic DNA molecules

    NASA Technical Reports Server (NTRS)

    Joyce, Gerald F. (Inventor); Breaker, Ronald R. (Inventor)

    1998-01-01

    The present invention discloses deoxyribonucleic acid enzymes--catalytic or enzymatic DNA molecules--capable of cleaving nucleic acid sequences or molecules, particularly RNA, in a site-specific manner, as well as compositions including same. Methods of making and using the disclosed enzymes and compositions are also disclosed.

  17. Molecules between the Stars.

    ERIC Educational Resources Information Center

    Verschuur, Gerrit L.

    1987-01-01

    Provides a listing of molecules discovered to date in the vast interstellar clouds of dust and gas. Emphasizes the recent discoveries of organic molecules. Discusses molecular spectral lines, MASERs (microwave amplification by stimulated emission of radiation), molecular clouds, and star birth. (TW)

  18. Porous organic molecules

    NASA Astrophysics Data System (ADS)

    Holst, James R.; Trewin, Abbie; Cooper, Andrew I.

    2010-11-01

    Most synthetic materials that show molecular-scale porosity consist of one-, two- or three-dimensional networks. Porous metal-organic frameworks in particular have attracted a lot of recent attention. By contrast, discrete molecules tend to pack efficiently in the solid state, leaving as little empty space as possible, which leads to non-porous materials. This Perspective discusses recent developments with discrete organic molecules that are porous in the solid state. Such molecules, which may be either crystalline or amorphous, can be categorized as either intrinsically porous (containing permanent covalent cavities) or extrinsically porous (inefficiently packed). We focus on the possible advantages of organic molecules over inorganic or hybrid systems in terms of molecular solubility, choice of components and functionalities, and structural mobility and responsiveness in non-covalent extended solids. We also highlight the potential for 'undiscovered' porous systems among the large number of cage-like organic molecules that are already known.

  19. Dynamics of Activated Molecules

    SciTech Connect

    Mullin, Amy S.

    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.

  20. Of Molecules and Models.

    ERIC Educational Resources Information Center

    Brinner, Bonnie

    1992-01-01

    Presents an activity in which models help students visualize both the DNA process and transcription. After constructing DNA, RNA messenger, and RNA transfer molecules; students model cells, protein synthesis, codons, and RNA movement. (MDH)

  1. Positronium ions and molecules

    NASA Technical Reports Server (NTRS)

    Ho, Y. K.

    1990-01-01

    Recent theoretical studies on positronium ions and molecules are discussed. A positronium ion is a three particle system consisting of two electrons in singlet spin state, and a positron. Recent studies include calculations of its binding energy, positron annihilation rate, and investigations of its doubly excited resonant states. A positronium molecule is a four body system consisting of two positrons and two electrons in an overall singlet spin state. The recent calculations of its binding energy against the dissociation into two positronium atoms, and studies of auto-detaching states in positronium molecules are discussed. These auto-dissociating states, which are believed to be part of the Rydberg series as a result of a positron attaching to a negatively charged positronium ion, Ps-, would appear as resonances in Ps-Ps scattering.

  2. Single-Molecule Bioelectronics

    PubMed Central

    Rosenstein, Jacob K.; Lemay, Serge G.; Shepard, Kenneth L.

    2014-01-01

    Experimental techniques which interface single biomolecules directly with microelectronic systems are increasingly being used in a wide range of powerful applications, from fundamental studies of biomolecules to ultra-sensitive assays. Here we review several technologies which can perform electronic measurements of single molecules in solution: ion channels, nanopore sensors, carbon nanotube field-effect transistors, electron tunneling gaps, and redox cycling. We discuss the shared features among these techniques that enable them to resolve individual molecules, and discuss their limitations. Recordings from each of these methods all rely on similar electronic instrumentation, and we discuss the relevant circuit implementations and potential for scaling these single-molecule bioelectronic interfaces to high-throughput arrayed sensing platforms. PMID:25529538

  3. MOLECULES IN {eta} CARINAE

    SciTech Connect

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf; Zapata, Luis A.; Rodriguez, Luis F.

    2012-04-10

    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  4. Polarization of deuterium molecules

    SciTech Connect

    J. F. J. van den Brand; H. J. Bulten; M. Ferro-Luzzi; Z.-L. Zhou; Ricardo Alarcon; T. Botto; M. Bouwhuis; Rolf Ent; Peter Heimberg; Douglas W. Higinbotham; Kees de Jager; J. Lang; D. J. de Lange; I. Passchier; H. R. Poolman; J. J. M. Steijger; O. Unal; H. de Vries

    1997-08-01

    For molecular systems, spin relaxation is expected to be suppressed compared to the case of atoms, since the paired electrons in a hydrogen or deuterium molecule are chemically stable, and only weakly interact with the spin of the nucleus. Such systems would be largely insensitive to polarization losses due to spin-exchange collisions, to the interaction of the electron spins with external fields (e.g. the RF-field of a bunched charged-particle beam), and/or to the presence of container walls. Here, we discuss the results of a recent experiment where we obtained evidence that nuclear polarization is maintained, when polarized atoms recombine to molecules on a copper surface (in a magnetic field of 23 mT and at a density of about 10{sup 12} molecules {center_dot} cm{sup -3}).

  5. Single molecule diffraction.

    PubMed

    Spence, J C H; Doak, R B

    2004-05-14

    For solving the atomic structure of organic molecules such as small proteins which are difficult to crystallize, the use of a jet of doped liquid helium droplets traversing a continuous high energy electron beam is proposed as a means of obtaining electron diffraction patterns (serial crystallography). Organic molecules (such as small proteins) within the droplet (and within a vitreous ice jacket) may be aligned by use of a polarized laser beam. Iterative methods for solving the phase problem are indicated. Comparisons with a related plan for pulsed x-ray diffraction from single proteins in a molecular beam are provided.

  6. Enzyme molecules as nanomotors.

    PubMed

    Sengupta, Samudra; Dey, Krishna K; Muddana, Hari S; Tabouillot, Tristan; Ibele, Michael E; Butler, Peter J; Sen, Ayusman

    2013-01-30

    Using fluorescence correlation spectroscopy, we show that the diffusive movements of catalase enzyme molecules increase in the presence of the substrate, hydrogen peroxide, in a concentration-dependent manner. Employing a microfluidic device to generate a substrate concentration gradient, we show that both catalase and urease enzyme molecules spread toward areas of higher substrate concentration, a form of chemotaxis at the molecular scale. Using glucose oxidase and glucose to generate a hydrogen peroxide gradient, we induce the migration of catalase toward glucose oxidase, thereby showing that chemically interconnected enzymes can be drawn together.

  7. Sweeping molecules with light

    NASA Astrophysics Data System (ADS)

    Hutzler, Nicholas R.

    2017-03-01

    Many areas of physics—precision measurements, quantum information, and physical chemistry, to name a few—are starting to benefit from the enormous advantages offered by cold and ultracold polar molecules. Molecules have more states, more interactions, and more chemical properties compared to atoms, which make them exciting to study but difficult to tame. In particular, the powerful techniques of atomic laser cooling cannot be naïvely applied to molecules due to their complicated structure. Developments over the past few years have made directly laser cooled and trapped molecules a reality, and now much effort is focused on making these samples larger, denser, and colder—an important step to realizing many of their exciting applications. A careful experimental and numerical study by Truppe et al (2017 New J. Phys. 19 022001) demonstrates a significant improvement and advance in understanding of one of the most limiting steps in laser cooling and trapping of molecules—slowing them from a molecular beam to a near-standstill, with small enough kinetic energy that they can be loaded into a trap.

  8. Disentangling DNA molecules.

    PubMed

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  9. Diversity in Biological Molecules

    ERIC Educational Resources Information Center

    Newbury, H. John

    2010-01-01

    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  10. Mighty Molecule Models

    ERIC Educational Resources Information Center

    Brown, Tom; Rushton, Greg; Bencomo, Marie

    2008-01-01

    As part of the SMATHematics Project: The Wonder of Science, The Power of Mathematics--a collaborative partnership between Kennesaw State University and two local school districts, fifth graders had the opportunity to puzzle out chemical formulas of propane, methanol, and other important molecules. In addition, they explored properties that…

  11. Algebraic theory of molecules

    NASA Technical Reports Server (NTRS)

    Iachello, Franco

    1995-01-01

    An algebraic formulation of quantum mechanics is presented. In this formulation, operators of interest are expanded onto elements of an algebra, G. For bound state problems in nu dimensions the algebra G is taken to be U(nu + 1). Applications to the structure of molecules are presented.

  12. Single molecules: Thermodynamic limits

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    2012-09-01

    Technologies aimed at single-molecule resolution of non-equilibrium systems increasingly require sophisticated new ways of thinking about thermodynamics. An elegant extension to standard fluctuation theory grants access to the kinetic intermediate states of these systems -- as DNA-pulling experiments now demonstrate.

  13. Disentangling DNA molecules

    NASA Astrophysics Data System (ADS)

    Vologodskii, Alexander

    2016-09-01

    The widespread circular form of DNA molecules inside cells creates very serious topological problems during replication. Due to the helical structure of the double helix the parental strands of circular DNA form a link of very high order, and yet they have to be unlinked before the cell division. DNA topoisomerases, the enzymes that catalyze passing of one DNA segment through another, solve this problem in principle. However, it is very difficult to remove all entanglements between the replicated DNA molecules due to huge length of DNA comparing to the cell size. One strategy that nature uses to overcome this problem is to create the topoisomerases that can dramatically reduce the fraction of linked circular DNA molecules relative to the corresponding fraction at thermodynamic equilibrium. This striking property of the enzymes means that the enzymes that interact with DNA only locally can access their topology, a global property of circular DNA molecules. This review considers the experimental studies of the phenomenon and analyzes the theoretical models that have been suggested in attempts to explain it. We describe here how various models of enzyme action can be investigated computationally. There is no doubt at the moment that we understand basic principles governing enzyme action. Still, there are essential quantitative discrepancies between the experimental data and the theoretical predictions. We consider how these discrepancies can be overcome.

  14. Three new 'nonterrestrial' molecules

    NASA Astrophysics Data System (ADS)

    Thaddeus, P.; Guelin, M.; Linke, R. A.

    1981-05-01

    Eight new interstellar lines have been detected from three molecules not previously observed spectroscopically in space or in the laboratory. One is a linear or nearly linear molecule with microwave constants B0 equals 21,337.15 plus or minus 0.06 MHz, D0 equals 21.4 plus or minus 1.5 kHz. This is the thioformyl ion HCS(plus), first identified because B0 and D0 are close to those calculated, and now confirmed by laboratory detection of one of the present lines (Gudeman et al.). The second molecule, also linear or nearly so, has microwave constants B0 equals 10,691,406 plus or minus 0.043 MHz, D0 equals 1.84 plus or minus 0.91 kHz close to those expected for the isoelectronic systems HOCO(plus) and HOCN; a choice between the two cannot be made on the basis of the available astronomical data. The existence of a third molecule is deduced from an unidentified line at 85,338 MHz that has been found in many sources, is fairly intense in several, and may be self-absorbed in Sgr B2.

  15. OMG: Open Molecule Generator.

    PubMed

    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.

  16. Bacterial invasion reconstructed molecule by molecule

    SciTech Connect

    Werner, James H

    2009-01-01

    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the point of

  17. Molecules in Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Berdyugina, Svetlana

    2015-08-01

    Molecules probe cool matter in the Universe and various astrophysical objects. Their ability to sense magnetic fields provides new insights into magnetic properties of these objects. During the past fifteen years we have carried out a theoretical study of molecular magnetic effects such as the Zeeman, Paschen-Back and Hanle effects and their applications for inferring magnetic structures and spatial inhomogeneities on the Sun, cool stars, brown dwarfs, and exoplanets from molecular spectro-polarimetry (e.g., Berdyugina 2011). Here, we present an overview of this study and compare our theoretical predictions with recent laboratory measurements of magnetic properties of some molecules. We present also a new web-based tool to compute molecular magnetic effects and polarized spectra which is supported by the ERC Advanced Grant HotMol.

  18. Strange skyrmion molecules

    NASA Astrophysics Data System (ADS)

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-01

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  19. Strange skyrmion molecules

    SciTech Connect

    Kopeliovich, Vladimir B.; Stern, Boris E.

    1997-05-20

    Composed skyrmions with B=2, strangeness content close to 0.5 and the binding energy of several tens of Mev are described. These skyrmions are obtained starting from the system of two B=1 hedgehogs located in different SU(2) subgroups of SU(3) and have the mass and baryon number distribution of molecular (dipole) type. The quantization of zero modes of skyrmion molecules and physics consequences of their existence are discussed.

  20. Model molecules mimicking asphaltenes.

    PubMed

    Sjöblom, Johan; Simon, Sébastien; Xu, Zhenghe

    2015-04-01

    Asphalthenes are typically defined as the fraction of petroleum insoluble in n-alkanes (typically heptane, but also hexane or pentane) but soluble in toluene. This fraction causes problems of emulsion formation and deposition/precipitation during crude oil production, processing and transport. From the definition it follows that asphaltenes are not a homogeneous fraction but is composed of molecules polydisperse in molecular weight, structure and functionalities. Their complexity makes the understanding of their properties difficult. Proper model molecules with well-defined structures which can resemble the properties of real asphaltenes can help to improve this understanding. Over the last ten years different research groups have proposed different asphaltene model molecules and studied them to determine how well they can mimic the properties of asphaltenes and determine the mechanisms behind the properties of asphaltenes. This article reviews the properties of the different classes of model compounds proposed and present their properties by comparison with fractionated asphaltenes. After presenting the interest of developing model asphaltenes, the composition and properties of asphaltenes are presented, followed by the presentation of approaches and accomplishments of different schools working on asphaltene model compounds. The presentation of bulk and interfacial properties of perylene-based model asphaltene compounds developed by Sjöblom et al. is the subject of the next part. Finally the emulsion-stabilization properties of fractionated asphaltenes and model asphaltene compounds is presented and discussed.

  1. Single Molecule Mechanochemistry

    NASA Astrophysics Data System (ADS)

    Li, Shaowei; Zhang, Yanxing; Ho, Wilson; Wu, Ruqian; Ruqian Wu, Yanxing Zhang Team; Wilson Ho, Shaowei Li Team

    Mechanical forces can be used to trigger chemical reactions through bending and stretching of chemical bonds. Using the reciprocating movement of the tip of a scanning tunneling microscope (STM), mechanical energy can be provided to a single molecule sandwiched between the tip and substrate. When the mechanical pulse center was moved to the outer ring feature of a CO molecule, the reaction rate was significantly increased compared with bare Cu surface and over Au atoms. First, DFT calculations show that the presence of CO makes the Cu cavity more attractive toward H2 Second, H2 prefers the horizontal adsorption geometry in the Cu-Cu and Au-Cu cavities and no hybridization occurs between the antibonding states of H2 and states of Cu atoms. While H2 loses electrons from its bonding state in all three cavities, the filling of its anti-bonding state only occurs in the CO-Cu cavity. Both make the CO-Cu cavity much more effectively to chop the H2 molecule. Work was supported by the National Science Foundation Center for Chemical Innovation on Chemistry at the Space-Time Limit (CaSTL) under Grant No. CHE-1414466.

  2. Photonic Molecule Lasers Revisited

    NASA Astrophysics Data System (ADS)

    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.

  3. Negative ions of polyatomic molecules.

    PubMed Central

    Christophorou, L G

    1980-01-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies. PMID:7428744

  4. Negative ions of polyatomic molecules.

    PubMed

    Christophorou, L G

    1980-06-01

    In this paper general concepts relating to, and recent advances in, the study of negative ions of polyatomic molecules area discussed with emphasis on halocarbons. The topics dealt with in the paper are as follows: basic electron attachment processes, modes of electron capture by molecules, short-lived transient negative ions, dissociative electron attachment to ground-state molecules and to "hot" molecules (effects of temperature on electron attachment), parent negative ions, effect of density, nature, and state of the medium on electron attachment, electron attachment to electronically excited molecules, the binding of attached electrons to molecules ("electron affinity"), and the basic and the applied significance of negative-ion studies.

  5. Watching single molecules dance

    NASA Astrophysics Data System (ADS)

    Mehta, Amit Dinesh

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

  6. Molecules in crystals

    NASA Astrophysics Data System (ADS)

    Spackman, Mark A.

    2013-04-01

    Hirshfeld surface analysis has developed from the serendipitous discovery of a novel partitioning of the crystal electron density into discrete molecular fragments, to a suite of computational tools used widely for the identification, analysis and discussion of intermolecular interactions in molecular crystals. The relationship between the Hirshfeld surface and very early ideas on the internal structure of crystals is outlined, and applications of Hirshfeld surface analysis are presented for three molecules of historical importance in the development of modern x-ray crystallography: hexamethylbenzene, hexamethylenetetramine and diketopiperazine.

  7. Ultra-cold molecule production.

    SciTech Connect

    Ramirez-Serrano, Jamie; Chandler, David W.; Strecker, Kevin; Rahn, Larry A.

    2005-12-01

    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.

  8. Covalent Chemistry beyond Molecules.

    PubMed

    Jiang, Juncong; Zhao, Yingbo; Yaghi, Omar M

    2016-03-16

    Linking molecular building units by covalent bonds to make crystalline extended structures has given rise to metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), thus bringing the precision and versatility of covalent chemistry beyond discrete molecules to extended structures. The key advance in this regard has been the development of strategies to overcome the "crystallization problem", which is usually encountered when attempting to link molecular building units into covalent solids. Currently, numerous MOFs and COFs are made as crystalline materials in which the large size of the constituent units provides for open frameworks. The molecular units thus reticulated become part of a new environment where they have (a) lower degrees of freedom because they are fixed into position within the framework; (b) well-defined spatial arrangements where their properties are influenced by the intricacies of the pores; and (c) ordered patterns onto which functional groups can be covalently attached to produce chemical complexity. The notion of covalent chemistry beyond molecules is further strengthened by the fact that covalent reactions can be carried out on such frameworks, with full retention of their crystallinity and porosity. MOFs are exemplars of how this chemistry has led to porosity with designed metrics and functionality, chemically-rich sequences of information within their frameworks, and well-defined mesoscopic constructs in which nanoMOFs enclose inorganic nanocrystals and give them new levels of spatial definition, stability, and functionality.

  9. Dihydrino molecule identification

    SciTech Connect

    Mills, R.L.; Good, W.R. ); Shaubach, R.M. )

    1994-01-01

    Three sets of heat production and [open quotes]ash[close quotes] identification data are presented. An exothermic reaction is reported wherein the electrons of hydrogen and deuterium atoms are stimulated to relax to quantized potential energy levels below that of the [open quotes]ground state[close quotes] via electrochemical reactants K[sup +] and K[sup +]; Pd[sup 2+] and Li[sup +]; or Pd and O[sub 2] of redox energy resonant with the energy hole that stimulates this transition. Calorimetry of pulsed current and continuous electrolysis of aqueous potassium carbonate (K[sup +]/K[sup +] electrocatalytic couple) at a nickel cathode were performed. The excess output power of 41 W exceeded by a factor >8 the total input power given by the product of the electrolysis voltage and current. The product of the exothermic reaction is atoms having electrons of energy below the ground state, which are predicted to form molecules. The predicted molecules were identified by their lack of reactivity with oxygen, by separation from molecular deuterium by cryofiltration, and by mass spectroscopic analysis. 15 refs., 12 figs., 9 tabs.

  10. Molecules Best Paper Award 2013.

    PubMed

    McPhee, Derek J

    2013-02-05

    Molecules has started to institute a "Best Paper" award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the second "Molecules Best Paper Award" for 2013.

  11. Biochips - Can molecules compute?

    NASA Astrophysics Data System (ADS)

    Tucker, J. B.

    1984-02-01

    In recent years the possibility has been considered to build 'biochip' computers, in which the silicon transistors of present machines would be replaced by large organic molecules or genetically engineered proteins. Two major advantages of such biochips over current devices would be related to vastly increased densities of computing elements, and entirely new styles of data processing, suited to such high-level tasks as pattern recognition and context-dependent analysis. The limitations of the semiconductor chip with respect to the density of elementary units due to size considerations and heat development could be overcome by making use of molecular switches. Attention is given to soliton switching, soliton logic, bulk molecular devices, analog biochips, 'intelligent' switches based on the employment of enzymes, robot vision, questions of biochip fabrication, protein engineering, and a strategy for the development of biochips.

  12. Molecules in the Spotlight

    SciTech Connect

    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.

  13. Fiber-mesh photonic molecule

    NASA Astrophysics Data System (ADS)

    Mishra, Subodha; Satpathy, Sashi

    2008-03-01

    Analogous to the photonic crystal, we introduce the concept of a fiber-mesh photonic molecule made up of optical fibers and study its transmission characteristics. We consider a specific example of a photonic molecule, inspired by the well-known C60 molecule, with the arms of the molecule formed out of single-moded optical fibers. The transmittance consists of sharp peaks determined by the pole structure of the scattering matrix in the complex energy plane. A molecule can be designed to control the positions and the widths of the transmission peaks, opening up the possibility of building new photonic devices such as high quality band-pass filters.

  14. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    DOEpatents

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  15. Organic Molecules in Meteorites

    NASA Astrophysics Data System (ADS)

    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 (<30%) consists of a rich organic inventory of soluble organic compounds, including key compounds important in terrestrial biochemistry [2-4]. Different carbonaceous 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

  16. Electron-excited molecule interactions

    SciTech Connect

    Christophorou, L.G. Tennessee Univ., Knoxville, TN . Dept. of Physics)

    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{sup 6} to 10{sup 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.

  17. Electrochromic Graphene Molecules

    DOE PAGES

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were foundmore » to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.« less

  18. Single molecule tracking

    DOEpatents

    Shera, E.B.

    1987-10-07

    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. Photons 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. 3 figs.

  19. Single molecule tracking

    DOEpatents

    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.

  20. Atmospheric trace molecule spectroscopy

    NASA Technical Reports Server (NTRS)

    Farmer, C. B.

    1982-01-01

    The Spacelab investigation entitled Atmospheric Trace Molecule Spectroscopy (ATMOS) is designed to obtain fundamental information related to the chemistry and physics of the Earth's upper atmosphere using the techniques of infrared absorption spectroscopy. There are two principal objectives to be met. The first is the determination, on a global scale, of the compositional structure of the upper atmosphere and its spatial variability. The establishment of this variability represents the first step toward determining the characteristic residence times for the upper atmospheric constituents; the magnitudes of their sources and sinks; and, ultimately, an understanding of their effects on the stability of the stratosphere. The second objective is to provide the high-resolution, calibrated spectral information which is essential for the detailed design of advanced instrumentation for subsequent global monitoring of specific species found to be critical to atmospheric stability. This information will be disseminated in the form of a three dimensional atlas of solar absorption spectra obtained over a range of latitudes, longitudes, and altitudes.

  1. Vibrational autoionization in polyatomic molecules.

    PubMed

    Pratt, S T

    2005-01-01

    The vibrationally autoionizing Rydberg states of small polyatomic molecules provide a fascinating laboratory in which to study fundamental nonadiabatic processes. In this review, recent results on the vibrational mode dependence of vibrational autoionization are discussed. In general, autoionization rates depend strongly on the character of the normal mode driving the process and on the electronic character of the Rydberg electron. Although quantitative calculations based on multichannel quantum defect theory are available for some polyatomic molecules, including H3, only qualitative information exists for most molecules. This review shows how qualitative information, such as Walsh diagrams along different normal coordinates of the molecule, can provide insight into the vibrational autoionization rates.

  2. Electrical Transport through Organic Molecules

    NASA Astrophysics Data System (ADS)

    Lau, C. N.; Chang, Shun-Chi; Williams, Stan

    2003-03-01

    We investigate electrical transport properties of single organic molecules using electromigration break junctions[1]. A self-assembled monolayer of various organic molecules such as 1,4-di(phenylethynyl-4'-methanethiol)benzene was grown on narrow metal wires, and single or a few molecules were incorporated into the junctions which were created by applying a large voltage and breaking the wires. The transport properties of these molecules were then measured at low temperatures. Latest experimental results will be discussed. [1] Park, J. et al, Nature, 417, 722 (2002); Liang W. et al, Nature, 417, 725 (2002).

  3. Electrochromic Graphene Molecules

    SciTech Connect

    Ji, Zhiqiang; Doorn, Stephen K.; Sykora, Milan

    2015-03-13

    Polyclic aromatic hydrocarbons, also called Graphene Molecules (GMs), with chemical composition C132H36(COOH)2 were synthesized in-situ on the surface of transparent nanocrystaline indium tin oxide (nc-ITO) electrodes. Their electronic structure was studied electrochemically and spectro-electrochemically. Variations in the potential applied onto the nc-ITO/GM electrodes induce only small changes in the observed current but they produce dramatic changes in the absorption of the GMs, which are associated with their oxidation and reduction. Analysis of the absorption changes using modified Nernst equation is used to determine standard potentials associated with the individual charge transfer processes. For the GMs prepared here these were found to be E1,ox 0 = 0.77± 0.01 V and E2,ox 0 = 1.24 ± 0.02 V vs. NHE for the first and second oxidation and E1,red 0 = -1.50 ± 0.04 V for the first reduction. The charge transfer processes are found to be non-ideal. The non-ideality factors associated with the oxidation and reduction processes suggest presence of strong interactions between the GM redox centers. Under the conditions of potential cycling GMs show rapid (seconds) color change with high contrast and stability. An electrochromic application is demonstrated wherein the GMs are used as the optically active component.

  4. Loosely-Bound Diatomic Molecules.

    ERIC Educational Resources Information Center

    Balfour, W. J.

    1979-01-01

    Discusses concept of covalent bonding as related to homonuclear diatomic molecules. Article draws attention to the existence of bound rare gas and alkaline earth diatomic molecules. Summarizes their molecular parameters and offers spectroscopic data. Strength and variation with distance of interatomic attractive forces is given. (Author/SA)

  5. Featured Molecules: Sucrose and Vanillin

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-04-01

    The WebWare molecules of the month for April relate to the sense of taste. Apple Fool, the JCE Classroom Activity, mentions sucrose and vanillin and their use as flavorings. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  6. Micro-Kelvin cold molecules.

    SciTech Connect

    Strecker, Kevin E.; Chandler, David W.

    2009-10-01

    We have developed a novel experimental technique for direct production of cold molecules using a combination of techniques from atomic optical and molecular physics and physical chemistry. The ability to produce samples of cold molecules has application in a broad spectrum of technical fields high-resolution spectroscopy, remote sensing, quantum computing, materials simulation, and understanding fundamental chemical dynamics. Researchers around the world are currently exploring many techniques for producing samples of cold molecules, but to-date these attempts have offered only limited success achieving milli-Kelvin temperatures with low densities. This Laboratory Directed Research and Development project is to develops a new experimental technique for producing micro-Kelvin temperature molecules via collisions with laser cooled samples of trapped atoms. The technique relies on near mass degenerate collisions between the molecule of interest and a laser cooled (micro-Kelvin) atom. A subset of collisions will transfer all (nearly all) of the kinetic energy from the 'hot' molecule, cooling the molecule at the expense of heating the atom. Further collisions with the remaining laser cooled atoms will thermally equilibrate the molecules to the micro-Kelvin temperature of the laser-cooled atoms.

  7. Enzyme molecules in solitary confinement.

    PubMed

    Liebherr, Raphaela B; Gorris, Hans H

    2014-09-12

    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. An optical conveyor for molecules.

    PubMed

    Weinert, Franz M; Braun, Dieter

    2009-12-01

    Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.

  9. Single Molecule Electronics and Devices

    PubMed Central

    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

  10. Adhesion molecules in vernal keratoconjunctivitis

    PubMed Central

    El-Asrar, A.; Geboes, K.; Al-Kharashi, S.; Tabbara, K.; Missotten, L.; Desmet, V.

    1997-01-01

    AIMS/BACKGROUND—Adhesion molecules play a key role in the selective recruitment of different leucocyte population to inflammatory sites. The purpose of the present study was to investigate the presence and distribution of adhesion molecules in the conjunctiva of patients with vernal keratoconjunctivitis (VKC).
METHODS—The presence and distribution of adhesion molecules were studied in 14 conjunctival biopsy specimens from seven patients with active VKC and in four normal conjunctival biopsy specimens. We used a panel of specific monoclonal antibodies (mAbs) directed against intercellular adhesion molecule-1 (ICAM-1), intercellular adhesion molecule-3 (ICAM-3), lymphocyte function associated antigen-1 (LFA-1), very late activation antigen-4 (VLA-4), vascular cell adhesion molecule-1 (VCAM-1), and endothelial leucocyte adhesion molecule-1 (ELAM-1). In addition, a panel of mAbs were used to characterise the composition of the inflammatory infiltrate.
RESULTS—In the normal conjunctiva, ICAM-1 was expressed on the vascular endothelium only, LFA-1 and ICAM-3 on epithelial and stromal mononuclear cells , and VLA-4 on stromal mononuclear cells. The expression of VCAM-1 and ELAM-1 was absent. The number of cells expressing adhesion molecules was found to be markedly increased in all VKC specimens. This was concurrent with a heavy inflammatory infiltrate. Strong ICAM-1 expression was induced on the basal epithelial cells, and vascular endothelial cells. Furthermore, ICAM-1 was expressed on stromal mononuclear cells. LFA-1 and ICAM-3 were expressed on the majority of epithelial and stromal infiltrating mononuclear cells. VLA-4 expression was noted on stromal mononuclear cells. Compared with controls, VKC specimens showed significantly more ICAM-3+, LFA-1+, and VLA-4+ cells. VCAM-1 and ELAM-1 were induced on the vascular endothelial cells.
CONCLUSIONS—Increased expression of adhesion molecules may play an important role in the pathogenesis of VKC.

 PMID

  11. Resolving metal-molecule interfaces at single-molecule junctions

    PubMed Central

    Komoto, Yuki; Fujii, Shintaro; Nakamura, Hisao; Tada, Tomofumi; Nishino, Tomoaki; Kiguchi, Manabu

    2016-01-01

    Electronic and structural detail at the electrode-molecule interface have a significant influence on charge transport across molecular junctions. Despite the decisive role of the metal-molecule interface, a complete electronic and structural characterization of the interface remains a challenge. This is in no small part due to current experimental limitations. Here, we present a comprehensive approach to obtain a detailed description of the metal-molecule interface in single-molecule junctions, based on current-voltage (I-V) measurements. Contrary to conventional conductance studies, this I-V approach provides a correlated statistical description of both, the degree of electronic coupling across the metal-molecule interface, and the energy alignment between the conduction orbital and the Fermi level of the electrode. This exhaustive statistical approach was employed to study single-molecule junctions of 1,4-benzenediamine (BDA), 1,4-butanediamine (C4DA), and 1,4-benzenedithiol (BDT). A single interfacial configuration was observed for both BDA and C4DA junctions, while three different interfacial arrangements were resolved for BDT. This multiplicity is due to different molecular adsorption sites on the Au surface namely on-top, hollow, and bridge. Furthermore, C4DA junctions present a fluctuating I-V curve arising from the greater conformational freedom of the saturated alkyl chain, in sharp contrast with the rigid aromatic backbone of both BDA and BDT. PMID:27221947

  12. Relative Sizes of Organic Molecules

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This computer graphic depicts the relative complexity of crystallizing large proteins in order to study their structures through x-ray crystallography. Insulin is a vital protein whose structure has several subtle points that scientists are still trying to determine. Large molecules such as insuline are complex with structures that are comparatively difficult to understand. For comparison, a sugar molecule (which many people have grown as hard crystals in science glass) and a water molecule are shown. These images were produced with the Macmolecule program. Photo credit: NASA/Marshall Space Flight Center (MSFC)

  13. Quantum Transport Through Heterocyclic Molecules

    NASA Astrophysics Data System (ADS)

    Maiti, Santanu K.; Karmakar, S. N.

    We explore electron transport properties in molecular wires made of heterocyclic molecules (pyrrole, furan and thiophene) by using the Green's function technique. Parametric calculations are given based on the tight-binding model to describe the electron transport in these wires. It is observed that the transport properties are significantly influenced by (a) the heteroatoms in the heterocyclic molecules and (b) the molecule-to-electrodes coupling strength. Conductance (g) shows sharp resonance peaks associated with the molecular energy levels in the limit of weak molecular coupling, while they get broadened in the strong molecular coupling limit. These resonances get shifted with the change of the heteroatoms in these heterocyclic molecules. All the essential features of the electron transfer through these molecular wires become much more clearly visible from the study of our current-voltage (I-V) characteristics, and they provide several key information in the study of molecular transport.

  14. Molecule-hugging graphene nanopores

    PubMed Central

    Garaj, Slaven; Liu, Song; Golovchenko, Jene A.; Branton, Daniel

    2013-01-01

    It has recently been recognized that solid-state nanopores in single-atomic-layer graphene membranes can be used to electronically detect and characterize single long charged polymer molecules. We have now fabricated nanopores in single-layer graphene that are closely matched to the diameter of a double-stranded DNA molecule. Ionic current signals during electrophoretically driven translocation of DNA through these nanopores were experimentally explored and theoretically modeled. Our experiments show that these nanopores have unusually high sensitivity (0.65 nA/Å) to extremely small changes in the translocating molecule’s outer diameter. Such atomically short graphene nanopores can also resolve nanoscale-spaced molecular structures along the length of a polymer, but do so with greatest sensitivity only when the pore and molecule diameters are closely matched. Modeling confirms that our most closely matched pores have an inherent resolution of ≤0.6 nm along the length of the molecule. PMID:23836648

  15. Fluorescence Microscopy of Single Molecules

    ERIC Educational Resources Information Center

    Zimmermann, Jan; van Dorp, Arthur; Renn, Alois

    2004-01-01

    The investigation of photochemistry and photophysics of individual quantum systems is described with the help of a wide-field fluorescence microscopy approach. The fluorescence single molecules are observed in real time.

  16. Moving Molecules and Mothball Madness.

    ERIC Educational Resources Information Center

    Strain, John

    1993-01-01

    Describes concrete demonstrations on the states of matter. In the first demonstration, students represent molecules; and, in the second demonstration, moth balls are heated to produce a change of state. (PR)

  17. [Adhesion molecules and diabetes mellitus].

    PubMed

    Urso, C; Hopps, E; Caimi, G

    2010-01-01

    Adhesion molecules play a significant role in leukocyte migration across the endothelium and are also involved in regulating immune system. It is shown that diabetic patients have an increase of soluble adhesion molecules (sICAM-1, sICAM-2, sVCAM-1, sE-selectin, sL-selectin, sP-selectin) considered an integral part of inflammatory state. This inflammation is responsible for the increased cardiovascular risk of these patients. There is a close link between hyperglycemia, oxidative stress, coagulopathy and inflammation and between these factors and the vascular damage. Various studies have showed the potential role of adhesion molecules in the pathogenesis of diabetic vasculopathy. They promote leukocyte recruitment, which is one of the initial steps in the genesis of atherosclerotic plaque. Adhesion molecules are also involved in the pathogenesis of diabetes mellitus type 1; sICAM-1 would have a particular immunomodulatory role in the process of destroying beta-cells and could be used as a subclinical marker of insulitis. Plasma levels of soluble adhesion molecules correlate with hyperglycemia, insulin resistance, dyslipidemia and obesity; they are associated with the development of nephropathy, retinopathy, myocardial infarction, stroke and obliterant peripheral arterial disease in diabetic type 1 and 2. Given the role of these molecules in endothelial dysfunction genesis and tissue damage associated with diabetes, they could constitute a therapeutic target for the prevention of genesis and progression of chronic complications of diabetic disease.

  18. Spin orbit driven ferromagnetic resonance and torques in single ferromagnetic layers

    NASA Astrophysics Data System (ADS)

    Maciá, Ferran; Pépin, Charles; Kent, A. D.

    2012-02-01

    The coupling of spin and charge may convert electrical currents into spin currents in non-magnetic metals. In non-magnetic metals with strong spin orbit (SO) interaction in combination with magnetic metals one can also us the effect to excite magnetization dynamics; electrical currents in the non-magnetic metal transform to spin currents and the spin currents diffuse to the magnetic metal interacting with the magnetic moments. The combination of non-magnetic metals and magnetic metals has been recently used to determine spin hall angles. Here we demonstrate that spin currents in a ferromagnetic layer associated with SO interactions can excite ferromagnetic precession in the same layer. We have studied Co|Ni multilayers with both in-plane anisotropy and weak out-of-plane anisotropy. Results show that the samples have strong SO interactions. We have injected microwaves into patterned samples with several geometries and measured the mixed voltage in the same leads. Oscillatory currents drive FMR in the thin-film layer. We show that SO torques are primarily responsible for the magnetic excitations in samples with strong SO interactions, whereas samples with a weaker SO barely respond to the injected microwaves and show asymmetric components from charge current induced Oersted fields.

  19. Controlling Magnetism in Spin-Orbit-Driven Oxides with Epitaxial Strain

    NASA Astrophysics Data System (ADS)

    Clancy, Patrick

    2015-03-01

    The layered perovskite iridates Sr2IrO4andBa2IrO4 are the prototypical spin-orbital Mott insulators, displaying a novel jeff = 1/2 ground state driven by strong 5d spin-orbit coupling effects. Efforts to understand, and ultimately control, this spin-orbit-induced ground state have led to a surge of interest in thin film iridates, which offer unique opportunities for the tuning of electronic and magnetic properties via epitaxial strain. We have performed complementary resonant magnetic x-ray scattering (RMXS) and resonant inelastic x-ray scattering (RIXS) measurements on epitaxial thin film samples of Sr2IrO4andBa2IrO4. By measuring 13 to 50 nm films grown on a variety of different substrates (PSO, GSO, STO, LSAT), we are able to investigate the impact of applied tensile and compressive strain on the magnetic structure, correlation lengths, and characteristic excitations of these materials. We find that the dispersion of the low-lying magnetic and orbital excitations is strongly affected by strain-induced structural changes, and show that epitaxial strain provides an effective method for tuning three distinct energy scales: the magnetic ordering temperature (TN) , the magnetic exchange interactions (J), and the non-cubic crystal field splitting (ΔCEF) . Perhaps most strikingly, we demonstrate that hard x-ray RIXS can be used to perform detailed magnetic dispersion measurements on thin film samples of 13 nm (~5 unit cells) or less. Work performed in collaboration with H. Gretarsson, A. Lupascu, J.A. Sears, Z. Nie, Y.-J. Kim (University of Toronto), Z. Islam, M.H. Upton, J. Kim, D. Casa, T. Gog, A.H. Said (Argonne National Laboratory), J. Nichols, J. Terzic, S.S.A. Seo, G. Cao (University of Kentucky), M. Uchida, D.G. Schlom, K.M. Shen (Cornell University), H. Stoll (University of Stuttgart), V.M. Katukuri, L.Hozoi, J. van den Brink (IFW Dresden).

  20. The transient response of ice volume to orbital-driven climate changes of the Late Pliocene

    NASA Astrophysics Data System (ADS)

    de Boer, Bas; Hunter, Stephen; Dolan, Aisling; Haywood, Alan

    2016-04-01

    The contribution to sea-level rise of the Antarctic and Greenland ice sheets in a warming climate is uncertain. A better understanding is evidently needed to make more rigorous projections of the impact of regional sea-level rise. A warm interval within the Late Pliocene (3.264 to 3.025 million years before present) can be used to gain a better understanding of the response of the ice sheets to a warming climate with CO2 levels close to or higher than present. Here, we will use a unique ice-sheet - sea-level model, ANICE-SELEN and couple this to the full-complexity intermediate-resolution FAMOUS climate model for the Late Pliocene interval. A first approach is presented here with a one-way coupling, using FAMOUS to force the ice-sheet models in a transient mode. The FAMOUS simulation is driven by PRISM3 boundary conditions (which were also used in PlioMIP phase 1), where we apply a changing orbit, with and without dynamic vegetation. This 40 kyr simulation is centred on the warm interglacial peak, MIS KM5c (3.225 to 3.185 Myr ago). This experiment will give a first indication of the response of the Greenland and Antarctic ice sheets to the climate of the Late Pliocene. The results are compared with the equilibrated response of the ice sheet on Greenland and Antarctica to the PlioMIP phase 1 climate model output, as done so for the PLISMIP experiments.

  1. Isolation of exchange- and spin-orbit-driven effects via manipulation of the axis of quantization

    SciTech Connect

    Komesu, Takashi; Waddill, G.D.; Yu, S.-W.; Butterfield, M.T.; Tobin, J.G.

    2010-11-19

    Double polarization photoelectron spectroscopy using circularly polarized x-rays and true spin detection has been performed using the 2p core levels of ultrathin films of Fe and Co. This includes both the separation into magnetization- and spin-specific spectra and an analysis of the polarization, asymmetry, and related quantities. It is shown how to selectively manipulate the manifestation of exchange- and spin-orbit effects simply by choosing different axes of quantization. Furthermore, the underlying simplicity of the results can be confirmed by comparison to a simple yet powerful single-electron picture.

  2. Raman Optical Activity Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    PubMed

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-09

    We present an efficient method for the calculation of the Raman optical activity (ROA) spectra for large molecules through the molecules-in-molecules (MIM) fragment-based method. The relevant higher energy derivatives from smaller fragments are used to build the property tensors of the parent molecule to enable the extension of the MIM method for evaluating ROA spectra (MIM-ROA). Two factors were found to be particularly important in yielding accurate results. First, the link-atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, yielding a mathematically rigorous method. Second, the long-range interactions between fragments are taken into account by using a less computationally expensive lower level of theory. The performance of the MIM-ROA model is calibrated on the enantiomeric pairs of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and ROA intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-ROA method is employed to predict the ROA spectra of d-maltose, α-D-cyclodextrin, and cryptophane-A, yielding spectra in excellent agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-ROA model for exploring ROA spectra of large molecules.

  3. Electrical conduction through DNA molecule.

    PubMed

    Abdalla, S

    2011-09-01

    Several disorder parameters, inside the DNA molecule, lead to localization of charge carriers inside potential wells in the lowest unoccupied and highest occupied molecular orbits (LUMO and HOMO) which affects drastically the electrical conduction through the molecule, and demonstrates that the band carriers play an essential role in the conduction mechanism. So, a model is presented to shed light on the role of electrons of the LUMO in the electrical conduction through the DNA molecule. DC-, AC-conductivity and dielectric permittivity experimental data are well fitted with the presented model giving evidence that the free carriers in the LUMO and HOMO are responsible to make the DNA molecule conductor, insulator or semiconductor. The obtained results show that the localized charge carriers in the DNA molecule are characterized by four different types of relaxation phenomena which are thermally activated by corresponding four activation energies at 0.56 eV, 0.33 eV, 0.24 eV, and 0.05 eV respectively. Moreover, the calculations after the model, at room temperature, show that the time of the relaxation times of the current carriers are in the order of 5 × 10(-2)s, 1.74 × 10(-4)s, 5 × 10(-7)s, and 1.6 × 10(-10)s, respectively.

  4. Small molecule fluoride toxicity agonists.

    PubMed

    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.

  5. Small Molecule Fluoride Toxicity Agonists

    PubMed Central

    Nelson1, James W.; Plummer, Mark S.; Blount, Kenneth F.; Ames, Tyler D.; Breaker, Ronald R.

    2015-01-01

    SUMMARY 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. PMID:25910244

  6. Small Molecule CXCR3 Antagonists.

    PubMed

    Andrews, Stephen P; Cox, Rhona J

    2016-04-14

    Chemokines and their receptors are known to play important roles in disease. More than 40 chemokine ligands and 20 chemokine receptors have been identified, but, to date, only two small molecule chemokine receptor antagonists have been approved by the FDA. The chemokine receptor CXCR3 was identified in 1996, and nearly 20 years later, new areas of CXCR3 disease biology continue to emerge. Several classes of small molecule CXCR3 antagonists have been developed, and two have shown efficacy in preclinical models of inflammatory disease. However, only one CXCR3 antagonist has been evaluated in clinical trials, and there remain many opportunities to further investigate known classes of CXCR3 antagonists and to identify new chemotypes. This Perspective reviews the known CXCR3 antagonists and considers future opportunities for the development of small molecules for clinical evaluation.

  7. Partial Dynamical Symmetry in Molecules

    NASA Astrophysics Data System (ADS)

    Ping, Jia-Lun; Chen, Jin-Quan

    1997-03-01

    It is shown that any Hamiltonian involving only one- and two-bond interactions for a molecule withnbonds and having a point groupPas its symmetry group may have theSn⊃Ppartial dynamical symmetry, i.e., the Hamiltonian can be solved analytically for a part of the states, called the unique states. For example, theXY6molecule has theS6⊃Ohpartial dynamical symmetry. The model of Iachello and Oss forncoupled anharmonic oscillators is revisited in terms of the partial dynamical symmetry. The energies are obtained analytically for the nine unique levels of theXY6molecule and the structures of the eigenstates are disclosed for the first time, while for non-unique states they are obtained by diagonalizing the Hamiltonian in theS6⊃Ohsymmetry adapted basis with greatly reduced dimension.

  8. Autonomous DNA-Molecule Computing

    NASA Astrophysics Data System (ADS)

    Komiya, Ken; Rose, John A.; Yamamura, Masayuki

    DNA molecules autonomously change their forms from the single strand to the double helix by specific binding between complementary sequences according to the Watson-Crick base pairing rule. This paring rule allows us to control connections among molecules and to construct various structures by sequence design. Further, the motion of constructed structures can also be designed by considering sequential bindings. Recently, the feasibility to utilize the programmed DNA structural change for information processing was studied. In the present paper, we report an efficient synthetic chain reaction based on autonomous binding of DNA to realize a computing system, which enable us to implement computational intelligence in vitro.

  9. Piezoresistivity in single DNA molecules

    PubMed Central

    Bruot, Christopher; Palma, Julio L.; Xiang, Limin; Mujica, Vladimiro; Ratner, Mark A.; Tao, Nongjian

    2015-01-01

    Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π–π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes. PMID:26337293

  10. Phase structure of soliton molecules

    SciTech Connect

    Hause, A.; Hartwig, H.; Seifert, B.; Stolz, H.; Boehm, M.; Mitschke, F.

    2007-06-15

    Temporal optical soliton molecules were recently demonstrated; they potentially allow further increase of data rates in optical telecommunication. Their binding mechanism relies on the internal phases, but these have not been experimentally accessible so far. Conventional frequency-resolved optical gating techniques are not suited for measurement of their phase profile: Their algorithms fail to converge due to zeros both in their temporal and their spectral profile. We show that the VAMPIRE (very advanced method of phase and intensity retrieval of E-fields) method performs reliably. With VAMPIRE the phase profile of soliton molecules has been measured, and further insight into the mechanism is obtained.

  11. Nucleic Acids as Information Molecules.

    ERIC Educational Resources Information Center

    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)

  12. Small Molecules Target Carcinogenic Proteins

    NASA Astrophysics Data System (ADS)

    Gradinaru, Claudiu

    2009-03-01

    An ingenious cellular mechanism of effecting protein localization is prenylation: the covalent attachment of a hydrophobic prenyl group to a protein that facilitates protein association with cell membranes. Fluorescence microscopy was used to investigate whether the oncogenic Stat3 protein can undergo artificial prenylation via high-affinity prenylated small-molecule binding agents and thus be rendered inactive by localization at the plasma membrane instead of nucleus. The measurements were performed on a home-built instrument capable of recording simultaneously several optical parameters (lifetime, polarization, color, etc) and with single-molecule sensitivity. A pH-invariant fluorescein derivative with double moiety was designed to bridge a prenyl group and a small peptide that binds Stat3 with high affinity. Confocal fluorescence images show effective localization of the ligand to the membrane of liposomes. Stat3 predominantly localizes at the membrane only in the presence of the prenylated ligand. Single-molecule FRET (fluorescence resonance energy transfer) between donor-labeled prenylated agents and acceptor-labeled, surface tethered Stat3 protein is used to determine the dynamic heterogeneity of the protein-ligand interaction and follow individual binding-unbinding events in real time. The data indicates that molecules can effect protein localization, validating a therapeutic design that influences protein activity via induced localization.

  13. Nanodevices for Single Molecule Studies

    NASA Astrophysics Data System (ADS)

    Craighead, H. G.; Stavis, S. M.; Samiee, K. T.

    During the last two decades, biotechnology research has resulted in progress in fields as diverse as the life sciences, agriculture and healthcare. While existing technology enables the analysis of a variety of biological systems, new tools are needed for increasing the efficiency of current methods, and for developing new ones altogether. Interest has grown in single molecule analysis for these reasons.

  14. Eckart frames for planar molecules

    NASA Astrophysics Data System (ADS)

    Wei, Hua

    2003-04-01

    Explicit analytic expressions of Eckart frames for planar molecules in Radau, Jacobi and bond coordinates have been presented. The orientation of the frame axis system with respect to the molecular plane at equilibrium is specified by an angle θ1e.

  15. Dissociation energy of molecules in dense gases

    NASA Technical Reports Server (NTRS)

    Kunc, J. A.

    1992-01-01

    A general approach is presented for calculating the reduction of the dissociation energy of diatomic molecules immersed in a dense (n = less than 10 exp 22/cu cm) gas of molecules and atoms. The dissociation energy of a molecule in a dense gas differs from that of the molecule in vacuum because the intermolecular forces change the intramolecular dynamics of the molecule, and, consequently, the energy of the molecular bond.

  16. Nano trap for polar molecules

    NASA Astrophysics Data System (ADS)

    Blümel, R.

    2012-07-01

    A new ac/dc monopole trap for neutral polar particles, introduced and explored by Blümel (2011 Phys. Rev. A 83 045402 and 2011 Eur. Phys. J. D 64 85-101), is significantly advanced in several directions. (1) Previously shown to work only for polar classical particles and polar macro-molecules, the trap is shown to work for polar diatomic molecules. (2) A homogeneous electric field, optionally switched on for improved stability in the angular direction, leads to stable trapping in higher order stability regions of the Mathieu equation. (3) Based on the Floquet formalism, analytical and numerical calculations are presented that show that the trap is quantum mechanically stable. (4) Definition and derivation of a quantum pseudo-potential allow a qualitative understanding of the quantum trapping mechanism. (5) It is shown that the proposed ac/dc trap may be realized experimentally using currently available scanning tunnelling microscopy technology.

  17. Optical highlighter molecules in neurobiology.

    PubMed

    Datta, Sandeep Robert; Patterson, George H

    2012-02-01

    The development of advanced optical methods has played a key role in propelling progress in neurobiology. Genetically-encoded fluorescent molecules found in nature have enabled labeling of individual neurons to study their physiology and anatomy. Here we discuss the recent use of both native and synthetic optical highlighter proteins to address key problems in neurobiology, including questions relevant to synaptic function, neuroanatomy, and the organization of neural circuits.

  18. Racemic fluids of hard molecules

    NASA Astrophysics Data System (ADS)

    Vatamanu, J.; Cann, N. M.

    2001-05-01

    The structure in four racemic fluids is explored using two integral equation theories: the reference interaction site method (RISM) [D. Chandler and H. C. Andersen, J. Chem. Phys. 57, 1930 (1972)] and the diagrammatically correct theory of Chandler, Silbey, and Ladanyi (CSL) [D. Chandler, R. Silbey, and B. M. Ladanyi, Mol. Phys. 46, 1335 (1982)]. Discrimination is measured by comparison of site pair distributions for sites on identical molecules with the corresponding distributions for sites on mirror-image molecules. We find that discrimination is largest for distributions between the smallest sites in the molecules. Between racemates, those consisting of more asymmetrical chiral molecules (i.e., with a bigger range of site sizes and bond lengths) show the largest discrimination. The indirect correlation function is shown to be nondiscriminating in racemates. Further, exact relationships between like-like and like-unlike differences in the other pair functions have been obtained. From these, the importance of the bridge functions in discrimination is evident. The CSL theory always satisfies the exact relationships, even with approximate bridge diagrams. RISM theory cannot satisfy these exact limits regardless of density and closure relation. We have found that RISM theory predicts qualitatively incorrect pair distributions at low densities, but that the difference in the distributions is more accurate. All bridge diagrams which contribute to O(ρo) have been enumerated and evaluated. Inclusion of these diagrams into the CSL theory leads to exact results at low density. However, we find that the inclusion of the ρo diagrams has dramatically improved the quality of the CSL theory at all densities.

  19. Metagenomic small molecule discovery methods

    PubMed Central

    Charlop-Powers, Zachary; Milshteyn, Aleksandr; Brady, Sean F.

    2014-01-01

    Metagenomic approaches to natural product discovery provide the means of harvesting bioactive small molecules synthesized by environmental bacteria without the requirement of first culturing these organisms. Advances in sequencing technologies and general metagenomic methods are beginning to provide the tools necessary to unlock the unexplored biosynthetic potential encoded by the genomes of uncultured environmental bacteria. Here, we highlight recent advances in sequence- and functional- based metagenomic approaches that promise to facilitate antibiotic discovery from diverse environmental microbiomes. PMID:25000402

  20. Intensity calculations of HCN molecules

    NASA Astrophysics Data System (ADS)

    Yasmin, Kausar

    2006-10-01

    Accurate spectroscopic data of HCN are required for many astronomical calculations and modeling. HCN molecules are present in the atmosphere of carbon stars and in galactic centers. Ro-vibrational energy levels and intensity calculations were carried out using the full coupled cluster model and radau coordinates. Accurate ab initio calculated potential energy surface^1 and dipole moment surface^2 were used for computation. The computed values were compared with Hitran^99.^

  1. Electron interactions with polar molecules

    SciTech Connect

    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.

  2. Small Molecules-Big Data.

    PubMed

    Császár, Attila G; Furtenbacher, Tibor; Árendás, Péter

    2016-11-17

    Quantum mechanics builds large-scale graphs (networks): the vertices are the discrete energy levels the quantum system possesses, and the edges are the (quantum-mechanically allowed) transitions. Parts of the complete quantum mechanical networks can be probed experimentally via high-resolution, energy-resolved spectroscopic techniques. The complete rovibronic line list information for a given molecule can only be obtained through sophisticated quantum-chemical computations. Experiments as well as computations yield what we call spectroscopic networks (SN). First-principles SNs of even small, three to five atomic molecules can be huge, qualifying for the big data description. Besides helping to interpret high-resolution spectra, the network-theoretical view offers several ideas for improving the accuracy and robustness of the increasingly important information systems containing line-by-line spectroscopic data. For example, the smallest number of measurements necessary to perform to obtain the complete list of energy levels is given by the minimum-weight spanning tree of the SN and network clustering studies may call attention to "weakest links" of a spectroscopic database. A present-day application of spectroscopic networks is within the MARVEL (Measured Active Rotational-Vibrational Energy Levels) approach, whereby the transitions information on a measured SN is turned into experimental energy levels via a weighted linear least-squares refinement. MARVEL has been used successfully for 15 molecules and allowed to validate most of the transitions measured and come up with energy levels with well-defined and realistic uncertainties. Accurate knowledge of the energy levels with computed transition intensities allows the realistic prediction of spectra under many different circumstances, e.g., for widely different temperatures. Detailed knowledge of the energy level structure of a molecule coming from a MARVEL analysis is important for a considerable number of modeling

  3. Quantum simulation with cold molecules

    NASA Astrophysics Data System (ADS)

    Rey, Ana Maria

    2014-03-01

    Recent experimental developments on cooling, trapping, manipulating and loading ultra-cold ground state molecules in an optical lattice have opened the door for the exploration of quantum magnetism and the observation of complex quantum dynamics. In this talk I will discuss recent developments towards the implementation of controllable spin lattice models in polar molecules with the spin degrees of freedom encoded in rotational states. The spin-spin couplings are generated by direct dipolar interactions and can be fully controlled by dc electromagnetic fields and microwaves. The spin models realized in this way are long range, anisotropic and can even feature direction-dependent spin interactions. They can emulate Hamiltonians ranging from the Heisenberg spin model, to Hamiltonians with symmetry protected topological phases to Hamiltonians without solid state counterpart. At JILA we have been able to realize for the first time a lattice spin model with fermionic KRb molecules pinned in a 3D lattice. We observe clear manifestation of dipolar exchange interactions in Ramsey spectroscopy even at substantially less than unit lattice filling. I will describe the new theoretical methods that we developed to model the spin dynamics and show that those reproduce the experimental observations. Even though so far the spin dynamics has been restricted to pinned molecules, in part to prevent chemical reactions, I will finish by presenting theoretical calculations supported by experimental measurement at JILA that demonstrate that the continuous quantum Zeno mechanism can actually suppress loss in this highly reactive system. This finding opens the exciting possibility of observing itinerant quantum magnetism in near term experiments. This work is supported by ARO, ARO-DARPA-OLE, NSF-PFC and NSF-PIF

  4. A single-molecule diode

    PubMed Central

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-01-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current–voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur–gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current–voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current–voltage characteristics, similar to the phenomena in a semiconductor diode. PMID:15956208

  5. A single-molecule diode.

    PubMed

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B; Mayor, Marcel

    2005-06-21

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic pi -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical pi-systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode.

  6. Simple molecules as complex systems

    PubMed Central

    Furtenbacher, Tibor; Árendás, Péter; Mellau, Georg; Császár, Attila G.

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H216O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an “ultra-small-world” property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  7. Mechanobiology of Short DNA Molecules: A Single Molecule Perspective

    NASA Astrophysics Data System (ADS)

    Raghunathan, Krishnan

    Mechanical properties of DNA are known to play a significant role in several biological processes like wrapping of DNA around histones and looping. Most of these cellular events occur on a DNA length scale of a few hundred basepairs. Single molecule methods have been highly successful in directly investigating heterogeneity in different biomolecular systems and serve as ideal tools to study the mechanical properties of DNA. However, their use in studying DNA of contour lengths less than a kilobase are fraught with experimental difficulties. The research presented in this thesis explores the behavior of short stretches of DNA (≤ 500bp) using existing and novel single molecule methods. We have quantified the variation in persistence lengths between sequences having different elasticity using a constant force axial optical tweezers. Our experiments have also revealed that this difference in persistence lengths manifests itself as a difference in looping lifetimes of lac repressor, in sequences having the aforementioned constructs as the intervening sequence between the operator sites. We have also developed a system to probe DNA dynamics in vivo. We have found that the active processes in the cell have distinct effects on dynamics of DNA and eliminating the active processes causes a 'phase transition' like behavior in the inside the cell. We are currently extending this technique to understand DNA dynamics inside bacterial systems. Our results provide vital insights into mechanical properties of DNA and the effect of athermal fluctuations on DNA dynamics.

  8. Water molecules orientation in surface layer

    NASA Astrophysics Data System (ADS)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  9. XUV ionization of aligned molecules

    SciTech Connect

    Kelkensberg, F.; Siu, W.; Gademann, G.; Rouzee, A.; Vrakking, M. J. J.; Johnsson, P.; Lucchini, M.; Lucchese, R. R.

    2011-11-15

    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  10. Molecules in Studio v. 1.0

    SciTech Connect

    Walker, La Tonya; Malczynski, Leonard

    2016-04-22

    A Powersim Studio implementation of the system dynamics’ ‘Molecules of Structure’. The original implementation was in Ventana’s Vensim language by James Hines. The molecules are fundamental constructs of the system dynamics simulation methodology.

  11. Characterization of Interstellar Organic Molecules

    NASA Astrophysics Data System (ADS)

    Gençaǧa, Deniz; Carbon, Duane F.; Knuth, Kevin H.

    2008-11-01

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  12. Electronic spectroscopy of diatomic molecules

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.

    1994-01-01

    This article provides an overview of the principal computational approaches and their accuracy for the study of electronic spectroscopy of diatomic molecules. We include a number of examples from our work that illustrate the range of application. We show how full configuration interaction benchmark calculations were instrumental in improving the understanding of the computational requirements for obtaining accurate results for diatomic spectroscopy. With this understanding it is now possible to compute radiative lifetimes accurate to within 10% for systems involving first- and second-row atoms. We consider the determination of the infrared vibrational transition probabilities for the ground states of SiO and NO, based on a globally accurate dipole moment function. We show how we were able to assign the a(sup "5)II state of CO as the upper state in the recently observed emission bands of CO in an Ar matrix. We next discuss the assignment of the photoelectron detachment spectra of NO and the alkali oxide negative ions. We then present several examples illustrating the state-of-the-art in determining radiative lifetimes for valence-valence and valence-Rydberg transitions. We next compare the molecular spectroscopy of the valence isoelectronic B2, Al2, and AlB molecules. The final examples consider systems involving transition metal atoms, which illustrate the difficulty in describing states with different numbers of d electrons.

  13. Organic Molecules in Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Gibb, Erika; Horne, David; Shenoy, Sachindev; Blake, Daniel; van Brunt, Kari; Brittain, Sean; Rettig, Terrence

    2008-08-01

    We propose to use NIRSPEC to search for organic molecules in circumstellar disks toward nearly edge-on T Tauri stars. The feasibility of this study has been recently illustrated by the NIRSPEC detection of HCN toward two edge-on T Tauri stars, GV Tau (Gibb et al. 2007) and IRS 46 (Lahuis et al. 2006), and Spitzer detections of C_2H_2, HCN, and CO_2 toward IRS 46 (Lahuis et al. 2006) and AA Tau (Carr & Najita 2008). We have selected 10 molecules that are predicted to be abundant based on chemical models, observations of high and low mass star forming regions, and comet comae. We will investigate compositional variations among the T Tauri population and compare that to comets and chemical models of disk chemistry. Through this, we can explore the chemistry occurring in the planet-forming regions of protoplanetary disks and investigate the evolution of organic volatiles, which can help establish the mechanism and timescale for planet formation.

  14. Exotic negative molecules in AMS

    NASA Astrophysics Data System (ADS)

    Golser, Robin; Gnaser, Hubert; Kutschera, Walter; Priller, Alfred; Steier, Peter; Wallner, Anton

    2007-06-01

    "The techniques and equipment developed for AMS studies are well suited for identifying exotic negative ions". With this sentence begins a pioneering paper by Roy Middleton and Jeff Klein (M&K) on small doubly-charged negative carbon clusters [Nucl. Instr. and Meth. B 123 (1997) 532]. M&K were the first to utilize Accelerator Mass Spectrometry to prove the existence of these clusters and a number of other exotic molecules. We review M&K's efforts and show how their work is being continued at other laboratories. The latest developments are: (1) the discovery of long-lived molecular hydrogen anions H2-,D2-and (2) the unambiguous identification of the smallest doubly-charged negative molecule (LiF3)2-. In particular we show new experimental data for D3-, and for (LiF3)2-, and we try to answer the question why M&K's search for this di-anion was unsuccessful.

  15. Characterization of Interstellar Organic Molecules

    SciTech Connect

    Gencaga, Deniz; Knuth, Kevin H.; Carbon, Duane F.

    2008-11-06

    Understanding the origins of life has been one of the greatest dreams throughout history. It is now known that star-forming regions contain complex organic molecules, known as Polycyclic Aromatic Hydrocarbons (PAHs), each of which has particular infrared spectral characteristics. By understanding which PAH species are found in specific star-forming regions, we can better understand the biochemistry that takes place in interstellar clouds. Identifying and classifying PAHs is not an easy task: we can only observe a single superposition of PAH spectra at any given astrophysical site, with the PAH species perhaps numbering in the hundreds or even thousands. This is a challenging source separation problem since we have only one observation composed of numerous mixed sources. However, it is made easier with the help of a library of hundreds of PAH spectra. In order to separate PAH molecules from their mixture, we need to identify the specific species and their unique concentrations that would provide the given mixture. We develop a Bayesian approach for this problem where sources are separated from their mixture by Metropolis Hastings algorithm. Separated PAH concentrations are provided with their error bars, illustrating the uncertainties involved in the estimation process. The approach is demonstrated on synthetic spectral mixtures using spectral resolutions from the Infrared Space Observatory (ISO). Performance of the method is tested for different noise levels.

  16. Is JPC = 3-+ molecule possible?

    NASA Astrophysics Data System (ADS)

    Zhu, Wei; Liu, Yan-Rui; Yao, Tao

    2015-02-01

    The confirmation of charged charmonium-like states indicates that heavy quark molecules should exist. Here we discuss the possibility of a molecule state with JPC = 3-+. In a one-boson-exchange model investigation for the S wave C = + D*D¯2* states, one finds that the strongest attraction is in the case J = 3 and I = 0 for both π and σ exchanges. Numerical analysis indicates that this hadronic bound state might exist if a phenomenological cutoff parameter around 2.3 GeV (1.5 GeV) is reasonable with a dipole (monopole) type form factor in the one-pion-exchange model. The cutoff for binding solutions may be reduced to a smaller value once the σ exchange contribution is included. If a state around the D*D¯2* threshold (≈4472 MeV) in the channel J/ψω (P wave) is observed, the heavy quark spin symmetry implies that it is not a cc¯ meson and the JPC are likely to be 3-+. Supported by National Natural Science Foundation of China (11275115), Shandong Province Natural Science Foundation (ZR2010AM023), SRF for ROCS, SEM, and Independent Innovation Foundation of Shandong University

  17. Time scales for molecule formation by ion-molecule reactions

    NASA Technical Reports Server (NTRS)

    Langer, W. D.; Glassgold, A. E.

    1976-01-01

    Analytical solutions are obtained for nonlinear differential equations governing the time-dependence of molecular abundances in interstellar clouds. Three gas-phase reaction schemes are considered separately for the regions where each dominates. The particular case of CO, and closely related members of the Oh and CH families of molecules, is studied for given values of temperature, density, and the radiation field. Nonlinear effects and couplings with particular ions are found to be important. The time scales for CO formation range from 100,000 to a few million years, depending on the chemistry and regime. The time required for essentially complete conversion of C(+) to CO in the region where the H3(+) chemistry dominates is several million years. Because this time is longer than or comparable to dynamical time scales for dense interstellar clouds, steady-state abundances may not be observed in such clouds.

  18. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K.; Hickey, Gregory S.

    1994-01-01

    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  19. Visualization of large elongated DNA molecules.

    PubMed

    Lee, Jinyong; Kim, Yongkyun; Lee, Seonghyun; Jo, Kyubong

    2015-09-01

    Long and linear DNA molecules are the mainstream single-molecule analytes for a variety of biochemical analysis within microfluidic devices, including functionalized surfaces and nanostructures. However, for biochemical analysis, large DNA molecules have to be unraveled, elongated, and visualized to obtain biochemical and genomic information. To date, elongated DNA molecules have been exploited in the development of a number of genome analysis systems as well as for the study of polymer physics due to the advantage of direct visualization of single DNA molecule. Moreover, each single DNA molecule provides individual information, which makes it useful for stochastic event analysis. Therefore, numerous studies of enzymatic random motions have been performed on a large elongated DNA molecule. In this review, we introduce mechanisms to elongate DNA molecules using microfluidics and nanostructures in the beginning. Secondly, we discuss how elongated DNA molecules have been utilized to obtain biochemical and genomic information by direct visualization of DNA molecules. Finally, we reviewed the approaches used to study the interaction of proteins and large DNA molecules. Although DNA-protein interactions have been investigated for many decades, it is noticeable that there have been significant achievements for the last five years. Therefore, we focus mainly on recent developments for monitoring enzymatic activity on large elongated DNA molecules.

  20. Ultrafast electron diffraction from aligned molecules

    SciTech Connect

    Centurion, Martin

    2015-08-17

    The aim of this project was to record time-resolved electron diffraction patterns of aligned molecules and to reconstruct the 3D molecular structure. The molecules are aligned non-adiabatically using a femtosecond laser pulse. A femtosecond electron pulse then records a diffraction pattern while the molecules are aligned. The diffraction patterns are then be processed to obtain the molecular structure.

  1. A single-molecule diode

    NASA Astrophysics Data System (ADS)

    Elbing, Mark; Ochs, Rolf; Koentopp, Max; Fischer, Matthias; von Hänisch, Carsten; Weigend, Florian; Evers, Ferdinand; Weber, Heiko B.; Mayor, Marcel

    2005-06-01

    We have designed and synthesized a molecular rod that consists of two weakly coupled electronic π -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical π -systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode. Author contributions: F.E., H.B.W., and M.M. designed research; M.E., R.O., M.K., M.F., F.E., H.B.W., and M.M. performed research; M.E., R.O., M.K., M.F., C.v.H., F.W., F.E., H.B.W., and M.M. contributed new reagents/analytic tools; M.E., R.O., M.K., C.v.H., F.E., H.B.W., and M.M. analyzed data; and F.E., H.B.W., and M.M. wrote the paper.This paper was submitted directly (Track II) to the PNAS office.Abbreviations: A, acceptor; D, donor; MCB, mechanically controlled break junction.Data deposition: The atomic coordinates have been deposited in the Cambridge Structural Database, Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, United Kingdom (CSD reference no. 241632).

  2. Behavior of atypical amphiphilic molecules

    NASA Astrophysics Data System (ADS)

    Ko, John

    1997-08-01

    The physical behavior of several atypical amphiphilic molecules was studied in various environments including micelles, model bilayer membranes, and emulsions. The molecules under investigation were nor-chenodeoxycholic acid (nor-CDCA), ursodeoxycholic acid (UDCA), sphingosine (Sp), sphingosine hydrochloride (SpċHCl), and tetrahydrolipstatin (THL). The bile acids, nor-CDCA and UDCA, were studied using 13C-Nuclear Magnetic Resonance ([13C) -NMR) in micelles of taurocholate and in bilayers of phosphatidylcholine. The pK a values of the bile acids in each environment were determined by [13C) -NMR and are as follows: 6.08 ±.03 for nor-CDCA and 6.27 ±.01 for UDCA in micelles, and 7.04 ± 12 for nor-CDCA and 6.89 ±.05 for UDCA in vesicles. Using line shape analysis, the transbilayer movement rate at 36oC for nor-CDCA and UDCA was calculated to be 580 sec--1 and 409 sec-1, respectively. [13C) -NMR titration of Sp gave pK a values of 9.09 ±.02 in micelles and 9.69 ±.21 in bilayers. Differential scanning calorimetry (DSC) and X-ray diffraction were used to establish the Spċwater and SpċHClċwater phase diagrams. Anhydrous and hydrated samples ranging from 5- 90% water were analyzed. The DSC thermograms traced out the transition temperatures of each molecule while the X- ray diffraction patterns revealed their chain and crystalline lattice packing structures. In general, sphingosine exists as a hydrated crystal with β packing phase below 43oC and melts into an Lα phase. Sphingosine hydrochloride, however, exists as a gel phase (L_beta or /beta/sp') below 42oC that swells to 61% hydration. At low water concentrations (0-64%), a lamellar liquid crystal phase (L_alpha) is formed above the chain melting transition of 42oC. At medium concentration (65%), a Hexagonal I phase is present, and at high water concentrations (66-90%), a micellar phase is present. THL, a specific inhibitor of lipases, was analyzed with [ 13C) -NMR to study its behavior in various environments

  3. Small-molecule arginase inhibitors.

    PubMed

    Ivanenkov, Yan A; Chufarova, Nina V

    2014-01-01

    Arginase is an enzyme that metabolizes L-arginine to L-ornithine and urea. In addition to its fundamental role in the hepatic ornithine cycle, it also influences the immune systems in humans and mice. Arginase participates in many inflammatory disorders by decreasing the synthesis of nitric oxide and inducing fibrosis and tissue regeneration. L-arginine deficiency, which is modulated by myeloid cell arginase, suppresses T-cell immune response. This mechanism plays a fundamental role in inflammation-associated immunosuppression. Pathogens can synthesize their own arginase to elude immune reaction. Small-molecule arginase inhibitors are currently described as promising therapeutics for the treatment of several diseases, including allergic asthma, inflammatory bowel disease, ulcerative colitis, cardiovascular diseases (atherosclerosis and hypertension), diseases associated with pathogens (e.g., Helicobacter pylori, Trypanosoma cruzi, Leishmania, Mycobacterium tuberculosis and Salmonella), cancer and induced or spontaneous immune disorders. This article summarizes recent patents in the area of arginase inhibitors and discusses their properties.

  4. Nonadiabatic calculations on hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Komasa, Jacek; Pachucki, Krzysztof

    Since its infancy quantum mechanics has treated hydrogen molecule as a test bed. Contemporary spectroscopy is able to supply the dissociation energy (D0) of H2 with the accuracy of 3 . 7 .10-4cm-1 , while current theoretical predictions are 10-3cm-1 in error. Both the uncertainties are already smaller than the quantum electrodynamic (QED) effects contributing to D0, which poses a particular challenge to theoreticians. Undoubtedly, in order to increase the predictive power of theory one has to not only account for the multitude of the tiny relativistic and QED effects but, especially, significantly increase precision of the largest component of D0--the nonrelativistic contribution. We approach the problem of solving the Schroedinger equation, equipped with new methodology, with the target precision of D0 set at the level of 10-7cm-1 .

  5. Electrokinetic concentration of charged molecules

    DOEpatents

    Singh, Anup K.; Neyer, David W.; Schoeniger, Joseph S.; Garguilo, Michael G.

    2002-01-01

    A method for separating and concentrating charged species from uncharged or neutral species regardless of size differential. The method uses reversible electric field induced retention of charged species, that can include molecules and molecular aggregates such as dimers, polymers, multimers, colloids, micelles, and liposomes, in volumes and on surfaces of porous materials. The retained charged species are subsequently quantitatively removed from the porous material by a pressure driven flow that passes through the retention volume and is independent of direction thus, a multi-directional flow field is not required. Uncharged species pass through the system unimpeded thus effecting a complete separation of charged and uncharged species and making possible concentration factors greater than 1000-fold.

  6. Special Issue: "Molecules against Alzheimer".

    PubMed

    Decker, Michael; Muñoz-Torrero, Diego

    2016-12-16

    This Special Issue, entitled "Molecules against Alzheimer", gathers a number of original articles, short communications, and review articles on recent research efforts toward the development of novel drug candidates, diagnostic agents and therapeutic approaches for Alzheimer's disease (AD), the most prevalent neurodegenerative disorder and a leading cause of death worldwide. This Special Issue contains many interesting examples describing the design, synthesis, and pharmacological profiling of novel compounds that hit one or several key biological targets, such as cholinesterases, β-amyloid formation or aggregation, monoamine oxidase B, oxidative stress, biometal dyshomeostasis, mitochondrial dysfunction, serotonin and/or melatonin systems, the Wnt/β-catenin pathway, sigma receptors, nicotinamide phosphoribosyltransferase, or nuclear erythroid 2-related factor. The development of novel AD diagnostic agents based on tau protein imaging and the use of lithium or intranasal insulin for the prevention or the symptomatic treatment of AD is also covered in some articles of the Special Issue.

  7. Laser optogalvanic spectroscopy of molecules

    NASA Technical Reports Server (NTRS)

    Webster, C. R.; Rettner, C. T.

    1983-01-01

    In laser optogalvanic (LOG) spectroscopy, a tunable laser is used to probe the spectral characteristics of atomic or molecular species within an electrical discharge in a low pressure gas. Optogalvanic signals arise when the impedance of the discharge changes in response to the absorption of laser radiation. The technique may, therefore, be referred to as impedance spectroscopy. This change in impedance may be monitored as a change in the voltage across the discharge tube. LOG spectra are recorded by scanning the wavelength of a chopped CW dye laser while monitoring the discharge voltage with a lock-in amplifier. LOG signals are obtained if the laser wavelength matches a transition in a species present in the discharge (or flame), and if the absorption of energy in the laser beam alters the impedance of the discharge. Infrared LOG spectroscopy of molecules has been demonstrated and may prove to be the most productive application in the field of optogalvanic techniques.

  8. Production and application of translationally cold molecules

    NASA Astrophysics Data System (ADS)

    Bethlem, Hendrick L.; Meijer, Gerard

    Inspired by the spectacular successes in the field of cold atoms, there is currently great interest in cold molecules. Cooling molecules is useful for various fundamental physics studies and gives access to an exotic regime in chemistry where the wave property of the molecules becomes important. Although cooling molecules has turned out to be considerably more difficult than cooling atoms, a number of methods to produce samples of cold molecules have been demonstrated over the last few years. This paper aims to review the application of cold molecules and the methods to produce them. Emphasis is put on the deceleration of polar molecules using time-varying electric fields. The operation principle of the array of electrodes that is used to decelerate polar molecules is described in analogy with, and using terminology from, charged-particle accelerators. It is shown that, by applying an appropriately timed high voltage burst, molecules can be decelerated while the phase-space density, i.e. the number of molecules per position-velocity interval, remains constant. In this way the high density and low temperature in the moving frame of a pulsed molecular beam can be transferred to the laboratory frame. Experiments on metastable CO in states that are either repelled by or attracted to high electric fields are presented. Loading of slow molecules into traps and storage rings is discussed.

  9. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, George D.; Rupp, Bernhard

    1996-01-01

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an x-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the x-ray diffraction pattern.

  10. Electrorheological crystallization of proteins and other molecules

    DOEpatents

    Craig, G.D.; Rupp, B.

    1996-06-11

    An electrorheological crystalline mass of a molecule is formed by dispersing the molecule in a dispersion fluid and subjecting the molecule dispersion to a uniform electrical field for a period of time during which time an electrorheological crystalline mass is formed. Molecules that may be used to form an electrorheological crystalline mass include any organic or inorganic molecule which has a permanent dipole and/or which is capable of becoming an induced dipole in the presence of an electric field. The molecules used to form the electrorheological crystalline mass are preferably macromolecules, such as biomolecules, such as proteins, nucleic acids, carbohydrates, lipoproteins and viruses. Molecules are crystallized by a method in which an electric field is maintained for a period of time after the electrorheological crystalline mass has formed during which time at least some of the molecules making up the electrorheological crystalline mass form a crystal lattice. The three dimensional structure of a molecule is determined by a method in which an electrorheological crystalline mass of the molecule is formed, an X-ray diffraction pattern of the electrorheological crystalline mass is obtained and the three dimensional structure of the molecule is calculated from the X-ray diffraction pattern. 4 figs.

  11. Observation of pendular butterfly Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-10-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  12. Deformation of DNA molecules by hydrodynamic focusing

    NASA Astrophysics Data System (ADS)

    Wong, Pak Kin; Lee, Yi-Kuen; Ho, Chih-Ming

    2003-12-01

    The motion of a DNA molecule in a solvent flow reflects the deformation of a nano/microscale flexible mass spring structure by the forces exerted by the fluid molecules. The dynamics of individual molecules can reveal both fundamental properties of the DNA and basic understanding of the complex rheological properties of long-chain molecules. In this study, we report the dynamics of isolated DNA molecules under homogeneous extensional flow. Hydrodynamic focusing generates homogeneous extensional flow with uniform velocity in the transverse direction. The deformation of individual DNA molecules in the flow was visualized with video fluorescence microscopy. A coil stretch transition was observed when the Deborah number (De) is larger than 0.8. With a sudden stopping of the flow, the DNA molecule relaxes and recoils. The longest relaxation time of T2 DNA was determined to be 0.63 s when scaling viscosity to 0.9 cP.

  13. Observation of pendular butterfly Rydberg molecules.

    PubMed

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-10-05

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  14. Observation of pendular butterfly Rydberg molecules

    PubMed Central

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H.; Ott, Herwig

    2016-01-01

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron–perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance. PMID:27703143

  15. High-harmonic spectroscopy of aligned molecules

    NASA Astrophysics Data System (ADS)

    Yun, Hyeok; Yun, Sang Jae; Lee, Gae Hwang; Nam, Chang Hee

    2017-01-01

    High harmonics emitted from aligned molecules driven by intense femtosecond laser pulses provide the opportunity to explore the structural information of molecules. The field-free molecular alignment technique is an expedient tool for investigating the structural characteristics of linear molecules. The underlying physics of field-free alignment, showing the characteristic revival structure specific to molecular species, is clearly explained from the quantum-phase analysis of molecular rotational states. The anisotropic nature of molecules is shown from the harmonic polarization measurement performed with spatial interferometry. The multi-orbital characteristics of molecules are investigated using high-harmonic spectroscopy, applied to molecules of N2 and CO2. In the latter case the two-dimensional high-harmonic spectroscopy, implemented using a two-color laser field, is applied to distinguish harmonics from different orbitals. Molecular high-harmonic spectroscopy will open a new route to investigate ultrafast dynamics of molecules.

  16. Methods and applications in single molecule electronics

    NASA Astrophysics Data System (ADS)

    Hihath, Joshua

    In recent years it has become possible to measure charge transport in a single molecule contacted to two metal electrodes. However, a thorough understanding of how a molecule behaves while contacted to two electrodes and how it interacts with its environment is still lacking. This thesis demonstrates various experimental methods for understanding and controlling charge transport in a single molecule junction and the application of these methods to various molecular systems to help elucidate the conduction mechanisms invoked. First, the conductance of DNA is examined in a controlled environment while varying the length, sequence, base-pair matching, bias, temperature, and electrochemical gate of the molecule. These studies show that the conductance of DNA is extremely sensitive to changes in length, sequence, and base-matching, but not as sensitive to temperature and electrochemical gate. Despite the variety of experimental methods applied, the subtleties of the conduction mechanism remain uncertain, and as such necessitate the development of additional tools for understanding the behavior of a single molecule junction. Next, the Conductance Screening Tool for Molecules (CSTM) is described. This is a new tool capable of creating 1000's of single molecules junctions in a matter of minutes. This tool has been used to study the conductance of alkanedithiols, molecules in an array, and single amino acid residues. This system allows for greater speed and flexibility in determining the conductance of a single molecule junction, and provides a capability for performing large-scale systematic studies of molecular systems to determine the conduction mechanism. Finally, an additional experimental method capable of extracting information about the interaction between a molecule and its environment is developed. Here, electron-phonon interactions in a single molecule contacted to two electrodes are studied. This method allows one to obtain a specific, chemical signature of a

  17. Geochemical Origin of Biological Molecules

    NASA Astrophysics Data System (ADS)

    Bassez, Marie-Paule

    2013-04-01

    A model for the geochemical origin of biological molecules is presented. Rocks such as peridotites and basalts, which contain ferromagnesian minerals, evolve in the presence of water. Their hydrolysis is an exothermic reaction which generates heat and a release of H2 and of minerals with modified structures. The hydrogen reacts with the CO2 embedded inside the rock or with the CO2 of the environment to form CO in an hydrothermal process. With the N2 of the environment, and with an activation source arising from cosmic radiation, ferromagnesian rocks might evolve towards the abiotic formation of biological molecules, such as peptide like macromolecules which produce amino acids after acid hydrolysis. The reactions concerned are described. The production of hydrothermal CO is discussed in geological sites containing ferromagnesian silicate minerals and the low intensity of the Earth's magnetic field during Paleoarchaean Era is also discussed. It is concluded that excitation sources arising from cosmic radiation were much more abundant during Paleoarchaean Era and that macromolecular structures of biological relevance might consequently form during Archaean Eon, as a product of the chemical evolution of the rocks and of their mineral contents. This synthesis of abiotically formed biological molecules is consecutively discussed for meteorites and other planets such as Mars. This model for the geochemical origin of biological molecules has first been proposed in 2008 in the context of reactions involving catalysers such as kaolinite [Bassez 2008a] and then presented in conferences and articles [Bassez 2008b, 2009, 2012; Bassez et al. 2009a to 2012b]. BASSEZ M.P. 2008a Synthèse prébiotique dans les conditions hydrothermales, CNRIUT'08, Lyon 29-30/05/2008, Conf. and open access article:http://liris.cnrs.fr/~cnriut08/actes/ 29 mai 11h-12h40. BASSEZ M.P. 2008b Prebiotic synthesis under hydrothermal conditions, ISSOL'08, P2-6, Firenze-Italy, 24-29/08/2008. Poster at the

  18. NMR studies of oriented molecules

    SciTech Connect

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  19. Cochleates bridged by drug molecules.

    PubMed

    Syed, Uwais M; Woo, Amy F; Plakogiannis, Fotios; Jin, Tuo; Zhu, Hua

    2008-11-03

    A new type of cochleate, able to microencapsulate water-soluble cationic drugs or peptides into its inter-lipid bi-layer space, was formed through interaction between negatively charged lipids and drugs or peptides acting as the inter-bi-layer bridges instead of multi-cationic metal ions. This new type of cochleate opened up to form large liposomes when treated with EDTA, suggesting that cationic organic molecules can be extracted from these cochleates in a way similar to multivalent metal ions from metal ion-bridged cochleates. Cochleates can be produced in sub-micron size using a method known as "hydrogel isolated cochleation" or simply by increasing the ratio of multivalent cationic peptides over negatively charged liposomes. When nanometer-sized cochleates and liposomes containing the same fluorescent labeled lipid component were incubated with human fibroblasts cells under identical conditions, cells exposed to cochleates showed bright fluorescent cell surfaces, whereas those incubated with liposomes did not. This result suggests that cochleates' edges made them fuse with the cell surfaces as compared to edge free liposomes. This mechanism of cochleates' fusion with cell membrane was supported by a bactericidal activity assay using tobramycin cochleates, which act by inhibiting intracellular ribosomes. Tobramycin bridged cochleates in nanometer size showed improved antibacterial activity than the drug's solution.

  20. Coordination programming of photofunctional molecules.

    PubMed

    Sakamoto, Ryota; Kusaka, Shinpei; Hayashi, Mikihiro; Nishikawa, Michihiro; Nishihara, Hiroshi

    2013-04-05

    Our recent achievements relating to photofunctional molecules are addressed. Section 1 discloses a new concept of photoisomerization. Pyridylpyrimidine-copper complexes undergo a ring inversion that can be modulated by the redox state of the copper center. In combination with an intermolecular photoelectron transfer (PET) initiated by the metal-to-ligand charge transfer (MLCT) transition of the Cu(I) state, we realize photonic regulation of the ring inversion. Section 2 reports on the first examples of heteroleptic bis(dipyrrinato)zinc(II) complexes. Conventional homoleptic bis(dipyrrinato)zinc(II) complexes suffered from low fluorescence quantum yields, whereas the heteroleptic ones feature bright fluorescence even in polar solvents. Section 3 describes our new findings on Pechmann dye, which was first synthesized in 1882. New synthetic procedures for Pechmann dye using dimethyl bis(arylethynyl)fumarate as a starting material gives rise to its new structural isomer. We also demonstrate potentiality of a donor-acceptor-donor type of Pechmann dye in organic electronics.

  1. Single Molecule Studies of Chromatin

    SciTech Connect

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  2. Aggregated Gas Molecules: Toxic to Protein?

    PubMed Central

    Zhang, Meng; Zuo, Guanghong; Chen, Jixiu; Gao, Yi; Fang, Haiping

    2013-01-01

    The biological toxicity of high levels of breathing gases has been known for centuries, but the mechanism remains elusive. Earlier work mainly focused on the influences of dispersed gas molecules dissolved in water on biomolecules. However, recent studies confirmed the existence of aggregated gas molecules at the water-solid interface. In this paper, we have investigated the binding preference of aggregated gas molecules on proteins with molecular dynamics simulations, using nitrogen (N2) gas and the Src-homology 3 (SH3) domain as the model system. Aggregated N2 molecules were strongly bound by the active sites of the SH3 domain, which could impair the activity of the protein. In contrast, dispersed N2 molecules did not specifically interact with the SH3 domain. These observations extend our understanding of the possible toxicity of aggregates of gas molecules in the function of proteins. PMID:23588597

  3. Broadband single-molecule excitation spectroscopy

    PubMed Central

    Piatkowski, Lukasz; Gellings, Esther; van Hulst, Niek F.

    2016-01-01

    Over the past 25 years, single-molecule spectroscopy has developed into a widely used tool in multiple disciplines of science. The diversity of routinely recorded emission spectra does underpin the strength of the single-molecule approach in resolving the heterogeneity and dynamics, otherwise hidden in the ensemble. In early cryogenic studies single molecules were identified by their distinct excitation spectra, yet measuring excitation spectra at room temperature remains challenging. Here we present a broadband Fourier approach that allows rapid recording of excitation spectra of individual molecules under ambient conditions and that is robust against blinking and bleaching. Applying the method we show that the excitation spectra of individual molecules exhibit an extreme distribution of solvatochromic shifts and distinct spectral shapes. Importantly, we demonstrate that the sensitivity and speed of the broadband technique is comparable to that of emission spectroscopy putting both techniques side-by-side in single-molecule spectroscopy. PMID:26794035

  4. Ballistic electron spectroscopy of individual buried molecules

    NASA Astrophysics Data System (ADS)

    Kirczenow, George

    2007-01-01

    A theoretical study is presented of the ballistic electron emission spectra (BEES) of individual insulating and conducting organic molecules chemisorbed on a silicon substrate and buried under a thin gold film. It is predicted that ballistic electrons injected into the gold film from a scanning tunneling microscope tip should be transmitted so weakly to the silicon substrate by alkane molecules of moderate length (decane, hexane) and their thiolates that individual buried molecules of this type will be difficult to detect in BEES experiments. However, resonant transmission by molecules containing unsaturated C-C bonds or aromatic rings is predicted to be strong enough for BEES spectra of individual buried molecules of these types to be measured. Calculated BEES spectra of molecules of both types are presented and the effects of some simple interstitial and substitutional gold defects that may occur in molecular films are also briefly discussed.

  5. Small-Molecule Carbohydrate-Based Immunostimulants.

    PubMed

    Marzabadi, Cecilia H; Franck, Richard W

    2017-02-03

    In this review, we discuss small-molecule, carbohydrate-based immunostimulants that target Toll-like receptor 4 (TLR-4) and cluster of differentiation 1D (CD1d) receptors. The design and use of these molecules in immunotherapy as well as results from their use in clinical trials are described. How these molecules work and their utilization as vaccine adjuvants are also discussed. Future applications and extensions for the use of these analogues as therapeutic agents will be outlined.

  6. Double photoionization of hydrocarbons and aromatic molecules

    NASA Astrophysics Data System (ADS)

    Wehlitz, R.

    2016-11-01

    This article reviews the recent progress in the field of double photoionization of hydrocarbons and aromatic molecules using synchrotron radiation. First I will describe the importance of carbon-based molecules, which are all around us and are literally part of our life. They exhibit intriguing properties some of which can be probed via double photoionization, i.e., the simultaneous emission of two electrons. Furthermore, I will discuss the different mechanisms that can lead to a doubly charged organic molecule and will highlight those findings by comparing them with the results for atoms and other (simple) molecules. Finally, I will give an outlook on future directions on this subject.

  7. Circularly Polarized Luminescence from Simple Organic Molecules.

    PubMed

    Sánchez-Carnerero, Esther M; Agarrabeitia, Antonia R; Moreno, Florencio; Maroto, Beatriz L; Muller, Gilles; Ortiz, María J; de la Moya, Santiago

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented.

  8. Second virial coefficients for chain molecules

    SciTech Connect

    Bokis, C.P.; Donohue, M.D. . Dept. of Chemical Engineering); Hall, C.K. . Dept. of Chemical Engineering)

    1994-01-01

    The importance of having accurate second virial coefficients in phase equilibrium calculations, especially for the calculation of dew points, is discussed. The square-well potentials results in a simple but inaccurate equation for the second virial coefficient for small, spherical molecules such as argon. Here, the authors present a new equation for the second virial coefficient of both spherical molecules and chain molecules which is written in a form similar to that for the square-well potential. This new equation is accurate in comparison to Monte Carlo simulation data on second virial coefficients for square-well chain molecules and with second virial coefficients obtained from experiments on n-alkanes.

  9. Conserved water molecules in bacterial serine hydroxymethyltransferases.

    PubMed

    Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

    2015-10-01

    Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments.

  10. Rovibrational cooling of molecules by optical pumping.

    PubMed

    Manai, I; Horchani, R; Lignier, H; Pillet, P; Comparat, D; Fioretti, A; Allegrini, M

    2012-11-02

    We demonstrate rotational and vibrational cooling of cesium dimers by optical pumping techniques. We use two laser sources exciting all the populated rovibrational states, except a target state that thus behaves like a dark state where molecules pile up thanks to absorption-spontaneous emission cycles. We are able to accumulate photoassociated cold Cs(2) molecules in their absolute ground state (v = 0, J = 0) with up to 40% efficiency. Given its simplicity, the method could be extended to other molecules and molecular beams. It also opens up general perspectives in laser cooling the external degrees of freedom of molecules.

  11. Negative refraction in Möbius molecules

    NASA Astrophysics Data System (ADS)

    Fang, Y. N.; Shen, Yao; Ai, Qing; Sun, C. P.

    2016-10-01

    We theoretically show the negative refraction existing in Möbius molecules. The negative refractive index is induced by the nontrivial topology of the molecules. With the Möbius boundary condition, the effective electromagnetic fields felt by the electron in a Möbius ring is spatially inhomogeneous. In this regard, the DN symmetry is broken in Möbius molecules and thus the magnetic response is induced through the effective magnetic field. Our findings provide an alternative architecture for negative refractive index materials based on the nontrivial topology of Möbius molecules.

  12. Production and Trapping of Ultracold Polar Molecules

    SciTech Connect

    David, DeMille

    2015-04-21

    We report a set of experiments aimed at the production and trapping of ultracold polar molecules. We begin with samples of laser-cooled and trapped Rb and Cs atoms, and bind them together to form polar RbCs molecules. The binding is accomplished via photoassociation, which uses a laser to catalyze the sticking process. We report results from investigation of a new pathway for photoassociation that can produce molecules in their absolute ground state of vibrational and rotational motion. We also report preliminary observations of collisions between these ground-state molecules and co-trapped atoms.

  13. The Arrangement of Information in DNA Molecules

    PubMed Central

    Thomas, Charles A.

    1966-01-01

    The anatomy of DNA molecules isolated from mature bacteriophage is reviewed. These molecules are linear, duplex DNA consisting mainly of uninterrupted polynucleotide chains. Certain phage (T5 and PB) contain four specifically located interruptions. While the nucleotide sequence of most of these molecules is unique (T5, T3, T7, λ), some are circular permutations of each other (T2, T4, P22). Partial degradation of these DNA molecules by exonuclease III predisposes some of them to form circles upon annealing, but indicating they are terminally redundant. PMID:5967428

  14. Ultracold Molecules: Physics in the Quantum Regime

    SciTech Connect

    Doyle, John

    2014-11-17

    Our research encompasses approaches to the trapping of diatomic molecules at low temperature plus the cooling and detection of polyatomic molecules in the kelvin temperature regime. We have cooled and trapped CaF and/or CaH molecules, loaded directly from a molecular beam. As part of this work, we are continuing to develop an important trapping technique, optical loading from a buffer-gas beam. This method was invented in our lab. We are also studying cold polyatomic molecules and their interactions with cold atoms.

  15. Theoretical spectra of floppy molecules

    NASA Astrophysics Data System (ADS)

    Chen, Hua

    2000-09-01

    Detailed studies of the vibrational dynamics of floppy molecules are presented. Six-D bound-state calculations of the vibrations of rigid water dimer based on several anisotropic site potentials (ASP) are presented. A new sequential diagonalization truncation approach was used to diagonalize the angular part of the Hamiltonian. Symmetrized angular basis and a potential optimized discrete variable representation for intermonomer distance coordinate were used in the calculations. The converged results differ significantly from the results presented by Leforestier et al. [J. Chem. Phys. 106 , 8527 (1997)]. It was demonstrated that ASP-S potential yields more accurate tunneling splittings than other ASP potentials used. Fully coupled 4D quantum mechanical calculations were performed for carbon dioxide dimer using the potential energy surface given by Bukowski et al [J. Chem. Phys., 110, 3785 (1999)]. The intermolecular vibrational frequencies and symmetry adapted force constants were estimated and compared with experiments. The inter-conversion tunneling dynamics was studied using the calculated virtual tunneling splittings. Symmetrized Radau coordinates and the sequential diagonalization truncation approach were formulated for acetylene. A 6D calculation was performed with 5 DVR points for each stretch coordinate, and an angular basis that is capable of converging the angular part of the Hamiltonian to 30 cm-1 for internal energies up to 14000 cm-1. The probability at vinylidene configuration were evaluated. It was found that the eigenstates begin to extend to vinylidene configuration from about 10000 cm-1, and the ra, coordinate is closely related to the vibrational dynamics at high energy. Finally, a direct product DVR was defined for coupled angular momentum operators, and the SDT approach were formulated. They were applied in solving the angular part of the Hamiltonian for carbon dioxide dimer problem. The results show the method is capable of giving very accurate

  16. Water: a responsive small molecule.

    PubMed

    Shultz, Mary Jane; Vu, Tuan Hoang; Meyer, Bryce; Bisson, Patrick

    2012-01-17

    Unique among small molecules, water forms a nearly tetrahedral yet flexible hydrogen-bond network. In addition to its flexibility, this network is dynamic: bonds are formed or broken on a picosecond time scale. These unique features make probing the local structure of water challenging. Despite the challenges, there is intense interest in developing a picture of the local water structure due to water's fundamental importance in many fields of chemistry. Understanding changes in the local network structure of water near solutes likely holds the key to unlock problems from analyzing parameters that determine the three dimensional structure of proteins to modeling the fate of volatile materials released into the atmosphere. Pictures of the local structure of water are heavily influenced by what is known about the structure of ice. In hexagonal I(h) ice, the most stable form of solid water under ordinary conditions, water has an equal number of donor and acceptor bonds; a kind of symmetry. This symmetric tetrahedral coordination is only approximately preserved in the liquid. The most obvious manifestation of this altered tetrahedral bonding is the greater density in the liquid compared with the solid. Formation of an interface or addition of solutes further modifies the local bonding in water. Because the O-H stretching frequency is sensitive to the environment, vibrational spectroscopy provides an excellent probe for the hydrogen-bond structure in water. In this Account, we examine both local interactions between water and small solutes and longer range interactions at the aqueous surface. Locally, the results suggest that water is not a symmetric donor or acceptor, but rather has a propensity to act as an acceptor. In interactions with hydrocarbons, action is centered at the water oxygen. For soluble inorganic salts, interaction is greater with the cation than the anion. The vibrational spectrum of the surface of salt solutions is altered compared with that of neat

  17. Tumor suppressor molecules and methods of use

    DOEpatents

    Welch, Peter J.; Barber, Jack R.

    2004-09-07

    The invention provides substantially pure tumor suppressor nucleic acid molecules and tumor suppressor polypeptides. The invention also provides hairpin ribozymes and antibodies selective for these tumor suppressor molecules. Also provided are methods of detecting a neoplastic cell in a sample using detectable agents specific for the tumor suppressor nucleic acids and polypeptides.

  18. The Distribution of Solubilized Molecules among Micelles.

    ERIC Educational Resources Information Center

    Miller, Dennis J.

    1978-01-01

    Conflicting views have been put forward on the derivation of the distribution of solubilized molecules among micelles. This stems from failure to consider the arrangement of the solubilized molecules in the micelles. In the treatment presented enthalpy effects are ignored as they are not amenable to a simple general theory. (Author/BB)

  19. How organic molecules can control electronic devices.

    PubMed

    Vilan, Ayelet; Cahen, David

    2002-01-01

    This article examines a somewhat counter-intuitive approach to molecular-based electronic devices. Control over the electronic energy levels at the surfaces of conventional semiconductors and metals is achieved by assembling on the solid surfaces, poorly organized, partial monolayers (MLs) of molecules instead of the more commonly used ideal ones. Once those surfaces become interfaces, these layers exert electrostatic rather than electrodynamic control over the resulting devices, based on both electrical monopole and dipole effects of the molecules. Thus electronic transport devices, incorporating molecules, can be constructed without current flow through the molecules. This is illustrated for a gallium arsenide (GaAs) sensor as well as for gold-silicon (Au-Si) and Au-GaAs diodes. Incorporating molecules into solid interfaces becomes possible, using a 'soft' electrical contacting procedure, so as not to damage the molecules. Because there are only a few molecular restrictions, this approach opens up possibilities for the use of more complex (including biologically active) molecules as it circumvents requirements for ideal MLs and for molecules that can tolerate actual electron transport through them.

  20. Decelerating and Trapping Large Polar Molecules.

    PubMed

    Patterson, David

    2016-11-18

    Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.

  1. Near-field single molecule spectroscopy

    SciTech Connect

    Xie, X.S.; Dunn, R.C.

    1995-02-01

    The high spatial resolution and sensitivity of near-field fluorescence microscopy allows one to study spectroscopic and dynamical properties of individual molecules at room temperature. Time-resolved experiments which probe the dynamical behavior of single molecules are discussed. Ground rules for applying near-field spectroscopy and the effect of the aluminum coated near-field probe on spectroscopic measurements are presented.

  2. Small Molecules in the Cone Snail Arsenal.

    PubMed

    Neves, Jorge L B; Lin, Zhenjian; Imperial, Julita S; Antunes, Agostinho; Vasconcelos, Vitor; Olivera, Baldomero M; Schmidt, Eric W

    2015-10-16

    Cone snails are renowned for producing peptide-based venom, containing conopeptides and conotoxins, to capture their prey. A novel small-molecule guanine derivative with unprecedented features, genuanine, was isolated from the venom of two cone snail species. Genuanine causes paralysis in mice, indicating that small molecules and not just polypeptides may contribute to the activity of cone snail venom.

  3. Nanoscience: Single-molecule instant replay

    NASA Astrophysics Data System (ADS)

    Camillone, Nicholas

    2016-11-01

    A nanoscale imaging method that uses ultrashort light pulses to initiate and follow the motion of a single molecule adsorbed on a solid surface opens a window onto the physical and chemical dynamics of molecules on surfaces. See Letter p.263

  4. Electronic and thermal properties of Biphenyl molecules

    NASA Astrophysics Data System (ADS)

    Medina, F. G.; Ojeda, J. H.; Duque, C. A.; Laroze, D.

    2015-11-01

    Transport properties of a single Biphenyl molecule coupled to two contacts are studied. We characterise this system by a tight-binding Hamiltonian. Based on the non-equilibrium Green's functions technique with a Landauer-Büttiker formalism the transmission probability, current and thermoelectrical power are obtained. We show that the Biphenyl molecule may have semiconductor behavior for certain values of the electrode-molecule-electrode junctions and different values of the angle between the two rings of the molecule. In addition, the density of states (DOS) is calculated to compare the bandwidths with the profile of the transmission probability. DOS allows us to explain the asymmetric shape with respect to the molecule's Fermi energy.

  5. Superresolution Imaging using Single-Molecule Localization

    PubMed Central

    Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

    2013-01-01

    Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

  6. The symmetry of single-molecule conduction.

    PubMed

    Solomon, Gemma C; Gagliardi, Alessio; Pecchia, Alessandro; Frauenheim, Thomas; Di Carlo, Aldo; Reimers, Jeffrey R; Hush, Noel S

    2006-11-14

    We introduce the conductance point group which defines the symmetry of single-molecule conduction within the nonequilibrium Green's function formalism. It is shown, either rigorously or to within a very good approximation, to correspond to a molecular-conductance point group defined purely in terms of the properties of the conducting molecule. This enables single-molecule conductivity to be described in terms of key qualitative chemical descriptors that are independent of the nature of the molecule-conductor interfaces. We apply this to demonstrate how symmetry controls the conduction through 1,4-benzenedithiol chemisorbed to gold electrodes as an example system, listing also the molecular-conductance point groups for a range of molecules commonly used in molecular electronics research.

  7. Chemical principles of single-molecule electronics

    NASA Astrophysics Data System (ADS)

    Su, Timothy A.; Neupane, Madhav; Steigerwald, Michael L.; Venkataraman, Latha; Nuckolls, Colin

    2016-03-01

    The field of single-molecule electronics harnesses expertise from engineering, physics and chemistry to realize circuit elements at the limit of miniaturization; it is a subfield of nanoelectronics in which the electronic components are single molecules. In this Review, we survey the field from a chemical perspective and discuss the structure-property relationships of the three components that form a single-molecule junction: the anchor, the electrode and the molecular bridge. The spatial orientation and electronic coupling between each component profoundly affect the conductance properties and functions of the single-molecule device. We describe the design principles of the anchor group, the influence of the electronic configuration of the electrode and the effect of manipulating the structure of the molecular backbone and of its substituent groups. We discuss single-molecule conductance switches as well as the phenomenon of quantum interference and then trace their fundamental roots back to chemical principles.

  8. Single molecule junction conductance and binding geometry

    NASA Astrophysics Data System (ADS)

    Kamenetska, Maria

    This Thesis addresses the fundamental problem of controlling transport through a metal-organic interface by studying electronic and mechanical properties of single organic molecule-metal junctions. Using a Scanning Tunneling Microscope (STM) we image, probe energy-level alignment and perform STM-based break junction (BJ) measurements on molecules bound to a gold surface. Using Scanning Tunneling Microscope-based break-junction (STM-BJ) techniques, we explore the effect of binding geometry on single-molecule conductance by varying the structure of the molecules, metal-molecule binding chemistry and by applying sub-nanometer manipulation control to the junction. These experiments are performed both in ambient conditions and in ultra high vacuum (UHV) at cryogenic temperatures. First, using STM imaging and scanning tunneling spectroscopy (STS) measurements we explore binding configurations and electronic properties of an amine-terminated benzene derivative on gold. We find that details of metal-molecule binding affect energy-level alignment at the interface. Next, using the STM-BJ technique, we form and rupture metal-molecule-metal junctions ˜104 times to obtain conductance-vs-extension curves and extract most likely conductance values for each molecule. With these measurements, we demonstrated that the control of junction conductance is possible through a choice of metal-molecule binding chemistry and sub-nanometer positioning. First, we show that molecules terminated with amines, sulfides and phosphines bind selectively on gold and therefore demonstrate constant conductance levels even as the junction is elongated and the metal-molecule attachment point is modified. Such well-defined conductance is also obtained with paracyclophane molecules which bind to gold directly through the pi system. Next, we are able to create metal-molecule-metal junctions with more than one reproducible conductance signatures that can be accessed by changing junction geometry. In the

  9. Quantum transport of the single metallocene molecule

    NASA Astrophysics Data System (ADS)

    Yu, Jing-Xin; Chang, Jing; Wei, Rong-Kai; Liu, Xiu-Ying; Li, Xiao-Dong

    2016-10-01

    The Quantum transport of three single metallocene molecule is investigated by performing theoretical calculations using the non-equilibrium Green's function method combined with density functional theory. We find that the three metallocen molecules structure become stretched along the transport direction, the distance between two Cp rings longer than the other theory and experiment results. The lager conductance is found in nickelocene molecule, the main transmission channel is the electron coupling between molecule and the electrodes is through the Ni dxz and dyz orbitals and the s, dxz, dyz of gold. This is also confirmed by the highest occupied molecular orbital resonance at Fermi level. In addition, negative differential resistance effect is found in the ferrocene, cobaltocene molecules, this is also closely related with the evolution of the transmission spectrum under applied bias.

  10. Extracting Models in Single Molecule Experiments

    NASA Astrophysics Data System (ADS)

    Presse, Steve

    2013-03-01

    Single molecule experiments can now monitor the journey of a protein from its assembly near a ribosome to its proteolytic demise. Ideally all single molecule data should be self-explanatory. However data originating from single molecule experiments is particularly challenging to interpret on account of fluctuations and noise at such small scales. Realistically, basic understanding comes from models carefully extracted from the noisy data. Statistical mechanics, and maximum entropy in particular, provide a powerful framework for accomplishing this task in a principled fashion. Here I will discuss our work in extracting conformational memory from single molecule force spectroscopy experiments on large biomolecules. One clear advantage of this method is that we let the data tend towards the correct model, we do not fit the data. I will show that the dynamical model of the single molecule dynamics which emerges from this analysis is often more textured and complex than could otherwise come from fitting the data to a pre-conceived model.

  11. Laser-induced Coulomb explosion of 1,4-diiodobenzene molecules: Studies of isolated molecules and molecules in helium nanodroplets

    NASA Astrophysics Data System (ADS)

    Christiansen, Lars; Nielsen, Jens H.; Christensen, Lauge; Shepperson, Benjamin; Pentlehner, Dominik; Stapelfeldt, Henrik

    2016-02-01

    Coulomb explosion of 1,4-diiodobenzene molecules, isolated or embedded in helium nanodroplets, is induced by irradiation with an intense femtosecond laser pulse. The recoiling ion fragments are probed by time-of-flight measurements and two-dimensional velocity map imaging. Correlation analysis of the emission directions of I+ ions recoiling from each end of the molecules reveals significant deviation from axial recoil, i.e., where the I+ ions leave strictly along the I-I symmetry axis. For isolated molecules, the relative angular distribution of the I+ ions is centered at 180∘, corresponding to perfect axial recoil, but with a full width at half maximum of 30∘. For molecules inside He droplets, the width of the distribution increases to 45∘. These results provide a direct measure of the accuracy of Coulomb explosion as a probe of the spatial orientation of molecules, which is particularly relevant in connection with laser-induced molecular alignment and orientation. In addition, our studies show how it is possible to identify fragmentation pathways of the Coulomb explosion for the isolated 1,4-diiodobenzene molecules. Finally, for the 1,4-diiodobenzene molecules in He droplets, it is shown that the angular correlation between fragments from the Coulomb explosion is preserved after they have interacted with the He environment.

  12. Attachment of second harmonic-active moiety to molecules for detection of molecules at interfaces

    DOEpatents

    Salafsky, Joshua S.; Eisenthal, Kenneth B.

    2005-10-11

    This invention provides methods of detecting molecules at an interface, which comprise labeling the molecules with a second harmonic-active moiety and detecting the labeled molecules at the interface using a surface selective technique. The invention also provides methods for detecting a molecule in a medium and for determining the orientation of a molecular species within a planar surface using a second harmonic-active moiety and a surface selective technique.

  13. Search for complex organic molecules in space

    NASA Astrophysics Data System (ADS)

    Ohishi, Masatoshi

    2016-07-01

    It was 1969 when the first organic molecule in space, H2CO, was discovered. Since then many organic molecules were discovered by using the NRAO 11 m (upgraded later to 12 m), Nobeyama 45 m, IRAM 30 m, and other highly sensitive radio telescopes as a result of close collaboration between radio astronomers and microwave spectroscopists. It is noteworthy that many famous organic molecules such as CH3OH, C2H5OH, (CH3)2O and CH3NH2 were detected by 1975. Organic molecules were found in so-called hot cores where molecules were thought to form on cold dust surfaces and then to evaporate by the UV photons emitted from the central star. These days organic molecules are known to exist not only in hot cores but in hot corinos (a warm, compact molecular clump found in the inner envelope of a class 0 protostar) and even protoplanetary disks. As was described above, major organic molecules were known since 1970s. It was very natural that astronomers considered a relationship between organic molecules in space and the origin of life. Several astronomers challenged to detect glycine and other prebiotic molecules without success. ALMA is expected to detect such important materials to further consider the gexogenous deliveryh hypothesis. In this paper I summarize the history in searching for complex organic molecules together with difficulties in observing very weak signals from larger species. The awfully long list of references at the end of this article may be the most useful part for readers who want to feel the exciting discovery stories.

  14. Symmetry calculation for molecules and transition states.

    PubMed

    Vandewiele, Nick M; Van de Vijver, Ruben; Van Geem, Kevin M; Reyniers, Marie-Françoise; Marin, Guy B

    2015-01-30

    The symmetry of molecules and transition states of elementary reactions is an essential property with important implications for computational chemistry. The automated identification of symmetry by computers is a very useful tool for many applications, but often relies on the availability of three-dimensional coordinates of the atoms in the molecule and hence becomes less useful when these coordinates are a priori unavailable. This article presents a new algorithm that identifies symmetry of molecules and transition states based on an augmented graph representation of the corresponding structures, in which both topology and the presence of stereocenters are accounted for. The automorphism group order of the graph associated with the molecule or transition state is used as a starting point. A novel concept of label-stereoisomers, that is, stereoisomers that arise after labeling homomorph substituents in the original molecule so that they become distinguishable, is introduced and used to obtain the symmetry number. The algorithm is characterized by its generic nature and avoids the use of heuristic rules that would limit the applicability. The calculated symmetry numbers are in agreement with expected values for a large and diverse set of structures, ranging from asymmetric, small molecules such as fluorochlorobromomethane to highly symmetric structures found in drug discovery assays. The new algorithm opens up new possibilities for the fast screening of the degree of symmetry of large sets of molecules.

  15. Controlling polar molecules in optical lattices

    SciTech Connect

    Kotochigova, S.; Tiesinga, E.

    2006-04-15

    We theoretically investigate the interaction of polar molecules with optical lattices and microwave fields. We demonstrate the existence of frequency windows in the optical domain where the complex internal structure of the molecule does not influence the trapping potential of the lattice. In such frequency windows the Franck-Condon factors are so small that near-resonant interaction of vibrational levels of the molecule with the lattice fields have a negligible contribution to the polarizability, and light-induced decoherences are kept to a minimum. In addition, we show that microwave fields can induce a tunable dipole-dipole interaction between ground-state rotationally symmetric (J=0) molecules. A combination of a carefully chosen lattice frequency and microwave-controlled interaction between molecules will enable trapping of polar molecules in a lattice and possibly realize molecular quantum logic gates. Our results are based on ab initio relativistic electronic structure calculations of the polar KRb and RbCs molecules combined with calculations of their rovibrational motion.

  16. Trapping and manipulating single molecules of DNA

    NASA Astrophysics Data System (ADS)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  17. Optically active quantum-dot molecules.

    PubMed

    Shlykov, Alexander I; Baimuratov, Anvar S; Baranov, Alexander V; Fedorov, Anatoly V; Rukhlenko, Ivan D

    2017-02-20

    Chiral molecules made of coupled achiral semiconductor nanocrystals, also known as quantum dots, show great promise for photonic applications owing to their prospective uses as configurable building blocks for optically active structures, materials, and devices. Here we present a simple model of optically active quantum-dot molecules, in which each of the quantum dots is assigned a dipole moment associated with the fundamental interband transition between the size-quantized states of its confined charge carriers. This model is used to analytically calculate the rotatory strengths of optical transitions occurring upon the excitation of chiral dimers, trimers, and tetramers of general configurations. The rotatory strengths of such quantum-dot molecules are found to exceed the typical rotatory strengths of chiral molecules by five to six orders of magnitude. We also study how the optical activity of quantum-dot molecules shows up in their circular dichroism spectra when the energy gap between the molecular states is much smaller than the states' lifetime, and maximize the strengths of the circular dichroism peaks by optimizing orientations of the quantum dots in the molecules. Our analytical results provide clear design guidelines for quantum-dot molecules and can prove useful in engineering optically active quantum-dot supercrystals and photonic devices.

  18. A quantum gas of polar molecules

    NASA Astrophysics Data System (ADS)

    Ni, Kang-Kuen

    Ultracold polar molecular gases promise new directions and exciting applications in precision measurements, ultracold chemistry, electric-field controlled collisions, dipolar quantum gases, and quantum information sciences. This thesis presents experimental realization of a near quantum degenerate gas of polar molecules, where the phase-space density of the gas achieved is more than 10 orders of magnitude higher than previous results. The near quantum degenerate gas of polar molecules is created using two coherent steps. First, atoms in an ultracold gas mixture are converted into extremely weakly bound molecules near a Fano-Feshbach resonance. Second, the weakly bound molecules are transferred to the ro-vibronic ground state using a coherent two-photon Raman technique. The fact that these ground-state molecules are polar is confirmed with a spectroscopic measurement of the permanent electric dipole moment. Finally, manipulation of the molecular hyperfine state is demonstrated; this allows molecules to be populated in a single quantum state, in particular, the lowest energy state. With an ultracold gas of molecules, full control of molecular internal state, and electric field as a new handle, ultracold molecular collisions, including ultracold chemical reactions and dipolar collisions, are studied.

  19. Line broadening of confined CO gas: from molecule-wall to molecule-molecule collisions with pressure.

    PubMed

    Hartmann, J-M; Boulet, C; Auwera, J Vander; El Hamzaoui, H; Capoen, B; Bouazaoui, M

    2014-02-14

    The infrared absorption in the fundamental band of CO gas confined in porous silica xerogel has been recorded at room temperature for pressures between about 5 and 920 hPa using a high resolution Fourier transform spectrometer. The widths of individual lines are determined from fits of measured spectra and compared with ab initio predictions obtained from requantized classical molecular dynamics simulations. Good agreement is obtained from the low pressure regime where the line shapes are governed by molecule-wall collisions to high pressures where the influence of molecule-molecule interactions dominates. These results, together with those obtained with a simple analytical model, indicate that both mechanisms contribute in a practically additive way to the observed linewidths. They also confirm that a single collision of a molecule with a wall changes its rotational state. These results are of interest for the determination of some characteristics of the opened porosity of porous materials through optical soundings.

  20. Giant molecules composed of polar molecules and atoms in mixed dimensions

    NASA Astrophysics Data System (ADS)

    Qi, Ran; Tan, Shina

    2014-05-01

    Two or three polar molecules, confined to one or two dimensions, can form stable bound states with a single atom living in three dimensions, if the molecule and the atom can interact resonantly such that their mixed dimensional scattering length is large. We call these bound states ``giant molecules'' since it's a molecule composed of smaller molecules and atoms. We study their properties using techniques including exact numerical solution, exact qunatum diffusion Monte Carlo (QMC), Born-Oppenheimer approximation (BOA), and semiclassical approximation. These bound states have a hierarchical structure reminiscent of the celestial systems.

  1. Single molecule microscopy and spectroscopy: concluding remarks.

    PubMed

    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.

  2. Probing Intermolecular Coupled Vibrations between Two Molecules

    NASA Astrophysics Data System (ADS)

    Han, Zhumin; Czap, Gregory; Xu, Chen; Chiang, Chi-lun; Yuan, Dingwang; Wu, Ruqian; Ho, W.

    2017-01-01

    Intermolecular interactions can induce energy shifts and coupling of molecular vibrations. However, the detection of intermolecular coupled vibrations has not been reported at the single molecule level. Here we detected an intermolecular coupled vibration between two CO molecules, one on the surface and another on the tip within the gap of a subkelvin scanning tunneling microscope, and analyzed the results by density functional calculations. We attribute the evolution of the energy and intensity of this coupled vibration as a function of tip-sample distance to the tilting and orbital alignment of the two CO molecules.

  3. Affibody molecules as engineered protein drugs

    PubMed Central

    Frejd, Fredrik Y; Kim, Kyu-Tae

    2017-01-01

    Affibody molecules can be used as tools for molecular recognition in diagnostic and therapeutic applications. There are several preclinical studies reported on diagnostic and therapeutic use of this molecular class of alternative scaffolds, and early clinical evidence is now beginning to accumulate that suggests the Affibody molecules to be efficacious and safe in man. The small size and ease of engineering make Affibody molecules suitable for use in multispecific constructs where AffiMabs is one such that offers the option to potentiate antibodies for use in complex disease. PMID:28336959

  4. Life at the Single Molecule Level

    SciTech Connect

    Xie, Xiaoliang Sunny

    2011-03-04

    In a living cell, gene expression—the transcription of DNA to messenger RNA followed by translation to protein—occurs stochastically, as a consequence of the low copy number of DNA and mRNA molecules involved. Can one monitor these processes in a living cell in real time? How do cells with identical genes exhibit different phenotypes? Recent advances in single-molecule imaging in living bacterial cells allow these questions to be answered at the molecular level in a quantitative manner. It was found that rare events of single molecules can have important biological consequences.

  5. Synaptic Cell Adhesion Molecules in Alzheimer's Disease

    PubMed Central

    Leshchyns'ka, Iryna

    2016-01-01

    Alzheimer's disease (AD) is a neurodegenerative brain disorder associated with the loss of synapses between neurons in the brain. Synaptic cell adhesion molecules are cell surface glycoproteins which are expressed at the synaptic plasma membranes of neurons. These proteins play key roles in formation and maintenance of synapses and regulation of synaptic plasticity. Genetic studies and biochemical analysis of the human brain tissue, cerebrospinal fluid, and sera from AD patients indicate that levels and function of synaptic cell adhesion molecules are affected in AD. Synaptic cell adhesion molecules interact with Aβ, a peptide accumulating in AD brains, which affects their expression and synaptic localization. Synaptic cell adhesion molecules also regulate the production of Aβ via interaction with the key enzymes involved in Aβ formation. Aβ-dependent changes in synaptic adhesion affect the function and integrity of synapses suggesting that alterations in synaptic adhesion play key roles in the disruption of neuronal networks in AD. PMID:27242933

  6. Single molecule fluorescence and force microscopy.

    PubMed

    Schütz, G J; Hinterdorfer, P

    2002-12-01

    The investigation of biomolecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states occurring highly correlated in space and time within an arrangement of various elements. Recent advances in the development of new microscopy techniques with sensitivity at the single molecule have gained access to essentially new types of information obtainable from imaging biomolecular samples. These methodologies are described here in terms of their applicability to the in vivo detection and visualization of molecular processes on surfaces, membranes, and cells. First examples of single molecule microscopy on cell membranes revealed new basic insight into the lateral organization of the plasma membrane, providing the captivating perspective of an ultra-sensitive methodology as a general tool to study local processes and heterogeneities in living cells.

  7. Variationally optimized basis orbitals for biological molecules

    NASA Astrophysics Data System (ADS)

    Ozaki, T.; Kino, H.

    2004-12-01

    Numerical atomic basis orbitals are variationally optimized for biological molecules such as proteins, polysaccharides, and deoxyribonucleic acid within a density functional theory. Based on a statistical treatment of results of a fully variational optimization of basis orbitals ( full optimized basis orbitals) for 43 biological model molecules, simple sets of preoptimized basis orbitals classified under the local chemical environment (simple preoptimized basis orbitals) are constructed for hydrogen, carbon, nitrogen, oxygen, phosphorous, and sulfur atoms, each of which contains double valence plus polarization basis function. For a wide variety of molecules we show that the simple preoptimized orbitals provide well convergent energy and physical quantities comparable to those calculated by the full optimized orbitals, which demonstrates that the simple preoptimized orbitals possess substantial transferability for biological molecules.

  8. Stochastic Models of Molecule Formation on Dust

    NASA Technical Reports Server (NTRS)

    Charnley, Steven; Wirstroem, Eva

    2011-01-01

    We will present new theoretical models for the formation of molecules on dust. The growth of ice mantles and their layered structure is accounted for and compared directly to observations through simulation of the expected ice absorption spectra

  9. SINGLE MOLECULE ENZYMOLOGY FINDS ITS STRIDE.

    PubMed

    Perkel, Jeffrey

    2015-10-01

    More techniques aimed at probing the nature of single molecules are being developed and advanced in biophysics labs. Jeffrey Perkel takes a look at the scientists leading the charge into the micro-world.

  10. Macronuclear gene-sized molecules of hypotrichs.

    PubMed Central

    Hoffman, D C; Anderson, R C; DuBois, M L; Prescott, D M

    1995-01-01

    The macronuclear genome of hypotrichous ciliates consists of DNA molecules of gene-sized length. A macronuclear DNA molecule contains a single coding region. We have analyzed the many hypotrich macronuclear DNA sequences sequenced by us and others. No highly conserved promoter sequences nor replication initiation sequences have been identified in the 5' nor in the 3' non-translated regions, suggesting that promoter function in hypotrichs may differ from other eukaryotes. The macronuclear genes are intron-poor; approximately 19% of the genes sequenced to date have one to three introns. Not all macronuclear DNA molecules may be transcribed; some macronuclear molecules may not have any coding function. Codon bias in hypotrichs is different in many respects from other ciliates and from other eukaryotes. PMID:7753617

  11. Dynamics of molecules in extreme rotational states

    PubMed Central

    Yuan, Liwei; Teitelbaum, Samuel W.; Robinson, Allison; Mullin, Amy S.

    2011-01-01

    We have constructed an optical centrifuge with a pulse energy that is more than 2 orders of magnitude larger than previously reported instruments. This high pulse energy enables us to create large enough number densities of molecules in extreme rotational states to perform high-resolution state-resolved transient IR absorption measurements. Here we report the first studies of energy transfer dynamics involving molecules in extreme rotational states. In these studies, the optical centrifuge drives CO2 molecules into states with J ∼ 220 and we use transient IR probing to monitor the subsequent rotational, translational, and vibrational energy flow dynamics. The results reported here provide the first molecular insights into the relaxation of molecules with rotational energy that is comparable to that of a chemical bond.

  12. Electronic Structure of Small Lanthanide Containing Molecules

    NASA Astrophysics Data System (ADS)

    Kafader, Jared O.; Ray, Manisha; Topolski, Josey E.; Chick Jarrold, Caroline

    2016-06-01

    Lanthanide-based materials have unusual electronic properties because of the high number of electronic degrees of freedom arising from partial occupation of 4f orbitals, which make these materials optimal for their utilization in many applications including electronics and catalysis. Electronic spectroscopy of small lanthanide molecules helps us understand the role of these 4f electrons, which are generally considered core-like because of orbital contraction, but are energetically similar to valence electrons. The spectroscopy of small lanthanide-containing molecules is relatively unexplored and to broaden this understanding we have completed the characterization of small cerium, praseodymium, and europium molecules using photoelectron spectroscopy coupled with DFT calculations. The characterization of PrO, EuH, EuO/EuOH, and CexOy molecules have allowed for the determination of their electron affinity, the assignment of numerous anion to neutral state transitions, modeling of anion/neutral structures and electron orbital occupation.

  13. Recovery of tritium from tritiated molecules

    DOEpatents

    Swansiger, W.A.

    1984-10-17

    This invention relates to the recovery of tritium from various tritiated molecules by reaction with uranium. More particularly, the invention relates to the recovery of tritium from tritiated molecules by reaction with uranium wherein the reaction is conducted in a reactor which permits the reaction to occur as a moving front reaction from the point where the tritium enters the reactor charged with uranium down the reactor until the uranium is exhausted.

  14. Hadronic molecules in the heavy baryon spectrum

    SciTech Connect

    Entem, D. R.; Fernández, F.; Ortega, P. G.

    2016-01-22

    We study possible baryon molecules in the non-strange heavy baryon spectrum. We include configurations with a heavy-meson and a light baryon. We find several structures, in particular we can understand the Λ{sub c}(2940) as a D*N molecule with J{sup P} = 3/2{sup −} quantum numbers. We also find D{sup (*)}Δ candidates for the recently discovered X{sub c}(3250) resonance.

  15. Do triatomic molecules echo atomic periodicity?

    SciTech Connect

    Hefferlin, R. Barrow, J.

    2015-03-30

    Demonstrations of periodicity among triatomic-molecular spectroscopic constants underscore the role of the periodic law as a foundation of chemistry. The objective of this work is to prepare for another test using vibration frequencies ν{sub 1} of free, ground-state, main-group triatomic molecules. Using data from four data bases and from computation, we have collected ν{sub 1} data for molecules formed from second period atoms.

  16. Modelling water molecules inside cyclic peptide nanotubes

    NASA Astrophysics Data System (ADS)

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

    Cyclic peptide nanotubes occur during the self-assembly process of cyclic peptides. Due to the ease of synthesis and ability to control the properties of outer surface and inner diameter by manipulating the functional side chains and the number of amino acids, cyclic peptide nanotubes have attracted much interest from many research areas. A potential application of peptide nanotubes is their use as artificial transmembrane channels for transporting ions, biomolecules and waters into cells. Here, we use the Lennard-Jones potential and a continuum approach to study the interaction of a water molecule in a cyclo[(- D-Ala- L-Ala)_4-] peptide nanotube. Assuming that each unit of a nanotube comprises an inner and an outer tube and that a water molecule is made up of a sphere of two hydrogen atoms uniformly distributed over its surface and a single oxygen atom at the centre, we determine analytically the interaction energy of the water molecule and the peptide nanotube. Using this energy, we find that, independent of the number of peptide units, the water molecule will be accepted inside the nanotube. Once inside the nanotube, we show that a water molecule prefers to be off-axis, closer to the surface of the inner nanotube. Furthermore, our study of two water molecules inside the peptide nanotube supports the finding that water molecules form an array of a 1-2-1-2 file inside peptide nanotubes. The theoretical study presented here can facilitate thorough understanding of the behaviour of water molecules inside peptide nanotubes for applications, such as artificial transmembrane channels.

  17. Trapping and Cooling of Polar Molecules

    DTIC Science & Technology

    2013-02-27

    force via radiative cycling in SrF molecules. We demonstrated the ability to create an effective cycling transition in SrF molecules, using only 2-3... Zeeman sublevels). With two lasers, we demonstrated up to 100 photon scattering events with loss too small to observe (ɝ%). The number of scattered...scattering. In the course of these measurements, we understood that the dark Zeeman and vibrational sublevels in the ground state of our cycling

  18. Laser-Assisted Single Molecule Refolding

    NASA Astrophysics Data System (ADS)

    Zhao, Rui; Marshall, Myles; Aleman, Elvin; Lamichhane, Rajan; Rueda, David

    2010-03-01

    In vivo, many RNA molecules can adopt multiple conformations depending on their biological context such as the HIV Dimerization Initiation Sequence (DIS) or the DsrA RNA in bacteria. It is quite common that the initial interaction between the two RNAs takes place via complementary unpaired regions, thus forming a so-called kissing complex. However, the exact kinetic mechanism by which the two RNA molecules reach the dimerized state is still not well understood. To investigate the refolding energy surface of RNA molecules, we have developed new technology based on the combination of single molecule spectroscopy with laser induced temperature jump kinetics, called Laser Assisted Single-molecule Refolding (LASR). LASR enables us to induce folding reactions of otherwise kinetically trapped RNAs at the single molecule level, and to characterize their folding landscape. LASR provides an exciting new approach to study molecular memory effects and kinetically trapped RNAs in general. LASR should be readily applicable to study DNA and protein folding as well.

  19. Electron-triggered motions in technomimetic molecules.

    PubMed

    Carella, Alexandre; Coudret, Christophe; Guirado, Gonzalo; Rapenne, Gwénaël; Vives, Guillaume; Launay, Jean-Pierre

    2007-01-14

    Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with motions triggered by electrons. The first part is devoted to our work in the field of molecular switches: after having demonstrated the possibility of controlling an intramolecular electron transfer by photoisomerisation, we are now trying to control the isomerisation, either by electrochemistry, or by embedding the photochromic compound in a self-assembled monolayer and testing the electrical conduction with a STM tip. In a second part, we present our strategy on controlling the rotation in a molecular rotary motor and the family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active groups, so that addressing the molecule with nano-electrodes would trigger rotation. The electrical control of the charge state of a molecule by a STM tip is developed in a final part.

  20. Single Molecule Raman Spectroscopy Under High Pressure

    NASA Astrophysics Data System (ADS)

    Fu, Yuanxi; Dlott, Dana

    2014-06-01

    Pressure effects on surface-enhanced Raman scattering spectra of Rhdoamine 6G adsorbed on silver nanoparticle surfaces was studied using a confocal Raman microscope. Colloidal silver nanoparticles were treated with Rhodamine 6G (R6G) and its isotopically substituted partner, R6G-d4. Mixed isotopomers let us identify single-molecule spectra, since multiple-molecule spectra would show vibrational transitions from both species. The nanoparticles were embedded into a poly vinyl alcohol film, and loaded into a diamond anvil cell for the high-pressure Raman scattering measurement. Argon was the pressure medium. Ambient pressure Raman scattering spectra showed few single-molecule spectra. At moderately high pressure ( 1GPa), a surprising effect was observed. The number of sites with observable spectra decreased dramatically, and most of the spectra that could be observed were due to single molecules. The effects of high pressure suppressed the multiple-molecule Raman sites, leaving only the single-molecule sites to be observed.

  1. Quantitative Aspects of Single Molecule Microscopy

    PubMed Central

    Ober, Raimund J.; Tahmasbi, Amir; Ram, Sripad; Lin, Zhiping; Ward, E. Sally

    2015-01-01

    Single molecule microscopy is a relatively new optical microscopy technique that allows the detection of individual molecules such as proteins in a cellular context. This technique has generated significant interest among biologists, biophysicists and biochemists, as it holds the promise to provide novel insights into subcellular processes and structures that otherwise cannot be gained through traditional experimental approaches. Single molecule experiments place stringent demands on experimental and algorithmic tools due to the low signal levels and the presence of significant extraneous noise sources. Consequently, this has necessitated the use of advanced statistical signal and image processing techniques for the design and analysis of single molecule experiments. In this tutorial paper, we provide an overview of single molecule microscopy from early works to current applications and challenges. Specific emphasis will be on the quantitative aspects of this imaging modality, in particular single molecule localization and resolvability, which will be discussed from an information theoretic perspective. We review the stochastic framework for image formation, different types of estimation techniques and expressions for the Fisher information matrix. We also discuss several open problems in the field that demand highly non-trivial signal processing algorithms. PMID:26167102

  2. Sol-gel method for encapsulating molecules

    DOEpatents

    Brinker, C. Jeffrey; Ashley, Carol S.; Bhatia, Rimple; Singh, Anup K.

    2002-01-01

    A method for encapsulating organic molecules, and in particular, biomolecules using sol-gel chemistry. A silica sol is prepared from an aqueous alkali metal silicate solution, such as a mixture of silicon dioxide and sodium or potassium oxide in water. The pH is adjusted to a suitably low value to stabilize the sol by minimizing the rate of siloxane condensation, thereby allowing storage stability of the sol prior to gelation. The organic molecules, generally in solution, is then added with the organic molecules being encapsulated in the sol matrix. After aging, either a thin film can be prepared or a gel can be formed with the encapsulated molecules. Depending upon the acid used, pH, and other processing conditions, the gelation time can be from one minute up to several days. In the method of the present invention, no alcohols are generated as by-products during the sol-gel and encapsulation steps. The organic molecules can be added at any desired pH value, where the pH value is generally chosen to achieve the desired reactivity of the organic molecules. The method of the present invention thereby presents a sufficiently mild encapsulation method to retain a significant portion of the activity of the biomolecules, compared with the activity of the biomolecules in free solution.

  3. Vibrational Cooling of Photoassociated Homonuclear Cold Molecules

    NASA Astrophysics Data System (ADS)

    Passagem, Henry; Ventura, Paulo; Tallant, Jonathan; Marcassa, Luis

    2015-05-01

    In this work, we produce vibrationally cold homonuclear Rb molecules using spontaneous optical pumping. The vibrationally cooled molecules are produced in three steps. In the first step, we use a photoassociation laser to produce molecules in high vibrational levels of the singlet ground state. Then in a second step, a 50 W broadband laser at 1071 nm, which bandwidth is about 2 nm, is used to transfer the molecules to lower vibrational levels via optical pumping through the excited state. This process transfers the molecules from vibrational levels around ν ~= 113 to a distribution of levels below ν = 35 . The molecules can be further cooled using a broadband light source near 685 nm. In order to obtain such broadband source, we have used a 5 mW superluminescent diode, which is amplified in a tapered amplifier using a double pass configuration. After the amplification, the spectrum is properly shaped and we end up with about 90 mW distributed in the 682-689 nm range. The final vibrational distribution is probed using resonance-enhanced multiphoton ionization with a pulsed dye laser near 670 nm operating at 4KHz. The results are presented and compared with theoretical simulations. This work was supported by Fapesp and INCT-IQ.

  4. Unwinding of circular helicoidal molecules vs. size

    NASA Astrophysics Data System (ADS)

    Zoli, Marco

    2015-04-01

    The thermodynamical stability of a set of circular double helical molecules is analyzed by path integral techniques. The minicircles differ only in i) the radius and ii) the number of base pairs (N) arranged along the molecule axis. Instead, the rise distance is kept constant. For any molecule size, the computational method simulates a broad ensemble of possible helicoidal configurations while the partition function is a sum over the path trajectories describing the base pair fluctuational states. The stablest helical repeat of every minicircle is determined by free-energy minimization. We find that, for molecules with N larger than 100, the helical repeat grows linearly with size and the twist number is constant. On the other hand, by reducing the size below 100 base pairs, the double helices sharply unwind and the twist number drops to one for N = 20. This is predicted as the minimum size for the existence of helicoidal molecules in the closed form. The helix unwinding appears as a strategy to release the bending stress associated to the circularization of the molecules.

  5. Molecules on si: electronics with chemistry.

    PubMed

    Vilan, Ayelet; Yaffe, Omer; Biller, Ariel; Salomon, Adi; Kahn, Antoine; Cahen, David

    2010-01-12

    Basic scientific interest in using a semiconducting electrode in molecule-based electronics arises from the rich electrostatic landscape presented by semiconductor interfaces. Technological interest rests on the promise that combining existing semiconductor (primarily Si) electronics with (mostly organic) molecules will result in a whole that is larger than the sum of its parts. Such a hybrid approach appears presently particularly relevant for sensors and photovoltaics. Semiconductors, especially Si, present an important experimental test-bed for assessing electronic transport behavior of molecules, because they allow varying the critical interface energetics without, to a first approximation, altering the interfacial chemistry. To investigate semiconductor-molecule electronics we need reproducible, high-yield preparations of samples that allow reliable and reproducible data collection. Only in that way can we explore how the molecule/electrode interfaces affect or even dictate charge transport, which may then provide a basis for models with predictive power.To consider these issues and questions we will, in this Progress Report, review junctions based on direct bonding of molecules to oxide-free Si.describe the possible charge transport mechanisms across such interfaces and evaluate in how far they can be quantified.investigate to what extent imperfections in the monolayer are important for transport across the monolayer.revisit the concept of energy levels in such hybrid systems.

  6. Spin-orbit driven Peierls transition and possible exotic superconductivity in CsW2O6

    NASA Astrophysics Data System (ADS)

    Streltsov, Sergey V.; Mazin, Igor I.; Heid, Rolf; Bohnen, Klaus-Peter

    2016-12-01

    We study ab initio a pyrochlore compound, CsW2O6 , which exhibits a yet unexplained metal-insulator transition. We find that (1) the reported low-T structure is likely inaccurate and the correct structure has a twice larger cell; (2) the insulating phase is not of a Mott or dimer-singlet nature, but a rare example of a three-dimensional Peierls transition, with a simultaneous condensation of three density waves; (3) the spin-orbit interaction plays a crucial role, forming well-nested bands. The high-T (HT) phase, if stabilized, could harbor a unique eg+i eg superconducting state that breaks time reversal symmetry, but is not chiral. This state was predicted in 1999, but not observed. We speculate about possible ways to stabilize the HT phase while keeping the conditions for superconductivity.

  7. Spin-orbit-driven magnetic structure and excitation in the 5d pyrochlore Cd2Os2O7

    DOE PAGES

    Calder, Stuart A; Vale, James G.; Bogdanov, Nikolay; ...

    2016-06-07

    Here, much consideration has been given to the role of spin-orbit coupling (SOC) in 5d oxides, particularly on the formation of novel electronic states and manifested metal-insulator transitions (MITs). SOC plays a dominant role in 5d5 iridates (Ir4+), undergoing MITs both concurrent (pyrochlores) and separated (perovskites) from the onset of magnetic order. However, the role of SOC for other 5d configurations is less clear. For example, 5d3 (Os5+) systems are expected to have an orbital singlet with reduced effective SOC. The pyrochlore Cd2Os2O7 nonetheless exhibits a MIT entwined with magnetic order phenomenologically similar to pyrochlore iridates. Here, we resolve themore » magnetic structure in Cd2Os2O7 with neutron diffraction and then via resonant inelastic X-ray scattering determine the salient electronic and magnetic energy scales controlling the MIT. In particular, SOC plays a subtle role in creating the electronic ground state but drives the magnetic order and emergence of a multiple spin-flip magnetic excitation.« less

  8. Unconventional magnetism in the spin-orbit-driven Mott insulators Ba3MIr2O9 (M=Sc,Y)

    NASA Astrophysics Data System (ADS)

    Dey, Tusharkanti; Kumar, R.; Mahajan, A. V.; Kaushik, S. D.; Siruguri, V.

    2014-05-01

    We have carried out detailed bulk and local probe studies on the hexagonal oxides Ba3MIr2O9 (M=Sc,Y), where Ir is expected to have a fractional oxidation state of +4.5. In the structure, Ir-Ir dimers are arranged in an edge-shared triangular network parallel to the ab plane. Whereas only weak anomalies are evident in the susceptibility data, clearer anomalies are present in the heat capacity data—around 10 K for Ba3ScIr2O9 and at 4 K for Ba3YIr2O9. Our 45Sc nuclear magnetic resonance (NMR) line shape (first-order quadrupole split) is symmetric at room temperature but becomes progressively asymmetric with decreasing temperatures indicating the presence of developing inequivalent Sc environments. This is suggestive of distortions in the structure which could arise from progressive tilt/rotation of the IrO6 octahedra with a decrease in temperature T. The 45Sc NMR spectral weight shifts near the reference frequency with decreasing T indicating the development of magnetic singlet regions. Around 10 K, a significant change in the spectrum takes place with a large intensity appearing near the reference frequency but with the spectrum remaining multipeak. It appears from our 45Sc NMR data that in Ba3ScIr2O9 significant disorder is still present below 10 K. In the case of Ba3YIr2O9, the 89Y NMR spectral lines are asymmetric at high temperatures but become nearly symmetric (single magnetic environment) below T ˜70 K. Our 89Y spectra and T1 measurements confirm the onset of long-range ordering from a bulk of the sample at 4 K in this compound. Our results suggest that Ba3YIr2O9 might be structurally distorted at room temperature (via, for example, tilt/rotations of the IrO6 octahedra) but becomes progressively a regular triangular lattice with decreasing T. The effective magnetic moments and magnetic entropy changes are strongly reduced in Ba3YIr2O9 as compared to those expected for a S =1/2 system. Similar effects have been found in other iridates which naturally have strong spin-orbit coupling.

  9. Spin-orbit driven magnetic insulating state with Jeff=1/2 character in a 4d oxide

    DOE PAGES

    Calder, S.; Li, Ling; Okamoto, Satoshi; ...

    2015-11-30

    The unusual magnetic and electronic ground states of 5d iridates has been shown to be driven by intrinsically enhanced spin-orbit coupling (SOC). The influence of appreciable but reduced SOC in creating the manifested magnetic insulating states in 4d oxides is less clear, with one hurdle being the existence of such compounds. Here we present experimental and theoretical results on Sr4RhO6 that reveal SOC dominated behavior. Neutron measurements show the octahedra are both spatially separated and locally ideal, making the electronic ground state susceptible to alterations by SOC. Magnetic ordering is observed with a similar structure to an analogous Jeff=1/2 Mottmore » iridate. We consider the underlying role of SOC in this rhodate with density functional theory and x-ray absorption spectroscopy and find a magnetic insulating ground state with Jeff =1/2 character.The unusual magnetic and electronic ground states of 5d iridates have been shown to be driven by intrinsically enhanced spin-orbit coupling (SOC). The influence of appreciable but reduced SOC in creating the manifested magnetic insulating states in 4d oxides is less clear, with one hurdle being the existence of such compounds. Here, we present experimental and theoretical results on Sr4RhO6 that reveal SOC dominated behavior. Neutron measurements show the octahedra are both spatially separated and locally ideal, making the electronic ground state susceptible to alterations by SOC. Magnetic ordering is observed with a similar structure to an analogous Jeff=1/2 Mott iridate. We consider the underlying role of SOC in this rhodate with density functional theory and x-ray absorption spectroscopy, and find a magnetic insulating ground state with Jeff=12 character.« less

  10. Spin-orbit-driven magnetic structure and excitation in the 5d pyrochlore Cd2Os2O7

    PubMed Central

    Calder, S.; Vale, J. G.; Bogdanov, N. A.; Liu, X.; Donnerer, C.; Upton, M. H.; Casa, D.; Said, A. H.; Lumsden, M. D.; Zhao, Z.; Yan, J. -Q.; Mandrus, D.; Nishimoto, S.; van den Brink, J.; Hill, J. P.; McMorrow, D. F.; Christianson, A. D.

    2016-01-01

    Much consideration has been given to the role of spin-orbit coupling (SOC) in 5d oxides, particularly on the formation of novel electronic states and manifested metal-insulator transitions (MITs). SOC plays a dominant role in 5d5 iridates (Ir4+), undergoing MITs both concurrent (pyrochlores) and separated (perovskites) from the onset of magnetic order. However, the role of SOC for other 5d configurations is less clear. For example, 5d3 (Os5+) systems are expected to have an orbital singlet with reduced effective SOC. The pyrochlore Cd2Os2O7 nonetheless exhibits a MIT entwined with magnetic order phenomenologically similar to pyrochlore iridates. Here, we resolve the magnetic structure in Cd2Os2O7 with neutron diffraction and then via resonant inelastic X-ray scattering determine the salient electronic and magnetic energy scales controlling the MIT. In particular, SOC plays a subtle role in creating the electronic ground state but drives the magnetic order and emergence of a multiple spin-flip magnetic excitation. PMID:27273216

  11. The reaction dynamics of alkali dimer molecules and electronically excited alkali atoms with simple molecules

    SciTech Connect

    Hou, Hongtao

    1995-12-01

    This dissertation presents the results from the crossed molecular beam studies on the dynamics of bimolecular collisions in the gas phase. The primary subjects include the interactions of alkali dimer molecules with simple molecules, and the inelastic scattering of electronically excited alkali atoms with O2. The reaction of the sodium dimers with oxygen molecules is described in Chapter 2. Two reaction pathways were observed for this four-center molecule-molecule reaction, i.e. the formations of NaO2 + Na and NaO + NaO. NaO2 products exhibit a very anisotropic angular distribution, indicating a direct spectator stripping mechanism for this reaction channel. The NaO formation follows the bond breaking of O2, which is likely a result of a charge transfer from Na2 to the excited state orbital of O2-. The scattering of sodium dimers from ammonium and methanol produced novel molecules, NaNH3 and Na(CH3OH), respectively. These experimental observations, as well as the discussions on the reaction dynamics and the chemical bonding within these molecules, will be presented in Chapter 3. The lower limits for the bond dissociation energies of these molecules are also obtained. Finally, Chapter 4 describes the energy transfer between oxygen molecules and electronically excited sodium atoms.

  12. Single-molecule detection with active transport

    NASA Astrophysics Data System (ADS)

    Ball, David Allan

    A glass capillary is used near the focal region of a custom-built confocal microscope to investigate the use of active transport for single-molecule detection in solution, with both one and two-photon laser excitation. The capillary tip has a diameter of several microns and is carefully aligned nearby to the sub-micron laser beam waist, collinear to the optical axis, so that a negative pressure-difference causes molecules to be drawn into the capillary, along the laser beam axis. The flow of solution, which is characterized by fluorescence correlation spectroscopy (FCS), can increase the single-molecule detection rate for slowly diffusing proteins by over a factor of 100, while the mean rate of photons during each burst is similar to that for random diffusional transport. Also, the flow is along the longest axis of the ellipsoidally-shaped confocal volume, which results in more collected photons per molecule than that for transverse flow at the same speed. When transport is dominated by flow, FCS can no longer distinguish molecules with differing translational diffusion, and hence a fluorescence fluctuation spectroscopy method based on differences in fluorescence brightness is investigated as a means for assaying different solution components, for applications in pharmaceutical drug discovery. Multi-channel fluctuation spectroscopy techniques can also be used for assays with the flow system and hence this dissertation also reports the characterization of a prototype 4-channel single-photon detector with a two-wavelength polarization-resolved optical set-up.

  13. Small Molecule Immunosensing Using Surface Plasmon Resonance

    PubMed Central

    Mitchell, John

    2010-01-01

    Surface plasmon resonance (SPR) biosensors utilize refractive index changes to sensitively detect mass changes at noble metal sensor surface interfaces. As such, they have been extensively applied to immunoassays of large molecules, where their high mass and use of sandwich immunoassay formats can result in excellent sensitivity. Small molecule immunosensing using SPR is more challenging. It requires antibodies or high-mass or noble metal labels to provide the required signal for ultrasensitive assays. Also, it can suffer from steric hindrance between the small antigen and large antibodies. However, new studies are increasingly meeting these and other challenges to offer highly sensitive small molecule immunosensor technologies through careful consideration of sensor interface design and signal enhancement. This review examines the application of SPR transduction technologies to small molecule immunoassays directed to different classes of small molecule antigens, including the steroid hormones, toxins, drugs and explosives residues. Also considered are the matrix effects resulting from measurement in chemically complex samples, the construction of stable sensor surfaces and the development of multiplexed assays capable of detecting several compounds at once. Assay design approaches are discussed and related to the sensitivities obtained. PMID:22163605

  14. Double point contact single molecule absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Howard, John Brooks

    Our primary objective with the presentation of this thesis is to utilize superconducting transport through microscopic objects to both excite and analyze the vibrational degrees of freedom of various molecules of a biological nature. The technique stems from a Josephson junction's ability to generate radiation that falls in the terahertz gap (≈ 10 THz) and consequently can be used to excite vibrational modes of simple and complex molecules. Analysis of the change in IV characteristics coupled with the differential conductance dIdV allows determination of both the absorption spectra and the vibrational modes of biological molecules. Presented here are both the theoretical foundations of superconductivity relevant to our experimental technique and the fabrication process of our samples. Comparisons between our technique and that of other absorption spectroscopy techniques are included as a means of providing a reference upon which to judge the merits of our novel procedure. This technique is meant to improve not only our understanding of the vibrational degrees of freedom of useful biological molecules, but also these molecule's structural, electronic and mechanical properties.

  15. Single-Molecule Imaging of Nuclear Transport

    PubMed Central

    Goryaynov, Alexander; Sarma, Ashapurna; Ma, Jiong; Yang, Weidong

    2010-01-01

    The utility of single molecule fluorescence microscopy approaches has been proven to be of a great avail in understanding biological reactions over the last decade. The investigation of molecular interactions with high temporal and spatial resolutions deep within cells has remained challenging due to the inherently weak signals arising from individual molecules. Recent works by Yang et al. demonstrated that narrow-field epifluorescence microscopy allows visualization of nucleocytoplasmic transport at the single molecule level. By the single molecule approach, important kinetics, such as nuclear transport time and efficiency, for signal-dependent and independent cargo molecules have been obtained. Here we described a protocol for the methodological approach with an improved spatiotemporal resolution of 0.4 ms and 12 nm. The improved resolution enabled us to capture transient active transport and passive diffusion events through the nuclear pore complexes (NPC) in semi-intact cells. We expect this method to be used in elucidating other binding and trafficking events within cells. PMID:20548283

  16. Classical interaction model for the water molecule.

    PubMed

    Baranyai, András; Bartók, Albert

    2007-05-14

    The authors propose a new classical model for the water molecule. The geometry of the molecule is built on the rigid TIP5P model and has the experimental gas phase dipole moment of water created by four equal point charges. The model preserves its rigidity but the size of the charges increases or decreases following the electric field created by the rest of the molecules. The polarization is expressed by an electric field dependent nonlinear polarization function. The increasing dipole of the molecule slightly increases the size of the water molecule expressed by the oxygen-centered sigma parameter of the Lennard-Jones interaction. After refining the adjustable parameters, the authors performed Monte Carlo simulations to check the ability of the new model in the ice, liquid, and gas phases. They determined the density and internal energy of several ice polymorphs, liquid water, and gaseous water and calculated the heat capacity, the isothermal compressibility, the isobar heat expansion coefficients, and the dielectric constant of ambient water. They also determined the pair-correlation functions of ambient water and calculated the energy of the water dimer. The accuracy of theirs results was satisfactory.

  17. Capillary condensation of short-chain molecules.

    PubMed

    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.

  18. Figuration and detection of single molecules

    NASA Astrophysics Data System (ADS)

    Nevels, R.; Welch, G. R.; Cremer, P. S.; Hemmer, P.; Phillips, T.; Scully, S.; Sokolov, A. V.; Svidzinsky, A. A.; Xia, H.; Zheltikov, A.; Scully, M. O.

    2012-08-01

    Recent advances in the description of atoms and molecules based on Dimensional scaling analysis, developed by Dudley Herschbach and co-workers, provided new insights into visualization of molecular structure and chemical bonding. Prof. Herschbach is also a giant in the field of single molecule scattering. We here report on the engineering of molecular detectors. Such systems have a wide range of application from medical diagnostics to the monitoring of chemical, biological and environmental hazards. We discuss ways to identify preselected molecules, in particular, mycotoxin contaminants using coherent laser spectroscopy. Mycotoxin contaminants, e.g. aflatoxin B1 which is present in corn and peanuts, are usually analysed by time-consuming microscopic, chemical and biological assays. We present a new approach that derives from recent experiments in which molecules are prepared by one (or more) femtosecond laser(s) and probed by another set. We call this technique FAST CARS (femto second adaptive spectroscopic technique for coherent anti-Stokes Raman spectroscopy). We propose and analyse ways in which FAST CARS can be used to identify preselected molecules, e.g. aflatoxin, rapidly and economically.

  19. Direct laser cooling of the BH molecule

    NASA Astrophysics Data System (ADS)

    Holland, Darren; Truppe, Stefan; Hendricks, Richard; Sauer, Ben; Tarbutt, Michael

    2015-03-01

    Ultracold polar molecules are of interest for a variety of applications, including tests of fundamental physics, ultracold chemistry, and simulation of many-body quantum systems. The laser cooling techniques that have been so successful in producing ultracold atoms are difficult to apply to molecules. Recently however, laser cooling has been applied successfully to a few molecular species, and a magneto-optical trap of SrF molecules has now been demonstrated. We have investigated the BH molecule as a candidate for laser cooling. We have produced a molecular beam of BH and have measured the branching ratios for the excited electronic state, A1 Π (v' = 0) , to decay to the various vibrational states of the ground electronic state, X1 Σ . We verify that the branching ratio for the spin-forbidden transition to an intermediate triplet state is inconsequentially small. We measure the frequency of the lowest rotational transition of the X state, and the hyperfine structure in the relevant levels of both the X and A states, and determine the nuclear electric quadrupole and magnetic dipole coupling constants. Our results show that a relatively simple laser cooling scheme can be used to cool, slow and trap BH molecules.

  20. Modelling the spectroscopic behaviour of hot molecules

    NASA Astrophysics Data System (ADS)

    Tennyson, Jonathan

    2010-05-01

    At elevated temperatures the molecules absorb and emit light in a very complicated fashion which is hard to characterise on the basis of laboraroty measurement. Computed line lists of molecule transitions therefore provide a vital input for models of hot atmospheres. I will describe the calculation and use of such line lists including the BT2 water line list [1], which contains some 500 million distinct rotation-vibration transitions. This linelist proved crucial in the detection of water in extrasolar planet HD189733b and has been used extensively in atmospheric modelling. Illustrations will be given at the meeting. A new linelist for the ammonia molecule has just been completed [2] which shows that standard compilations for this molecule need to be improved. Progress on a more extensive linelist for hot ammonia and linelists for other molecules will be discussed at the meeting. [1] R.J. Barber, J. Tennyson, G.J. Harris and R.N. Tolchenov, Mon. Not. R. Astr. Soc., 368, 1087-1094 (2006) [2] S.N. Yurchenko, R.J. Barber, A. Yachmenev, W. Theil, P. Jensen and J. Tennyson, J. Phys. Chem. A, 113, 11845-11855 (2009).

  1. Mining for Molecules in the Milky Way

    NASA Astrophysics Data System (ADS)

    2008-06-01

    Scientists are using the giant Robert C. Byrd Green Bank Telescope (GBT) to go prospecting in a rich molecular cloud in our Milky Way Galaxy. They seek to discover new, complex molecules in interstellar space that may be precursors to life. The GBT and Molecules The Robert C. Byrd Green Bank Telescope and some molecules it has discovered. CREDIT: Bill Saxton, NRAO/AUI/NSF "Clouds like this one are the raw material for new stars and planets. We know that complex chemistry builds prebiotic molecules in such clouds long before the stars and planets are formed. There is a good chance that some of these interstellar molecules may find their way to the surface of young planets such as the early Earth, and provide a head start for the chemistry of life. For the first time, we now have the capability to make a very thorough and methodical search to find all the chemicals in the clouds," said Anthony Remijan, of the National Radio Astronomy Observatory (NRAO). In the past three years, Remijan and his colleagues have used the GBT to discover ten new interstellar molecules, a feat unequalled in such a short time by any other team or telescope. The scientists discovered those molecules by looking specifically for them. However, they now are changing their strategy and casting a wide net designed to find whatever molecules are present, without knowing in advance what they'll find. In addition, they are making their data available freely to other scientists, in hopes of speeding the discovery process. The research team presented its plan to the American Astronomical Society's meeting in St. Louis, MO. As molecules rotate and vibrate, they emit radio waves at specific frequencies. Each molecule has a unique pattern of such frequencies, called spectral lines, that constitutes a "fingerprint" identifying that molecule. Laboratory tests can determine the pattern of spectral lines that identifies a specific molecule. Most past discoveries came from identifying a molecule's pattern in

  2. Assembling Ultracold Polar Molecules From Single Atoms

    NASA Astrophysics Data System (ADS)

    Liu, Lee R.; Hutzler, Nicholas R.; Yu, Yichao; Zhang, Jessie T.; Ni, Kang-Kuen

    2016-05-01

    Ultracold polar molecules are promising candidates for studying quantum many-body phenomena and building quantum information systems, due to their long-range, anisotropic, and tunable interactions. This calls for a technique to create low entropy samples of ultracold polar molecules with a large dipole moment. The lowest entropy molecular gas to date was created from atomic quantum gases in bulk or in optical lattices. The entropy is limited by that of the constituent atomic gases. We propose a method that addresses this limitation by assembling sodium cesium (NaCs) molecules from individually manipulated atoms. First, we load single Na and Cs atoms in separate optical tweezers from MOTs. We will cool them to their motional ground state using Raman sideband cooling and then merge them into a single tweezer. The tweezer confinement provides enhanced wavefunction overlap between the atom pair and molecule states. Using coherent two-photon techniques, we will then transfer the atom pair into a molecule. Our method offers reduced apparatus complexity and cycle time, single-site manipulation and imaging resolution, and should be readily extended to different species.

  3. Localized single molecule isotherms of DNA molecules at confined liquid-solid interfaces.

    PubMed

    Liang, Heng; Cheng, Xiaoliang; Ma, Yinfa

    2009-03-15

    The study of dynamics and thermodynamics of single biological molecules at confined liquid-solid interfaces is crucially important, especially in the case of low-copy number molecules in a single cell. Using a high-throughput single molecule imaging system and Lagrangian coordinates of single molecule images, we discovered that the local equilibrium isotherms of single lambdaDNA molecules at a confined liquid-solid interface varied from a stair type for the regions of single or double molecular DNA to a mild "S" type for the regions of triple molecular DNA spots, which does not agree with the conventional equilibrium isotherms in the literature. Single molecule images in time sequence for different lambdaDNA concentrations were statistically analyzed by measuring preferential partitioning from shearing effects, which were used to measure the local velocity of DNA molecules by directly observing the migration of DNA fluorescence spots for the 12 continuous images. The local linear velocity of hydrodynamic flow was calculated by the Hagen-Poiseuille equation in different microregions with a local Lagrangian approach. The local single molecule isotherms for the tracked molecules in the regions of single, double, or triple molecular DNA layers within the laminar flows were obtained according to the average local velocities of both the stochastic molecule events and the corresponding local Poiseuille flows. A millisecond and microvolume approach to directly determine local single molecule isotherms at confined liquid-solid interfaces was established, and the microspace scale effects on the types of isotherms were discovered. This study may have significant impact on preparations of low-copy number proteins in a single cell, membrane separations, and other bioseparation studies.

  4. Prebiotically Important Molecules in Orion KL

    NASA Astrophysics Data System (ADS)

    Kuan, Yi-Jehng; Chuang, Yo-Ling

    Many interstellar, complex organic molecules are known to be prebiotically important and have essential functions in terrestrial biochemistry. Observations of complex organic molecular species in molecular clouds can thus enable us to test the origin of the primitive organic material found in the Solar System. Interstellar pyrimidine and glycine, the building block of nucleic acid and the simplest amino acid, respectively, are key molecules for astrobiology and were both detected in meteorites and comets. Although the formation of prebiotic molecules in extraterrestrial environments and their contribution to prebiotic chemistry and the origin of life remains unsettled, the connection between interstellar organic chemistry, meteoritic pyrimidines and amino acids, and the emergence of life on the early Earth would be strengthened with the discovery of interstellar pyrimidine and glycine. We have therefore observed the Orion KL hot molecular core to search for interstellar pyrimidine and for the confirmation of interstellar glycine using the ALMA array. We will present some of the encouraging, positive results.

  5. Hydrogen sulfide and polysulfides as signaling molecules

    PubMed Central

    KIMURA, Hideo

    2015-01-01

    Hydrogen sulfide (H2S) is a familiar toxic gas that smells of rotten eggs. After the identification of endogenous H2S in the mammalian brain two decades ago, studies of this molecule uncovered physiological roles in processes such as neuromodulation, vascular tone regulation, cytoprotection against oxidative stress, angiogenesis, anti-inflammation, and oxygen sensing. Enzymes that produce H2S, such as cystathionine β-synthase, cystathionine γ-lyase, and 3-mercaptopyruvate sulfurtransferase have been studied intensively and well characterized. Polysulfides, which have a higher number of inner sulfur atoms than that in H2S, were recently identified as potential signaling molecules that can activate ion channels, transcription factors, and tumor suppressors with greater potency than that of H2S. This article focuses on our contribution to the discovery of these molecules and their metabolic pathways and mechanisms of action. PMID:25864468

  6. Torsional and rotational couplings in nonrigid molecules

    NASA Astrophysics Data System (ADS)

    Omiste, Juan J.; Madsen, Lars Bojer

    2017-02-01

    We analyze theoretically the interplay between the torsional and the rotational motion of an aligned biphenyl-like molecule. To do so, we consider a transition between two electronic states with different internal torsional potentials, induced by means of a resonant laser pulse. The change in the internal torsional potential provokes the motion of the torsional wave packet in the excited electronic state, modifying the structure of the molecule, and hence, its inertia tensor. We find that this process has a strong impact on the rotational wave function, displaying different behavior depending on the electronic states involved and their associated torsional potentials. We describe the dynamics of the system by considering the degree of alignment and the expectation values of the angular momentum operators for the overall rotation of the molecule.

  7. Ionization of glycerin molecule by electron impact

    NASA Astrophysics Data System (ADS)

    Zavilopulo, A. N.; Shpenik, O. B.; Markush, P. P.; Kontrosh, E. E.

    2015-07-01

    The methods and results of studying the yield of positive ions produced due to direct and dissociative electron impact ionization of the glycerin molecule are described. The experiment is carried out using two independent setups, namely, a setup with a monopole mass spectrometer employing the method of crossing electron and molecular beams and a setup with a hypocycloidal electron spectrometer with the gas-filled cell. The mass spectra of the glycerin molecule are studied in the range of mass numbers of 10-95 amu at various temperatures. The energy dependences of the effective cross sections of the glycerin molecular ions produced by a monoenergetic electron beam are obtained and analyzed; using these dependences, the appearance energies of fragment ions are determined. The dynamics of the glycerin molecule fragment ions formation is investigated in the temperature range of 300-340 K.

  8. Electrostatic trapping of metastable NH molecules

    SciTech Connect

    Hoekstra, Steven; Metsaelae, Markus; Zieger, Peter C.; Scharfenberg, Ludwig; Gilijamse, Joop J.; Meijer, Gerard; Meerakker, Sebastiaan Y. T. van de

    2007-12-15

    We report on the Stark deceleration and electrostatic trapping of {sup 14}NH (a{sup 1}{delta}) radicals. In the trap, the molecules are excited on the spin-forbidden A{sup 3}{pi}<-a{sup 1}{delta} transition and detected via their subsequent fluorescence to the X{sup 3}{sigma}{sup -} ground state. The 1/e trapping time is 1.4{+-}0.1 s, from which a lower limit of 2.7 s for the radiative lifetime of the a{sup 1}{delta}, v=0, J=2 state is deduced. The spectral profile of the molecules in the trapping field is measured to probe their spatial distribution. Electrostatic trapping of metastable NH followed by optical pumping of the trapped molecules to the electronic ground state is an important step toward accumulation of these radicals in a magnetic trap.

  9. Small molecule modifiers of circadian clocks.

    PubMed

    Chen, Zheng; Yoo, Seung-Hee; Takahashi, Joseph S

    2013-08-01

    Circadian clocks orchestrate 24-h oscillations of essential physiological and behavioral processes in response to daily environmental changes. These clocks are remarkably precise under constant conditions yet highly responsive to resetting signals. With the molecular composition of the core oscillator largely established, recent research has increasingly focused on clock-modifying mechanisms/molecules. In particular, small molecule modifiers, intrinsic or extrinsic, are emerging as powerful tools for understanding basic clock biology as well as developing putative therapeutic agents for clock-associated diseases. In this review, we will focus on synthetic compounds capable of modifying the period, phase, or amplitude of circadian clocks, with particular emphasis on the mammalian clock. We will discuss the potential of exploiting these small molecule modifiers in both basic and translational research.

  10. Protein Scaffolding for Small Molecule Catalysts

    SciTech Connect

    Baker, David

    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.

  11. Featured Molecules: Ascorbic Acid and Methylene Blue

    NASA Astrophysics Data System (ADS)

    Coleman, William F.; Wildman, Randall J.

    2003-05-01

    The WebWare molecules of the month for May are featured in several articles in this issue. "Arsenic: Not So Evil After All?" discusses the pharmaceutical uses of methylene blue and its development as the first synthetic drug used against a specific disease. The JCE Classroom Activity "Out of the Blue" and the article "Greening the Blue Bottle" feature methylene blue and ascorbic acid as two key ingredients in the formulation of the blue bottle. You can also see a colorful example of these two molecules in action on the cover. "Sailing on the 'C': A Vitamin Titration with a Twist" describes an experiment to determine the vitamin C (ascorbic acid) content of citrus fruits and challenges students, as eighteenth-century sea captains, to decide the best fruit to take on a long voyage. Fully manipulable (Chime) versions of these and other molecules are available at Only@JCE Online.

  12. Simple and advanced ferromagnet/molecule spinterfaces

    NASA Astrophysics Data System (ADS)

    Gruber, M.; Ibrahim, F.; Djedhloul, F.; Barraud, C.; Garreau, G.; Boukari, S.; Isshiki, H.; Joly, L.; Urbain, E.; Peter, M.; Studniarek, M.; Da Costa, V.; Jabbar, H.; Bulou, H.; Davesne, V.; Halisdemir, U.; Chen, J.; Xenioti, D.; Arabski, J.; Bouzehouane, K.; Deranlot, C.; Fusil, S.; Otero, E.; Choueikani, F.; Chen, K.; Ohresser, P.; Bertran, F.; Le Fèvre, P.; Taleb-Ibrahimi, A.; Wulfhekel, W.; Hajjar-Garreau, S.; Wetzel, P.; Seneor, P.; Mattana, R.; Petroff, F.; Scheurer, F.; Weber, W.; Alouani, M.; Beaurepaire, E.; Bowen, M.

    2016-10-01

    Spin-polarized charge transfer between a ferromagnet and a molecule can promote molecular ferromagnetism 1, 2 and hybridized interfacial states3, 4. Observations of high spin-polarization of Fermi level states at room temperature5 designate such interfaces as a very promising candidate toward achieving a highly spin-polarized, nanoscale current source at room temperature, when compared to other solutions such as half-metallic systems and solid-state tunnelling over the past decades. We will discuss three aspects of this research. 1) Does the ferromagnet/molecule interface, also called an organic spinterface, exhibit this high spin-polarization as a generic feature? Spin-polarized photoemission experiments reveal that a high spin-polarization of electronics states at the Fermi level also exist at the simple interface between ferromagnetic cobalt and amorphous carbon6. Furthermore, this effect is general to an array of ferromagnetic and molecular candidates7. 2) Integrating molecules with intrinsic properties (e.g. spin crossover molecules) into a spinterface toward enhanced functionality requires lowering the charge transfer onto the molecule8 while magnetizing it1,2. We propose to achieve this by utilizing interlayer exchange coupling within a more advanced organic spinterface architecture. We present results at room temperature across the fcc Co(001)/Cu/manganese phthalocyanine (MnPc) system9. 3) Finally, we discuss how the Co/MnPc spinterface's ferromagnetism stabilizes antiferromagnetic ordering at room temperature onto subsequent molecules away from the spinterface, which in turn can exchange bias the Co layer at low temperature10. Consequences include tunnelling anisotropic magnetoresistance across a CoPc tunnel barrier11. This augurs new possibilities to transmit spin information across organic semiconductors using spin flip excitations12.

  13. Connexin Channel Permeability to Cytoplasmic Molecules

    PubMed Central

    Harris, Andrew L.

    2007-01-01

    Connexin channels are known to be permeable to a variety of cytoplasmic molecules. The first observation of second messenger junctional permeability, made ∼30 years ago, sparked broad interest in gap junction channels as mediators of intercellular molecular signaling. Since then, much has been learned about the diversity of connexin channels with regard to isoform diversity, tissue and developmental distribution, modes of channel regulation, assembly and expression, biochemical modification and permeability, all of which appear to be dynamically regulated. This information has expanded the potential roles of connexin channels in development, physiology and disease, and made their elucidation much more complex - 30 years ago such an orchestra of junctional dynamics was unanticipated. Only recently, however, have investigators been able to directly address, in this more complex framework, the key issue: What specific biological molecules, second messengers and others, are able to permeate the various types of connexin channels, and how well? An important related issue, given the ever-growing list of connexin-related pathologies, is how these permeabilities are altered by disease-causing connexin mutations. Together, many studies show that a variety of cytoplasmic molecules can permeate the different types of connexin channels. A few studies reveal differences in permeation by different molecules through a particular type of connexin channel, and differences in permeation by a particular molecule through different types of connexin channels. This article describes and evaluates the various methods used to obtain these data, presents an annotated compilation of the results, and discusses the findings in the context of what can be inferred about mechanism of selectivity and potential relevance to signaling. The data strongly suggest that highly specific interactions take place between connexin pores and specific biological molecular permeants, and that those

  14. Chiral Molecules Revisited by Broadband Microwave Spectroscopy

    NASA Astrophysics Data System (ADS)

    Schnell, Melanie

    2014-06-01

    Chiral molecules have fascinated chemists for more than 150 years. While their physical properties are to a very good approximation identical, the two enantiomers of a chiral molecule can have completely different (bio)chemical activities. For example, the right-handed enantiomer of carvone smells of spearmint while the left-handed one smells of caraway. In addition, the active components of many drugs are of one specific handedness, such as in the case of ibuprofen. However, in nature as well as in pharmaceutical applications, chiral molecules often exist in mixtures with other chiral molecules. The analysis of these complex mixtures to identify the molecular components, to determine which enantiomers are present, and to measure the enantiomeric excesses (ee) remains a challenging task for analytical chemistry, despite its importance for modern drug development. We present here a new method of differentiating enantiomers of chiral molecules in the gas phase based on broadband rotational spectroscopy. The phase of the acquired signal bares the signature of the enantiomer, as it depends upon the combined quantity, μ_a μ_b μ_c, which is of opposite sign between enantiomers. It thus also provides information on the absolute configuration of the particular enantiomer. Furthermore, the signal amplitude is proportional to the ee. A significant advantage of our technique is its inherent mixture compatibility due to the fingerprint-like character of rotational spectra. In this contribution, we will introduce the technique and present our latest results on chiral molecule spectroscopy and enantiomer differentiation. D. Patterson, M. Schnell, J.M. Doyle, Nature 497 (2013) 475-477 V.A. Shubert, D. Schmitz, D. Patterson, J.M. Doyle, M. Schnell, Angewandte Chemie International Edition 53 (2014) 1152-1155

  15. Single-molecule electrophoresis. Final report

    SciTech Connect

    Castro, A.; Shera, E.B.

    1996-05-22

    A novel method for the detection and identification of single molecules in solution has been devised, computer-simulated, and experimentally achieved. The technique involves the determination of electrophoretic velocities by measuring the time required by individual molecules to travel a fixed distance between two laser beams. Computer simulations of the process were performed beforehand in order to estimate the experimental feasibility of the method, and to determine the optimum values for the various experimental parameters. Examples of the use of the technique for the ultrasensitive detection and identification of rhodamine-6G, a mixture of DNA restriction fragments, and a mixture of proteins in aqueous solution are presented.

  16. Enhancing single-molecule fluorescence with nanophotonics.

    PubMed

    Acuna, Guillermo; Grohmann, Dina; Tinnefeld, Philip

    2014-10-01

    Single-molecule fluorescence spectroscopy has become an important research tool in the life sciences but a number of limitations hinder the widespread use as a standard technique. The limited dynamic concentration range is one of the major hurdles. Recent developments in the nanophotonic field promise to alleviate these restrictions to an extent that even low affinity biomolecular interactions can be studied. After motivating the need for nanophotonics we introduce the basic concepts of nanophotonic devices such as zero mode waveguides and nanoantennas. We highlight current applications and the future potential of nanophotonic approaches when combined with biological systems and single-molecule spectroscopy.

  17. Nonadiabatic transitions in electrostatically trapped ammonia molecules

    SciTech Connect

    Kirste, Moritz; Schnell, Melanie; Meijer, Gerard; Sartakov, Boris G.

    2009-05-15

    Nonadiabatic transitions are known to be major loss channels for atoms in magnetic traps but have thus far not been experimentally reported upon for trapped molecules. We have observed and quantified losses due to nonadiabatic transitions for three isotopologues of ammonia in electrostatic traps by comparing the trapping times in traps with a zero and a nonzero electric field at the center. Nonadiabatic transitions are seen to dominate the overall loss rate even for the present samples that are at relatively high temperatures of 30 mK. It is anticipated that losses due to nonadiabatic transitions in electric fields are omnipresent in ongoing experiments on cold molecules.

  18. Single molecule study of silicon quantum dots

    NASA Astrophysics Data System (ADS)

    So, Woong Young; Li, Qi; Jin, Rongchao; Peteanu, Linda

    2016-09-01

    Recently, fluorescent Silicon (Si) Quantum Dots (QDs) have attracted much interest due to their high quantum yield, use of non-toxic and environmentally-benign chemicals, and water-solubility. However, more research is necessary to understand the energy level characteristics and single molecule behavior to enable their development for imaging applications. Therefore, single molecule time-resolved fluorescence spectroscopy of fluorescent Si QDs (cyan, green, and yellow) is needed. A rigorous analysis of time-resolved photon correlation spectroscopy and fluorescence lifetime data on single Si QDs at room temperature is presented.

  19. Small molecule inhibitors of ebola virus infection.

    PubMed

    Picazo, Edwige; Giordanetto, Fabrizio

    2015-02-01

    Ebola viruses are extremely virulent and highly transmissible. They are responsible for sporadic outbreaks of severe hemorrhagic fevers with human mortality rates of up to 90%. No prophylactic or therapeutic treatments in the form of vaccine, biologicals or small molecule, currently exist. Yet, a wealth of antiviral research on ebola virus is being generated and potential inhibitors have been identified in biological screening and medicinal chemistry programs. Here, we detail the state-of-the-art in small molecule inhibitors of ebola virus infection, with >60 examples, including approved drugs, compounds currently in clinical trials, and more exploratory leads, and summarize the associated in vitro and in vivo evidence for their effectiveness.

  20. Collisional Transitions in Interstellar Asymmetric Top Molecules

    NASA Astrophysics Data System (ADS)

    Chandra, Suresh

    2012-07-01

    For the study of a molecule in interstellar space or in circumstellar envelopes of an evolved star, one has to deal with a multi-level system in the molecule. These levels are connected through radiative as well as collisional transitions. The NLTE effects in a molecule come in the picture only when collisional transitions are present. Computation of collisional rates is quite cumbersome task. Besides emission and absorption, two anomalous phenomena: (i) MASER action and (ii) Anomalous absorption (Absorption against the CMB) are shown by some molecules in interstellar space. Both of these phenomena are good examples of NLTE prevailing in the interstellar space and circumstellar envelopes of evolved stars. In the present talk, we shall discuss about the collisional transitions between rotational levels in a molecule. The collisional rate coefficients for the rotational transition J τ → J' τ' at the kinetic temperature T, averaged over the Maxwellian distribution are C(J τ → J' τ'|T) = \\Big(\\frac{8 k T}{π μ}\\Big)^{1/2} \\Big(\\frac{1}{k T}\\Big)^2 \\int_0^\\infty σ (J τ → J' τ'|E) E {e}^{-E/kT} {d} E where μ is the reduced mass of the system and the cross section σ(J τ → J' τ'|E) for the transition is \\begin{eqnarray} σ (J τ → J' τ'|E) = \\sum_{L M M'} S(J, τ, J', τ'|L, M, M') q(L, M, M'|E) The q(L, M, M'|E) are the parameters which can be obtained from the software MOLSCAT. The spectroscopic coefficients, S ( J, τ, J', τ'|L, M, M'), depend on the wave-functions of the molecules and on the angular momentum coupling factors: S(J, τ, J', τ'|L, M, M') = \\sum_{p, p', q, q'} g^p_{J τ} g^q_{J τ} g^{p'}_{J' τ'} g^{q'}_{J' τ'} \\big \\big Here, \\big represents the Clebsch-Gorden coefficient. The g-coefficients can be obtained from laboratory analysis of the molecule and the parameters q(L, M, M'|E) can be obtained with the help of the software MOLSCAT for a

  1. Cavity sideband cooling of trapped molecules

    SciTech Connect

    Kowalewski, Markus; Vivie-Riedle, Regina de; Morigi, Giovanna; Pinkse, Pepijn W. H.

    2011-09-15

    The efficiency of cavity sideband cooling of trapped molecules is theoretically investigated for the case in which the infrared transition between two rovibrational states is used as a cycling transition. The molecules are assumed to be trapped either by a radiofrequency or optical trapping potential, depending on whether they are charged or neutral, and confined inside a high-finesse optical resonator that enhances radiative emission into the cavity mode. Using realistic experimental parameters and COS as a representative molecular example, we show that in this setup, cooling to the trap ground state is feasible.

  2. Cold Light from Hot Atoms and Molecules

    SciTech Connect

    Lister, Graeme; Curry, John J.

    2011-05-11

    The introduction of rare earth atoms and molecules into lighting discharges led to great advances in efficacy of these lamps. Atoms such as Dy, Ho and Ce provide excellent radiation sources for lighting applications, with rich visible spectra, such that a suitable combination of these elements can provide high quality white light. Rare earth molecules have also proved important in enhancing the radiation spectrum from phosphors in fluorescent lamps. This paper reviews some of the current aspects of lighting research, particularly rare earth chemistry and radiation, and the associated fundamental atomic and molecular data.

  3. The origin of life. [genetically important molecules

    NASA Technical Reports Server (NTRS)

    Horowitz, N. H.; Hubbard, J. S.

    1974-01-01

    Research in the areas of precambrian paleontology, chemical evolution of genetically important monomers, prebiotic dehydration-condensation reactions, organic compounds in meteorites and interstellar space, and biological exploration of the planets is summarized. Fossils in precambrian cherts and findings of eukaryotic cells are described, and recent investigations of prebiotic conditions, energy sources, and starting materials for genetic molecules are outlined. Studies of homogeneous and heterogeneous dehydrations and of nonaqueous thermal dehydrations are described. The detection of amino acids, purines, and pyrimidines in meteorites and of biologically significant molecules in interstellar clouds is discussed, as well as the possibilities of life on Jupiter, Mars, and Titan.

  4. The Interactions Between Nitrogen and Oxygen Molecules

    NASA Technical Reports Server (NTRS)

    Meador, Willard E., Jr.

    1960-01-01

    Lippincott's delta-function model for atomic interactions is analyzed, both physically and mathematically, and extended, by differentiation between K- and L-shell electrons and the introduction of a variable parameter in the expression for the delta-function strength, to cover homonuclear molecules more complex than hydrogen. In addition, modifications are made which allow treatments of diatomic, heteronuclear molecules. This theory, in conjunction with a reasonably extensive study of resonance, dispersion, and configuration interaction phenomena, as well as the use of simple quantum mechanical arguments, is then applied to the N2-N2, N2-O2, and O2-O2 interactions.

  5. Aharonov-Bohm effects in entangled molecules.

    PubMed

    Kimball, J C; Frisch, H L

    2004-08-27

    Molecules which are magnetic and conducting, if suitably entangled (e.g., catenanes and knots) could exhibit Aharonov-Bohm effects which can be viewed as particular examples of a Berry phase. The corrections to the quantum energy levels reflect the entangled geometry of the molecules and, while small (they are proportional to the square of the fine structure constant), may be observable. We illustrate these corrections for a number of catenated and knotted structures. For couplings between the components of a catenane (link), the Aharonov-Bohm corrections are determined by integer-valued linking numbers. For knots, the Aharonov-Bohm correction is proportional to the geometric writhe of the knot.

  6. Concentrating molecules in a simple microchannel.

    PubMed

    Jiang, Hai; Daghighi, Yasaman; Chon, Chan Hee; Li, Dongqing

    2010-07-15

    A simple method is proposed and tested to concentrate sample molecules from a dilute solution in a microchannel by electrokinetic means. The microfluidic chip has a straight microchannel connecting two wells and three electrodes. This method uses electrokinetic trapping and flow control simultaneously to concentrate a charged species of interest. A numerical model of the sample concentration process is presented in this paper. Using a fluorescent dye as the sample molecules, experimental investigation into the concentration process was performed. The 90 times of the concentration increase was achieved in 110 s. The numerical simulations of the concentrating and the subsequent dispensing processes agree well with the experimental results.

  7. A toy model for a diatomic molecule

    NASA Astrophysics Data System (ADS)

    Hecker Denschlag, Johannes

    2016-08-01

    We introduce a toy model for a diatomic molecule which is based on coupling electronic and nuclear spins to a rigid rotor. Despite its simplicity, the model can be used scientifically to analyze and understand complex molecular hyperfine spectra. In addition, the model has educational value as a number of fundamental symmetries and conservation laws of the molecule can be studied. Because of its simple structure, the model can be readily implemented as a computer program with comparatively short computing times on the order of a few seconds.

  8. Photoassociative production of ultracold heteronuclear ytterbium molecules

    SciTech Connect

    Borkowski, Mateusz; Ciurylo, Roman; Yamazaki, Rekishu; Takahashi, Yoshiro; Hara, Hideaki; Taie, Shintaro; Sugawa, Seiji; Takasu, Yosuke; Enomoto, Katsunari

    2011-09-15

    We report observations of photoassociation (PA) spectra near the intercombination line in isotopic mixtures of ultracold ytterbium gases. Several heteronuclear bound states have been found for the excited {sup 170}Yb{sup 174}Yb and {sup 174}Yb{sup 176}Yb molecules. We develop a single-channel mass-scaled interaction model for the excited state molecule which well reproduces the measured bound state energies. This is an important step toward optical control of interactions in mixtures of ultracold ytterbium gases using heteronuclear optical Feshbach resonances. The model developed is applicable in collisions of other similar systems, such as cadmium and mercury.

  9. Evidence of water molecules--a statistical evaluation of water molecules based on electron density.

    PubMed

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias

    2015-04-27

    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

  10. Making More-Complex Molecules Using Superthermal Atom/Molecule Collisions

    NASA Technical Reports Server (NTRS)

    Shortt, Brian; Chutjian, Ara; Orient, Otto

    2008-01-01

    A method of making more-complex molecules from simpler ones has emerged as a by-product of an experimental study in outer-space atom/surface collision physics. The subject of the study was the formation of CO2 molecules as a result of impingement of O atoms at controlled kinetic energies upon cold surfaces onto which CO molecules had been adsorbed. In this study, the O/CO system served as a laboratory model, not only for the formation of CO2 but also for the formation of other compounds through impingement of rapidly moving atoms upon molecules adsorbed on such cold interstellar surfaces as those of dust grains or comets. By contributing to the formation of increasingly complex molecules, including organic ones, this study and related other studies may eventually contribute to understanding of the origins of life.

  11. Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data

    PubMed Central

    Mabuchi, Hideo; Herschlag, Daniel

    2012-01-01

    Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data. PMID:22363412

  12. The origin of small and large molecule behavior in the vibrational relaxation of highly excited molecules

    NASA Astrophysics Data System (ADS)

    Gordon, Robert J.

    1990-04-01

    An explanation is proposed for the qualitatively different types of behavior that have been reported for the vibrational relaxation of highly excited diatomic and polyatomic molecules. It is argued that all of the diatomic molecules that have been studied in bulk relax adiabatically at room temperature. In contrast, large polyatomic molecules have low frequency modes which act at ``doorway'' modes for the rest of the molecules, producing an impulsive relaxation mechanism. The theoretical work of Nesbitt and Hynes showed that impulsive collisions result in an exponential decay of the average vibrational energy of a Morse oscillator, whereas adiabatic collisions produce nonexponential power law behavior. We propose that this result explains a large body of data for the vibrational relaxation of small and large molecules.

  13. The origin of small and large molecule behavior in the vibrational relaxation of highly excited molecules

    SciTech Connect

    Gordon, R.J. )

    1990-04-01

    An explanation is proposed for the qualitatively different types of behavior that have been reported for the vibrational relaxation of highly excited diatomic and polyatomic molecules. It is argued that all of the diatomic molecules that have been studied in bulk relax adiabatically at room temperature. In contrast, large polyatomic molecules have low frequency modes which act at doorway'' modes for the rest of the molecules, producing an impulsive relaxation mechanism. The theoretical work of Nesbitt and Hynes showed that impulsive collisions result in an exponential decay of the average vibrational energy of a Morse oscillator, whereas adiabatic collisions produce nonexponential power law behavior. We propose that this result explains a large body of data for the vibrational relaxation of small and large molecules.

  14. Strategy to discover diverse optimal molecules in the small molecule universe.

    PubMed

    Rupakheti, Chetan; Virshup, Aaron; Yang, Weitao; Beratan, David N

    2015-03-23

    The small molecule universe (SMU) is defined as a set of over 10(60) synthetically feasible organic molecules with molecular weight less than ∼500 Da. Exhaustive enumerations and evaluation of all SMU molecules for the purpose of discovering favorable structures is impossible. We take a stochastic approach and extend the ACSESS framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 , 7296 - 7303 ) to develop diversity oriented molecular libraries that can generate a set of compounds that is representative of the small molecule universe and that also biases the library toward favorable physical property values. We show that the approach is efficient compared to exhaustive enumeration and to existing evolutionary algorithms for generating such libraries by testing in the NKp fitness landscape model and in the fully enumerated GDB-9 chemical universe containing 3 × 10(5) molecules.

  15. Single Molecule Conductance of Oligothiophene Derivatives

    NASA Astrophysics Data System (ADS)

    Dell, Emma J.

    This thesis studies the electronic properties of small organic molecules based on the thiophene motif. If we are to build next-generation devices, advanced materials must be designed which possess requisite electronic functionality. Molecules present attractive candidates for these ad- vanced materials since nanoscale devices are particularly sought after. However, selecting a molecule that is suited to a certain electronic function remains a challenge, and characterization of electronic behavior is therefore critical. Single molecule conductance measurements are a powerful tool to determine properties on the nanoscale and, as such, can be used to investigate novel building blocks that may fulfill the design requirements of next-generation devices. Combining these conductance results with strategic chemical synthesis allows for the development of new families of molecules that show attractive properties for future electronic devices. Since thiophene rings are the fruitflies of organic semiconductors on the bulk scale, they present an intriguing starting point for building functional materials on the nanoscale, and therefore form the structural basis of all molecules studied herein. First, the single-molecule conductance of a family of bithiophene derivatives was measured. A broad distribution in the single-molecule conductance of bithiophene was found compared with that of a biphenyl. This increased breadth in the conductance distribution was shown to be explained by the difference in 5-fold symmetry of thiophene rings as compared to the 6-fold symmetry of benzene rings. The reduced symmetry of thiophene rings results in a restriction on the torsion angle space available to these molecules when bound between two metal electrodes in a junction, causing each molecular junction to sample a different set of conformers in the conductance measurements. By contrast, the rotations of biphenyl are essentially unimpeded by junction binding, allowing each molecular junction

  16. The Molecules of the Cell Membrane.

    ERIC Educational Resources Information Center

    Bretscher, Mark S.

    1985-01-01

    Cell membrane molecules form a simple, two-dimensional liquid controlling what enters and leaves the cell. Discusses cell membrane molecular architecture, plasma membranes, epithelial cells, cycles of endocytosis and exocytosis, and other topics. Indicates that some cells internalize, then recycle, membrane area equivalent to their entire surface…

  17. Single-molecule techniques for drug discovery.

    PubMed

    Skinner, Gary M; Visscher, Koen

    2004-08-01

    Single-molecule techniques offer a number of key benefits over conventional in vitro assay methods for drug screening, as they use less material and unlock the ability to observe transient states. By observing such states, it should be possible to screen for chemical compounds that isolate these steps. The benefit of this is twofold: (a) inhibitors can be found that target key phases in biochemical processes, e.g., transcription initiation; and (b) the total number of drug targets increases as many biochemical processes consist of many transient steps, e.g., transcription promoter binding, initiation, elongation, and termination. Although single-molecule methods offer exciting opportunities for new ways of discovering drugs, there are a number of obstacles to their adoption for drug screening. The main hurdle is to develop robust apparatus that will allow many thousands of individual single molecule experiments to be performed in parallel. By using recently developed integrated microfluidics technology, this hurdle may be overcome. Here, a number of potential single-molecule approaches to drug screening are presented along with a discussion of the benefits and technical obstacles that must be overcome.

  18. [Drug treatments, from chlorpromazine to new molecules].

    PubMed

    Gaillard, Adeline; Poirier, Marie-France

    2013-01-01

    The history of drug treatments, and particularly the discovery of certain molecules, led toan evolution in psychiatric practices. The discovery of the therapeutic properties of chlorpromazine in 1952 by Jean Delay and Pierre Deniker revolutionised the relational process between patients and caregivers.The perspectives are encouraging, notably in the areas of schizophrenia and mood disorders.

  19. Cooperative Ligand Binding to Linear Chain Molecules

    ERIC Educational Resources Information Center

    Applequist, Jon

    1977-01-01

    Summarizes the Ising model of ligand binding as it applies to cooperative binding to long chain molecules. Also presents some illustrations which help to visualize the connection between the interaction parameters and the shape of the binding isotherm. (Author/MR)

  20. Complex organic molecules and star formation

    NASA Astrophysics Data System (ADS)

    Bacmann, A.; Faure, A.

    2014-12-01

    Star forming regions are characterised by the presence of a wealth of chemical species. For the past two to three decades, ever more complex organic species have been detected in the hot cores of protostars. The evolution of these molecules in the course of the star forming process is still uncertain, but it is likely that they are partially incorporated into protoplanetary disks and then into planetesimals and the small bodies of planetary systems. The complex organic molecules seen in star forming regions are particularly interesting since they probably make up building blocks for prebiotic chemistry. Recently we showed that these species were also present in the cold gas in prestellar cores, which represent the very first stages of star formation. These detections question the models which were until now accepted to account for the presence of complex organic molecules in star forming regions. In this article, we shortly review our current understanding of complex organic molecule formation in the early stages of star formation, in hot and cold cores alike and present new results on the formation of their likely precursor radicals.

  1. The formation of molecules in protostellar winds

    NASA Technical Reports Server (NTRS)

    Glassgold, A. E.; Mamon, G. A.; Huggins, P. J.

    1991-01-01

    The production and destruction processes for molecules in very fast protostellar winds are analyzed and modeled with a one-dimensional chemical kinetics code. Radial density and temperature distributions suggested by protostellar theory are explored as are a range of mass-loss rates. The efficiency of in situ formation of heavy molecules is found to be high if the wind temperature falls sufficiently rapidly, as indicated by theory. The degree of molecular conversion is a strong function of the mass-loss rate and of density gradients associated with the acceleration and collimation of the wind. Even in cases where essentially all of the heavy atoms are processed into molecules, a significant fraction of atomic hydrogen remains so that hghly molecular, protostellar winds are able to emit the 21-cm line. Although CO has a substantial abundance in most models relevant to very young protostars, high abundances of other molecules such as SiO and H2O signify more complete association characteristic of winds containing regions of very high density. Although the models apply only to regions close to the protostar, they are in qualitative accord with recent observations at much larger distances of both atomic and molecular emission from extremely high-velocity flow.

  2. Measurement of dichroism in aligned molecules

    NASA Astrophysics Data System (ADS)

    Lavorel, B.; Babilotte, Ph.; Karras, G.; Billard, F.; Hertz, E.; Faucher, O.

    2016-10-01

    We present dichroism measurements in molecules prealigned with a short and intense laser pulse, using a balanced detection and a pump-probe scheme. The birefringence signal is recorded under the same irradiation conditions along with the dichroism one. Our results show that the dichroism signal is of comparable order of magnitude as the one originating from birefringence and reflects the degree of alignment. The balanced detection scheme directly provides an heterodyne signal for both birefringence and dichroism. Experiments are first conducted in air and then in pure nitrogen and carbon dioxide gases. A general approach allows us to explain the temporal shape of the dichroic response and to extract the imaginary part of the polarizability anisotropy. Furthermore, a simple model invoking the finite response time of the molecule to the probe excitation provides a complementary perspective. Using this model, the phase shift between the oscillations of the probe electric field and the induced polarization can be estimated. We find that the phase shift corresponds to a time delay of about 130 as (10-18s) in both molecules. Calculation of the energy flow between the probe field and the molecules taking into account the phase shift is compared to the experimental data.

  3. Trapping polar molecules in an ac trap

    SciTech Connect

    Bethlem, Hendrick L.; Veldhoven, Jacqueline van; Schnell, Melanie; Meijer, Gerard

    2006-12-15

    Polar molecules in high-field seeking states cannot be trapped in static traps as Maxwell's equations do not allow a maximum of the electric field in free space. It is possible to generate an electric field that has a saddle point by superposing an inhomogeneous electric field to an homogeneous electric field. In such a field, molecules are focused along one direction, while being defocused along the other. By reversing the direction of the inhomogeneous electric field the focusing and defocusing directions are reversed. When the fields are being switched back and forth at the appropriate rate, this leads to a net focusing force in all directions. We describe possible electrode geometries for creating the desired fields and discuss their merits. Trapping of {sup 15}ND{sub 3} ammonia molecules in a cylindrically symmetric ac trap is demonstrated. We present measurements of the spatial distribution of the trapped cloud as a function of the settings of the trap and compare these to both a simple model assuming a linear force and to full three-dimensional simulations of the experiment. With the optimal settings, molecules within a phase-space volume of 270 mm{sup 3} (m/s){sup 3} remain trapped. This corresponds to a trap depth of about 5 mK and a trap volume of about 20 mm{sup 3}.

  4. Stability of Matter-Antimatter Molecules

    SciTech Connect

    Wong, Cheuk-Yin; Lee, Teck-Ghee

    2011-01-01

    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{sub 1}{sup +}, m{sub 2}{sup -}, {bar m}{sub 2}{sup +}, {bar m}{sub 1}{sup -}) possess bound states if their constituent mass ratio m{sub 1}/m{sub 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 ({mu}{sup +}e{sup 0})-(e{sup +}{mu}{sup -}), ({pi}{sup +}e{sup -})-(e{sup +}{pi}{sup -}), (K{sup +}e{sup -})-(e{sup +}K{sup -}), (pe{sup -})-(e{sup +}{bar p}), (p{mu}{sup -})-({mu}{sup +}{bar p}), and (K{sup +}{mu}{sup -})-({mu}{sup +}K{sup -}), which satisfy the stability condition. We estimate the molecular annihilation lifetimes in their s states.

  5. Antiangiogenic and anticancer molecules in cartilage.

    PubMed

    Patra, Debabrata; Sandell, Linda J

    2012-01-19

    Cartilage is one of the very few naturally occurring avascular tissues where lack of angiogenesis is the guiding principle for its structure and function. This has attracted investigators who have sought to understand the biochemical basis for its avascular nature, hypothesising that it could be used in designing therapies for treating cancer and related malignancies in humans through antiangiogenic applications. Cartilage encompasses primarily a specialised extracellular matrix synthesised by chondrocytes that is both complex and unique as a result of the myriad molecules of which it is composed. Of these components, a few such as thrombospondin-1, chondromodulin-1, the type XVIII-derived endostatin, SPARC (secreted protein acidic and rich in cysteine) and the type II collagen-derived N-terminal propeptide (PIIBNP) have demonstrated antiangiogenic or antitumour properties in vitro and in vivo preclinical trials that involve several complicated mechanisms that are not completely understood. Thrombospondin-1, endostatin and the shark-cartilage-derived Neovastat preparation have also been investigated in human clinical trials to treat several different kinds of cancers, where, despite the tremendous success seen in preclinical trials, these molecules are yet to show success as anticancer agents. This review summarises the current state-of-the-art antiangiogenic characterisation of these molecules, highlights their most promising aspects and evaluates the future of these molecules in antiangiogenic applications.

  6. Mapping Conceptual Change in Matter and Molecules.

    ERIC Educational Resources Information Center

    Fellows, Nancy

    To analyze a student's conceptual changes, analyzing transcriptions of writing and verbal statements may not provide enough information. In a study of 25 sixth graders learning about matter and molecules, concept mapping of students' stated ideas was used to analyze the kinds of organizational changes the students made to use new science…

  7. Progress in Computational Electron-Molecule Collisions

    NASA Astrophysics Data System (ADS)

    Rescigno, Tn

    1997-10-01

    The past few years have witnessed tremendous progress in the development of sophisticated ab initio methods for treating collisions of slow electrons with isolated small molecules. Researchers in this area have benefited greatly from advances in computer technology; indeed, the advent of parallel computers has made it possible to carry out calculations at a level of sophistication inconceivable a decade ago. But bigger and faster computers are only part of the picture. Even with today's computers, the practical need to study electron collisions with the kinds of complex molecules and fragments encountered in real-world plasma processing environments is taxing present methods beyond their current capabilities. Since extrapolation of existing methods to handle increasingly larger targets will ultimately fail as it would require computational resources beyond any imagined, continued progress must also be linked to new theoretical developments. Some of the techniques recently introduced to address these problems will be discussed and illustrated with examples of electron-molecule collision calculations we have carried out on some fairly complex target gases encountered in processing plasmas. Electron-molecule scattering continues to pose many formidable theoretical and computational challenges. I will touch on some of the outstanding open questions.

  8. Small molecule control of bacterial biofilms

    PubMed Central

    Worthington, Roberta J.; Richards, Justin J.

    2012-01-01

    Bacterial biofilms are defined as a surface attached community of bacteria embedded in a matrix of extracellular polymeric substances that they have produced. When in the biofilm state, bacteria are more resistant to antibiotics and the host immune response than are their planktonic counterparts. Biofilms are increasingly recognized as being significant in human disease, accounting for 80% of bacterial infections in the body and diseases associated with bacterial biofilms include: lung infections of cystic fibrosis, colitis, urethritis, conjunctivitis, otitis, endocarditis and periodontitis. Additionally, biofilm infections of indwelling medical devices are of particular concern, as once the device is colonized infection is virtually impossible to eradicate. Given the prominence of biofilms in infectious diseases, there has been an increased effort toward the development of small molecules that will modulate bacterial biofilm development and maintenance. In this review, we highlight the development of small molecules that inhibit and/or disperse bacterial biofilms through non-microbicidal mechanisms. The review discuses the numerous approaches that have been applied to the discovery of lead small molecules that mediate biofilm development. These approaches are grouped into: 1) the identification and development of small molecules that target one of the bacterial signaling pathways involved in biofilm regulation, 2) chemical library screening for compounds with anti-biofilm activity, and 3) the identification of natural products that possess anti-biofilm activity, and the chemical manipulation of these natural products to obtain analogues with increased activity. PMID:22733439

  9. Uranium-mediated activation of small molecules.

    PubMed

    Arnold, Polly L

    2011-08-28

    Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power.

  10. Graphene-porphyrin single-molecule transistors.

    PubMed

    Mol, Jan A; Lau, Chit Siong; Lewis, Wilfred J M; Sadeghi, Hatef; Roche, Cecile; Cnossen, Arjen; Warner, Jamie H; Lambert, Colin J; Anderson, Harry L; Briggs, G Andrew D

    2015-08-21

    We demonstrate a robust graphene-molecule-graphene transistor architecture. We observe remarkably reproducible single electron charging, which we attribute to insensitivity of the molecular junction to the atomic configuration of the graphene electrodes. The stability of the graphene electrodes allow for high-bias transport spectroscopy and the observation of multiple redox states at room-temperature.

  11. Predicting the Stability of Hypervalent Molecules

    ERIC Educational Resources Information Center

    Mitchell, Tracy A.; Finnocchio, Debbie; Kua, Jeremy

    2007-01-01

    An exercise is described which introduces students to using concepts in thermochemistry to predict relative stability of a hypervalent molecule. Students will compare the energies of formation for both fluoride and the hydride by calculations and they will also explore the issue of partial ionic character in polar covalent bonds.

  12. Polypetide signaling molecules in plant development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intercellular communication mediated by small signaling molecules is a key mechanism for coordinating plant growth and development. In the past few years, polypeptide signals have been shown to play prominent roles in processes as diverse as shoot and root meristem maintenance, vascular differentiat...

  13. Comprehensive Map of Molecules Implicated in Obesity

    PubMed Central

    Agrawal, Stuti

    2016-01-01

    Obesity is a global epidemic affecting over 1.5 billion people and is one of the risk factors for several diseases such as type 2 diabetes mellitus and hypertension. We have constructed a comprehensive map of the molecules reported to be implicated in obesity. A deep curation strategy was complemented by a novel semi-automated text mining system in order to screen 1,000 full-length research articles and over 90,000 abstracts that are relevant to obesity. We obtain a scale free network of 804 nodes and 971 edges, composed of 510 proteins, 115 genes, 62 complexes, 23 RNA molecules, 83 simple molecules, 3 phenotype and 3 drugs in “bow-tie” architecture. We classify this network into 5 modules and identify new links between the recently discovered fat mass and obesity associated FTO gene with well studied examples such as insulin and leptin. We further built an automated docking pipeline to dock orlistat as well as other drugs against the 24,000 proteins in the human structural proteome to explain the therapeutics and side effects at a network level. Based upon our experiments, we propose that therapeutic effect comes through the binding of one drug with several molecules in target network, and the binding propensity is both statistically significant and different in comparison with any other part of human structural proteome. PMID:26886906

  14. Chain-like molecules confined in nanopores

    NASA Astrophysics Data System (ADS)

    Huber, Patrick; Soprunyuk, Viktor; Hofmann, Tommy; Knorr, Klaus

    2004-03-01

    We present an x-ray diffraction study on chain-like molecules, i.e. a selection of n-alkane molecules, embedded in the pores of nanoporous silica matrices. The lengths of the hydrocarbon chains are comparable to the mean diameter ( 7nm) of the tubular like nanopores which leads to drastic geometric restrictions. Diffraction patterns, recorded on heating and cooling between 200 K and 310 K, elucidate how the structure and phase behavior of the molecules is affected by the random substrate disorder and the confinement. The confined n-alkanes form close-packed structures by aligning parallel to the pore axis. In the case of the medium-length hydrocarbon chains one basic ordering principle known from the bulk crystalline state, i.e. the lamellar ordering of the molecules, is quenched[1], whereas for shorter n-alkanes this ordering principle survives[2]. The confined solids mimic the orientational order-disorder transitions known from the 3D unconfined crystals albeit in a modified fashion. 1. P. Huber, D. Wallacher, J. Albers, K. Knorr, Europhysics Letters, in press; 2. P. Huber, D. Wallacher, J. Albers, K. Knorr, Journal of Physics: Condensed Matter 15, 309 (2003).

  15. Organic molecules in translucent interstellar clouds.

    PubMed

    Krełowski, Jacek

    2014-09-01

    Absorption spectra of translucent interstellar clouds contain many known molecular bands of CN, CH+, CH, OH, OH(+), NH, C2 and C3. Moreover, one can observe more than 400 unidentified absorption features, known as diffuse interstellar bands (DIBs), commonly believed to be carried by complex, carbon-bearing molecules. DIBs have been observed in extragalactic sources as well. High S/N spectra allow to determine precisely the corresponding column densities of the identified molecules, rotational temperatures which differ significantly from object to object in cases of centrosymmetric molecular species, and even the (12)C/(13)C abundance ratio. Despite many laboratory based studies of possible DIB carriers, it has not been possible to unambiguously link these bands to specific species. An identification of DIBs would substantially contribute to our understanding of chemical processes in the diffuse interstellar medium. The presence of substructures inside DIB profiles supports the idea that DIBs are very likely features of gas phase molecules. So far only three out of more than 400 DIBs have been linked to specific molecules but none of these links was confirmed beyond doubt. A DIB identification clearly requires a close cooperation between observers and experimentalists. The review presents the state-of-the-art of the investigations of the chemistry of interstellar translucent clouds i.e. how far our observations are sufficient to allow some hints concerning the chemistry of, the most common in the Galaxy, translucent interstellar clouds, likely situated quite far from the sources of radiation (stars).

  16. Tunneling ionization of vibrationally excited nitrogen molecules

    NASA Astrophysics Data System (ADS)

    Kornev, Aleksei S.; Zon, Boris A.

    2015-09-01

    Ionization of molecular nitrogen plays an important role in the process of light-filament formation in air. In the present paper we theoretically investigated tunneling ionization of the valence 3 σg and 1 πu shells in a N2 molecule using a strong near-infrared laser field. This research is based on our previously proposed theory of anti-Stokes-enhanced tunneling ionization with quantum accounting for the vibrationally excited states of the molecules [A. S. Kornev and B. A. Zon, Phys. Rev. A 86, 043401 (2012), 10.1103/PhysRevA.86.043401]. We demonstrated that if the N2 molecule is ionized from the ground vibrational state, then the contribution of the 1 πu orbital is 0.5%. In contrast, for vibrationally excited states with a certain angle between the light polarization vector and the molecule axis, both shells can compete and even reverse their contributions due to the anti-Stokes mechanism. The structure constants of molecular orbitals are extracted from numerical solutions to the Hartree-Fock equations. This approach correctly takes into account the exchange interaction. Quantum consideration of vibrational motion results in the occurrence of the critical vibrational state, the tunneling ionization from which has the maximum rate. The numbers of the critical vibrational states are different for different valence shells. In addition, quantum description of vibrations changes the rate of ionization from the ground vibrational state by 20%-40% in comparison with the quasiclassical results.

  17. Molecule diagram from earth-grown crystals

    NASA Technical Reports Server (NTRS)

    2004-01-01

    Like many chemicals in the body, the three-dimensional structure of insulin is extremely complex. When grown on the ground, insulin crystals do not grow as large or as ordered as researchers desire--obscuring the blueprint of the insulin molecules.

  18. Vibrationally Excited Molecules for Chemical Laser

    DTIC Science & Technology

    Briefly reported are studies on elementary, exothermic, atom-molecule reactions in the hopes of discovering basic features of chemical reaction into specific internal energy vibrational modes of the reaction products. The long- range goal of such studies would hopefully be the prediction of specific chemical reactions which might be promising candidates for chemical laser systems.

  19. Molecules of significance in planetary aeronomy

    NASA Technical Reports Server (NTRS)

    Mohan, H.

    1979-01-01

    This monograph is basically devoted to spectroscopic information of the molecules of planetary interest. Only those molecules have been dealt with which have been confirmed spectroscopically to be present in the atmosphere of major planets of our solar system and play an important role in the aeronomy of the respective planets. An introduction giving the general conditions of planets and their atmospheres including the gaseous molecules is given. Some typical planetary spectra is presented and supported with a discussion on some basic concepts of optical absorption and molecular parameters that are important to the study of planetary atmospheres. Quantities like dipole moments, transition probabilities, Einstein coefficients and line strengths, radiative life times, absorption cross sections, oscillator strengths, line widths and profiles, equivalent widths, growth curves, bond strengths, electronic transition moments, Franck-Condon factors and r-centroids, etc., are discussed. Spectroscopic information and relevant data of 6 diatomic (HF, HCL, CO, H2, O2, N2) and 6 polyatomic (CO2, N2), O3, HeO, NH3, CH4) molecules are presented.

  20. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-05-30

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  1. Method for sequencing nucleic acid molecules

    DOEpatents

    Korlach, Jonas; Webb, Watt W.; Levene, Michael; Turner, Stephen; Craighead, Harold G.; Foquet, Mathieu

    2006-06-06

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  2. Molecules for Fluorescence Detection of Specific Chemicals

    NASA Technical Reports Server (NTRS)

    Fedor, Steve

    2008-01-01

    A family of fluorescent dye molecules has been developed for use in on-off fluorescence detection of specific chemicals. By themselves, these molecules do not fluoresce. However, when exposed to certain chemical analytes in liquid or vapor forms, they do fluoresce (see figure). These compounds are amenable to fixation on or in a variety of substrates for use in fluorescence-based detection devices: they can be chemically modified to anchor them to porous or non-porous solid supports or can be incorporated into polymer films. Potential applications for these compounds include detection of chemical warfare agents, sensing of acidity or alkalinity, and fluorescent tagging of proteins in pharmaceutical research and development. These molecules could also be exploited for use as two-photon materials for photodynamic therapy in the treatment of certain cancers and other diseases. A molecule in this family consists of a fluorescent core (such as an anthracene or pyrene) attached to two end groups that, when the dye is excited by absorption of light, transfer an electron to the core, thereby quenching the fluorescence. The end groups can be engineered so that they react chemically with certain analytes. Upon reaction, electrons on the end groups are no longer available for transfer to the core and, consequently, the fluorescence from the core is no longer quenched. The chemoselectivity of these molecules can be changed by changing the end groups. For example, aniline end groups afford a capability for sensing acids or acid halides (including those contained in chemical warfare agents). Pyridine or bipyridyl end groups would enable sensing of metal ions. Other chemicals that can be selectively detected through suitable choice of end groups include glucose and proteins. Moreover, the fluorescent cores can be changed to alter light-absorption and -emission characteristics: anthracene cores fluoresce at wavelengths around 500 nm, whereas perylene cores absorb and emit at

  3. Single-molecule Michaelis-Menten equations.

    PubMed

    Kou, S C; Cherayil, Binny J; Min, Wei; English, Brian P; Xie, X Sunney

    2005-10-20

    This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble kinetics, it contains more information than the ensemble data; in particular, it provides crucial information on dynamic disorder, the apparent fluctuation of the catalytic rates due to the interconversion among the enzyme's conformers with different catalytic rate constants. In the presence of dynamic disorder, f(t) exhibits a highly stretched multiexponential decay at high substrate concentrations and a monoexponential decay at low substrate concentrations. We derive a single-molecule Michaelis-Menten equation for the reciprocal of the first moment of f(t), 1/, which shows a hyperbolic dependence on the substrate concentration [S], similar to the ensemble enzymatic velocity. We prove that this single-molecule Michaelis-Menten equation holds under many conditions, in particular when the intercoversion rates among different enzyme conformers are slower than the catalytic rate. However, unlike the conventional interpretation, the apparent catalytic rate constant and the apparent Michaelis constant in this single-molecule Michaelis-Menten equation are complicated functions of the catalytic rate constants of individual conformers. We also suggest that the randomness parameter r, defined as <(t - )2> / t2, can serve as an indicator for dynamic disorder in the catalytic step of the enzymatic reaction, as it becomes larger than unity at high substrate concentrations in the presence of dynamic disorder.

  4. Chiral Sensitivity in Electron-Molecule Interactions

    NASA Astrophysics Data System (ADS)

    Dreiling, Joan

    2015-09-01

    All molecular forms of life possess a chiral asymmetry, with amino acids and sugars found respectively in L- and D-enantiomers only. The primordial origin of this enantiomeric excess is unknown. One possible explanation is given by the Vester- Ulbricht hypothesis, which suggests that left-handed electrons present in beta-radiation, produced by parity-violating weak decays, interacted with biological precursors and preferentially destroyed one of the two enantiomers. Experimental tests of this idea have thus far yielded inconclusive results. We show direct evidence for chirally-dependent bond breaking through a dissociative electron attachment (DEA) reaction when spin-polarized electrons are incident on gas-phase chiral molecules. This provides unambiguous evidence for a well-defined, chirally-sensitive destructive molecular process and, as such, circumstantial evidence for the Vester-Ulbricht hypothesis. I will also present the results of our systematic study of the DEA asymmetry for different chiral halocamphor molecules. Three halocamphor molecules were investigated: 3-bromocamphor (C10H15BrO), 3-iodocamphor(C10H15IO), and 10-iodocamphor. The DEA asymmetries collected for bromocamphor and iodocamphor are qualitatively different, suggesting that the atomic number of the heaviest atom in the molecule plays a crucial role in the asymmetric interactions. The DEA asymmetry data for 3- and 10-iodocamphor have the same qualitative behavior, but the 10-iodocamphor asymmetry is about twice as large at the lowest energies investigated, so the location of the heavy atom in the camphor molecule also affects the asymmetries. This work was performed at the University of Nebraska-Lincoln. This project is funded by NSF Grant PHY-1206067.

  5. Mechanical coupling between myosin molecules causes differences between ensemble and single-molecule measurements.

    PubMed

    Walcott, Sam; Warshaw, David M; Debold, Edward P

    2012-08-08

    In contracting muscle, individual myosin molecules function as part of a large ensemble, hydrolyzing ATP to power the relative sliding of actin filaments. The technological advances that have enabled direct observation and manipulation of single molecules, including recent experiments that have explored myosin's force-dependent properties, provide detailed insight into the kinetics of myosin's mechanochemical interaction with actin. However, it has been difficult to reconcile these single-molecule observations with the behavior of myosin in an ensemble. Here, using a combination of simulations and theory, we show that the kinetic mechanism derived from single-molecule experiments describes ensemble behavior; but the connection between single molecule and ensemble is complex. In particular, even in the absence of external force, internal forces generated between myosin molecules in a large ensemble accelerate ADP release and increase how far actin moves during a single myosin attachment. These myosin-induced changes in strong binding lifetime and attachment distance cause measurable properties, such as actin speed in the motility assay, to vary depending on the number of myosin molecules interacting with an actin filament. This ensemble-size effect challenges the simple detachment limited model of motility, because even when motility speed is limited by ADP release, increasing attachment rate can increase motility speed.

  6. Novel Applications of Buffer-gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules

    NASA Astrophysics Data System (ADS)

    Drayna, Garrett Korda

    Cold gases of atoms and molecules provide a system for the exploration of a diverse set of physical phenomena. For example, cold gasses of magnetically and electrically polar atoms and molecules are ideal systems for quantum simulation and quantum computation experiments, and cold gasses of large polar molecules allow for novel spectroscopic techniques. Buffer-gas cooling is a robust and widely applicable method for cooling atoms and molecules to temperatures of approximately 1 Kelvin. In this thesis, I present novel applications of buffer-gas cooling to obtaining gases of trapped, ultracold atoms and diatomic molecules, as well as the study of the cooling of large organic molecules. In the first experiment of this thesis, a buffer-gas beam source of atoms is used to directly load a magneto-optical trap. Due to the versatility of the buffer-gas beam source, we obtain trapped, sub-milliKelvin gases of four different lanthanide species using the same experimental apparatus. In the second experiment of this thesis, a buffer-gas beam is used as the initial stage of an experiment to directly laser cool and magneto-optically trap the diatomic molecule CaF. In the third experiment of this thesis, buffer-gas cooling is used to study the cooling of the conformational state of large organic molecules. We directly observe conformational relaxation of gas-phase 1,2-propanediol due to cold collisions with helium gas. Lastly, I present preliminary results on a variety of novel applications of buffer-gas cooling, such as mixture analysis, separation of chiral mixtures, the measurement of parity-violation in chiral molecules, and the cooling and spectroscopy of highly unstable reaction intermediates.

  7. Electron Transfer-Induced Fragmentation in (Bio)Molecules by Atom-Molecule Collisions

    NASA Astrophysics Data System (ADS)

    Limão-Vieira, Paulo; da Silva, Filipe Ferreira; Gómez-Tejedor, Gustavo García

    Ion-pair formation to gas phase molecules induced by electron transfer has been studied by investigating the products of collisions between fast potassium atoms and target molecules using a crossed molecular-beam technique. The negative ions formed in such collisions are TOF mass analysed. As far as (bio)molecules are concerned, TOF mass spectra at different collision energies reveal interesting anionic patterns with reduced fragmentation at lower impact energies. In the unimolecular decomposition of the temporary negative ion (TNI), complex internal rearrangement may involve the cleavage and formation of new bonds. In this chapter we report some of the recent achievements in negative ion formation of some polyatomic molecules with the special attention to biological relevant targets.

  8. Rotational dynamics of simple asymmetric molecules

    NASA Astrophysics Data System (ADS)

    Fragiadakis, D.; Roland, C. M.

    2015-02-01

    Molecular dynamic simulations were carried out on rigid diatomic molecules, which exhibit both α (structural) and β (secondary) dynamics. The relaxation scenarios range from onset behavior, in which a distinct α process emerges on cooling, to merging behavior, associated with two relaxation peaks that converge at higher temperature. These properties, as well as the manifestation of the β peak as an excess wing, depend not only on thermodynamic conditions, but also on both the symmetry of the molecule and the correlation function (odd or even) used to analyze its dynamics. These observations help to reconcile divergent results obtained from different experiments. For example, the β process is more intense and the α-relaxation peak is narrower in dielectric relaxation spectra than in dynamic light scattering or NMR measurements. In the simulations herein, this follows from the weaker contribution of the secondary relaxation to even-order correlation functions, related to the magnitude of the relevant angular jumps.

  9. Pollen tube guidance by attractant molecules: LUREs.

    PubMed

    Okuda, Satohiro; Higashiyama, Tetsuya

    2010-01-01

    Sexual reproduction in flowering plants requires pollen-tube guidance, which is thought to be mediated by chemoattractants derived from target ovules. To date, however, no convincing evidence has been reported of a particular molecule being the true attractant. Emerging data indicate that two synergid cells, which are on either side of the egg cell, emit a diffusible, species-specific signal to attract the pollen tube at the last step of pollen-tube guidance. Recently, it was demonstrated that LUREs (LURE1 and LURE2), cysteine-rich polypeptides secreted from the synergid cell, are the key molecules in pollen-tube guidance. In this review, we summarize the mechanism of pollen-tube guidance, with special focus on gametophytic guidance and the attractants.

  10. Theory of single molecule emission spectroscopy

    SciTech Connect

    Bel, Golan; Brown, Frank L. H.

    2015-05-07

    A general theory and calculation framework for the prediction of frequency-resolved single molecule photon counting statistics is presented. Expressions for the generating function of photon counts are derived, both for the case of naive “detection” based solely on photon emission from the molecule and also for experimentally realizable detection of emitted photons, and are used to explicitly calculate low-order photon-counting moments. The two cases of naive detection versus physical detection are compared to one another and it is demonstrated that the physical detection scheme resolves certain inconsistencies predicted via the naive detection approach. Applications to two different models for molecular dynamics are considered: a simple two-level system and a two-level absorber subject to spectral diffusion.

  11. Computer display and manipulation of biological molecules

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Hart, J.; Rein, R.

    1978-01-01

    This paper describes a computer model that was designed to investigate the conformation of molecules, macromolecules and subsequent complexes. Utilizing an advanced 3-D dynamic computer display system, the model is sufficiently versatile to accommodate a large variety of molecular input and to generate data for multiple purposes such as visual representation of conformational changes, and calculation of conformation and interaction energy. Molecules can be built on the basis of several levels of information. These include the specification of atomic coordinates and connectivities and the grouping of building blocks and duplicated substructures using symmetry rules found in crystals and polymers such as proteins and nucleic acids. Called AIMS (Ames Interactive Molecular modeling System), the model is now being used to study pre-biotic molecular evolution toward life.

  12. Computational mass spectrometry for small molecules

    PubMed Central

    2013-01-01

    The identification of small molecules from mass spectrometry (MS) data remains a major challenge in the interpretation of MS data. This review covers the computational aspects of identifying small molecules, from the identification of a compound searching a reference spectral library, to the structural elucidation of unknowns. In detail, we describe the basic principles and pitfalls of searching mass spectral reference libraries. Determining the molecular formula of the compound can serve as a basis for subsequent structural elucidation; consequently, we cover different methods for molecular formula identification, focussing on isotope pattern analysis. We then discuss automated methods to deal with mass spectra of compounds that are not present in spectral libraries, and provide an insight into de novo analysis of fragmentation spectra using fragmentation trees. In addition, this review shortly covers the reconstruction of metabolic networks using MS data. Finally, we list available software for different steps of the analysis pipeline. PMID:23453222

  13. Exploring X(5568) as a meson molecule

    NASA Astrophysics Data System (ADS)

    Agaev, S. S.; Azizi, K.; Sundu, H.

    2016-10-01

    The parameters, i.e. the mass and current coupling of the exotic X(5568) state observed by the D0 Collaboration as well as the decay width of the process X → B_s0π+, are explored using the Boverline{K} molecule assumption on its structure. Employed computational methods include QCD two-point and light-cone sum rules, the latter being considered in the soft-meson approximation. The obtained results are compared with the data of the D0 Collaboration as well as with the predictions of the diquark-antidiquark model. This comparison strengthens a diquark-antidiquark picture for the X(5568) state rather than a meson molecule structure.

  14. Illuminating single molecules in condensed matter.

    PubMed

    Moerner, W E; Orrit, M

    1999-03-12

    Efficient collection and detection of fluorescence coupled with careful minimization of background from impurities and Raman scattering now enable routine optical microscopy and study of single molecules in complex condensed matter environments. This ultimate method for unraveling ensemble averages leads to the observation of new effects and to direct measurements of stochastic fluctuations. Experiments at cryogenic temperatures open new directions in molecular spectroscopy, quantum optics, and solid-state dynamics. Room-temperature investigations apply several techniques (polarization microscopy, single-molecule imaging, emission time dependence, energy transfer, lifetime studies, and the like) to a growing array of biophysical problems where new insight may be gained from direct observations of hidden static and dynamic inhomogeneity.

  15. Trace Molecules in Giant Planet Atmospheres

    NASA Astrophysics Data System (ADS)

    Huestis, D. L.; Smith, G. P.

    2010-12-01

    Chemical kinetics matters in the upper atmospheres of giant planets in our solar system and in extrasolar systems. The composition of a volume of gas depends not only on where it is, but also on how it got there. The giant planets in our own solar system still have much to teach us about what we will be observing on extrasolar giant planets and how to interpret what we observe. Some molecules, such as CO, C2H2, C2H6, PH3, and NH3, which we call tracer molecules, provide remotely observable signatures of vertical transport. PH3 and NH3 especially have complicated thermochemistry and chemical kinetics that, until recently, have been poorly understood. Based on analysis of recent literature, we have identified new chemical mechanisms for interconverting NH3 and N2 and for interconverting PH3 and NH4-H2PO4.

  16. Semaphorins: a new class of immunoregulatory molecules

    PubMed Central

    Takegahara, Noriko; Kumanogoh, Atsushi; Kikutani, Hitoshi

    2005-01-01

    The immune and nervous systems play distinct roles in maintaining physiological homeostasis. Recent data indicates that these systems influence one another and share many proteins and pathways that are essential for their normal function and development. Molecules originally shown to be critical for the development of proper immune responses have recently been found to function in the nervous system. Conversely, neuronal guidance cues can modulate immune functions. Although semaphorins were originally identified as axon guidance factors active during neuronal development, several recent studies have identified indispensable functions for these molecules in the immune system. This review provides an overview of the rapidly emerging functions of semaphorins and their receptors in the immune system. PMID:16147531

  17. Photodestruction rates for cometary parent molecules

    NASA Astrophysics Data System (ADS)

    Crovisier, J.

    1994-02-01

    New evaluations of the photodestruction rates for several molecules of cometary interest are presented along with a critical comparison with other estimations from 1976 to 1993, and a summary of the need for future laboratory measurements. Photodestruction rates for a heliocentric distance of 1 AU (assuming the quiet Sun reference spectrum of Huebner and Carpenter) are tabulated for molecules from the water group, hydrocarbons, CO group, CHO species, nitrogen compounds, and sulfur compounds. Inspection of the table shows reasonable agreement between new and previously calculated photodestruction rates. Further work is needed on unstable species, photodissociation channel and quantum yields, temperature effects, kinematics and anistropic ejection of the fragments, and the effects of solar radiation field variations.

  18. Is the focus on "molecules" obsolete?

    PubMed

    Whitesides, George M

    2013-01-01

    The technologies developed in analytical chemistry have defined in spectacular detail the properties of molecules. The field now faces enormously important and interesting problems of which molecules are only a part: for example, understanding the nature of life; helping to manage megacities, oceans, and atmospheres; and making health care (especially diagnostics) affordable and relevant. The emergence of these problems involving molecular systems raises the issue of how (and what) analytical chemistry should teach. Historically, it has been essential to chemistry in teaching the science of measurement. As complicated analytical techniques proliferate, it must consider how to balance teaching the uses of sophisticated devices and the fundamentals of analysis and measurement. This review (by an admiring but nonanalytical chemist) sketches the essential role of analytical methods--especially simple ones made up on the spot--in guiding research in new fields, with examples from self-assembled monolayers, soft lithography, paper diagnostics, and self-assembly; and suggests issues in teaching.

  19. Modeling of Single Molecule Cytoplasmic Dynein

    NASA Astrophysics Data System (ADS)

    Yu, Clare

    2010-03-01

    A living cell has an infrastructure much like that of a city. We will describe the transportation system that consists of roads (filaments) and molecular motors (proteins) that haul cargo along these roads. Dynein is one type of motor protein that walks along microtubules towards the nucleus of the cell. Dynein is more complicated in its structure and function than other motors. Experiments have found that, unlike other motors, dynein can take different size steps along microtubules depending on load and ATP concentration. We use Monte Carlo simulations to model the molecular motor function of cytoplasmic dynein at the single molecule level. The theory relates dynein's enzymatic properties to its mechanical force production. Our simulations reproduce the main features of recent single molecule experiments. We make testable predictions that should guide future experiments related to dynein function.

  20. Chirally-sensitive electron-molecule interactions

    NASA Astrophysics Data System (ADS)

    Dreiling, J. M.; Gay, T. J.

    2015-09-01

    All molecular forms of life have chemically-specific handedness. However, the origin of these asymmetries is not understood. A possible explanation was suggested by Vester and Ulbricht immediately following the discovery of parity violation in 1957: chiral beta radiation in cosmic rays may have preferentially destroyed one enantiomeric form of various biological precursors. In the experiments reported here, we observed chiral specificity in two electron- molecule interactions: quasi-elastic scattering and dissociative electron attachment. Using low- energy longitudinally spin-polarized (chiral) electrons as substitutes for beta rays, we found that chiral bromocamphor molecules exhibited both a transmission and dissociative electron attachment rate that depended on their handedness for a given direction of incident electron spin. Consequently, these results, especially those with dissociative electron attachment, connect the universal chiral asymmetry of the weak force with a molecular breakup process, thereby demonstrating the viability of the Vester-Ulbricht hypothesis.

  1. The X(3872) boson: Molecule or charmonium

    SciTech Connect

    Suzuki, Mahiko

    2005-08-01

    It has been argued that the mystery boson X(3872) is a molecular state consisting of primarily D{sup 0}{bar D}*{sup 0} + {bar D}{sup 0}D*{sup 0}. In contrast, apparent puzzles and potential difficulties have been pointed out for the charmonium assignment of X(3872). They examine several aspects of these alternatives by semi-quantitative methods since quantitatively accurate results are often hard to reach on them. they point out that some of the observed properties of X(3872), in particular, the binding and the production rates are incompatible with the molecule interpretation. Despite puzzles and obstacles, X(3872) may fit more likely to the excited {sup 3}P{sub 1} charmonium than to the molecule after the mixing of c{bar c} with D{bar D}* + {bar D}D* is taken into account.

  2. Imaging Genetic Molecules At Atomic Resolution

    NASA Technical Reports Server (NTRS)

    Coles, L. Stephen

    1993-01-01

    Proposed method of imaging informational polymeric biological molecules at atomic resolution enables determination of sequences of component monomers about 10 to the 3rd power to 10 to the 4th power times as fast as conventional methods do. Accelerates research on genetic structures of animals and plants. Also contributes significantly to imaging processes like scanning electron microscopy (SEM), atomic-force microscopy (AFM), and scanning tunneling microscopy (STM) in cases in which necessary to locate or identify small specimens on relatively large backgrounds and subtract background images to obtain images of specimens in isolation. V-grooves on silicon wafer laid out in square pattern, intersections of which marked to identify coordinates. Specimen molecules held in grooves for reproducible positioning and scanning by AFM or STM.

  3. Automated imaging system for single molecules

    DOEpatents

    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.

  4. Organic small molecule-based optical coatings

    NASA Astrophysics Data System (ADS)

    Schulz, U.; Präfke, C.; Munzert, P.; Kaiser, N.

    2011-09-01

    A small molecule is a low molecular weight organic compound which is by definition not a polymer. Therefore, physical vapor deposition by evaporation as common for inorganic oxides is often possible. Organic layers can be useful as components of interference stacks for different functions. A number of organic compounds have interesting UV absorption characteristics and can be used to protect UV-sensitive polymers such as polycarbonate. In addition, organic layers can be applied to generate nanostructured thin films with a very low effective refractive index, as shown recently for polymers. A structured organic single layer can be applied as an antireflective (AR) coating for a glass lens. The applicability of several small molecule compounds will be discussed in this paper.

  5. Is the Focus on ``Molecules'' Obsolete?

    NASA Astrophysics Data System (ADS)

    Whitesides, George M.

    2013-06-01

    The technologies developed in analytical chemistry have defined in spectacular detail the properties of molecules. The field now faces enormously important and interesting problems of which molecules are only a part: for example, understanding the nature of life; helping to manage megacities, oceans, and atmospheres; and making health care (especially diagnostics) affordable and relevant. The emergence of these problems involving molecular systems raises the issue of how (and what) analytical chemistry should teach. Historically, it has been essential to chemistry in teaching the science of measurement. As complicated analytical techniques proliferate, it must consider how to balance teaching the uses of sophisticated devices and the fundamentals of analysis and measurement. This review (by an admiring but nonanalytical chemist) sketches the essential role of analytical methods—especially simple ones made up on the spot—in guiding research in new fields, with examples from self-assembled monolayers, soft lithography, paper diagnostics, and self-assembly; and suggests issues in teaching.

  6. Late Stage Azidation of Complex Molecules

    PubMed Central

    2016-01-01

    Selective functionalization of complex scaffolds is a promising approach to alter the pharmacological profiles of natural products and their derivatives. We report the site-selective azidation of benzylic and aliphatic C–H bonds in complex molecules catalyzed by the combination of Fe(OAc)2 and a PyBox ligand. The same system also catalyzes the trifluoromethyl azidation of olefins to form derivatives of natural products containing both fluorine atoms and azides. In general, both reactions tolerate a wide range of functional groups and occur with predictable regioselectivity. Azides obtained by functionalization of C–H and C=C bonds were converted to the corresponding amines, amides, and triazoles, thus providing a wide variety of nitrogen-containing complex molecules. PMID:27800554

  7. Electron correlation dynamics in atoms and molecules.

    PubMed

    Nest, M; Ludwig, M; Ulusoy, I; Klamroth, T; Saalfrank, P

    2013-04-28

    In this paper, we present quantum dynamical calculations on electron correlation dynamics in atoms and molecules using explicitly time-dependent ab initio configuration interaction theory. The goals are (i) to show that in which cases it is possible to switch off the electronic correlation by ultrashort laser pulses, and (ii) to understand the temporal evolution and the time scale on which it reappears. We characterize the appearance of correlation through electron-electron scattering when starting from an uncorrelated state, and we identify pathways for the preparation of a Hartree-Fock state from the correlated, true ground state. Exemplary results for noble gases, alkaline earth elements, and selected molecules are provided. For Mg we show that the uncorrelated state can be prepared using a shaped ultrashort laser pulse.

  8. Manipulating Kondo temperature via single molecule switching.

    PubMed

    Iancu, Violeta; Deshpande, Aparna; Hla, Saw-Wai

    2006-04-01

    Two conformations of isolated single TBrPP-Co molecules on a Cu(111) surface are switched by applying +2.2 V voltage pulses from a scanning tunneling microscope tip at 4.6 K. The TBrPP-Co has a spin-active cobalt atom caged at its center, and the interaction between the spin of this cobalt atom and free electrons from the Cu(111) substrate can cause a Kondo resonance. Tunneling spectroscopy data reveal that switching from the saddle to a planar molecular conformation enhances spin-electron coupling, which increases the associated Kondo temperature from 130 to 170 K. This result demonstrates that the Kondo temperature can be manipulated just by changing molecular conformation without altering chemical composition of the molecule.

  9. Targeted Protein Degradation by Small Molecules.

    PubMed

    Bondeson, Daniel P; Crews, Craig M

    2017-01-06

    Protein homeostasis networks are highly regulated systems responsible for maintaining the health and productivity of cells. Whereas therapeutics have been developed to disrupt protein homeostasis, more recently identified techniques have been used to repurpose homeostatic networks to effect degradation of disease-relevant proteins. Here, we review recent advances in the use of small molecules to degrade proteins in a selective manner. First, we highlight all-small-molecule techniques with direct clinical application. Second, we describe techniques that may find broader acceptance in the biomedical research community that require little or no synthetic chemistry. In addition to serving as innovative research tools, these new approaches to control intracellular protein levels offer the potential to develop novel therapeutics targeting proteins that are not currently pharmaceutically vulnerable.

  10. Investigation of electron attachment in polyatomic molecules

    NASA Astrophysics Data System (ADS)

    Dowell, J. T.

    1980-05-01

    Electron attachment to polyatomic molecules was studied using molecular beams of variable temperature crossed with an electron of high energy resolution. Species investigated include sulfur hexafluoride, molybdenum hexafluoride, and tungsten oxide polymers. New results were obtained in sulfur hexafluoride demonstrating importance of internal energy for the dissociative attachment in molybdenum hexafluoride. Tungsten oxide vapor exhibits both monomer and dimer negative ion formation near zero energy, apparently from dissociative attachment to the trimer.

  11. Collision integrals for isotopic hydrogen molecules.

    NASA Technical Reports Server (NTRS)

    Brown, N. J.; Munn, R. J.

    1972-01-01

    The study was undertaken to determine the effects of reduced mass and differences in asymmetry on the collision integrals and thermal diffusion factors of isotopic hydrogen systems. Each system selected for study consisted of two diatoms, one in the j = 0 rotation state and the other in the j = 1 state. The molecules interacted with a Lennard-Jones type potential modified to include angular terms. A set of cross sections and collision integrals were obtained for each system.

  12. Controlling quantum transport through a single molecule.

    PubMed

    Cardamone, David M; Stafford, Charles A; Mazumdar, Sumit

    2006-11-01

    We investigate multiterminal quantum transport through single monocyclic aromatic annulene molecules, and their derivatives, using the nonequilibrium Green function approach within the self-consistent Hartree-Fock approximation. We propose a new device concept, the quantum interference effect transistor, that exploits perfect destructive interference stemming from molecular symmetry and controls current flow by introducing decoherence and/or elastic scattering that break the symmetry. This approach overcomes the fundamental problems of power dissipation and environmental sensitivity that beset nanoscale device proposals.

  13. Small Talk: Children's Everyday `Molecule' Ideas

    NASA Astrophysics Data System (ADS)

    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.

  14. 'Single molecule': theory and experiments, an introduction.

    PubMed

    Riveline, Daniel

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins--molecular motors--have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'.

  15. 'Single molecule': theory and experiments, an introduction

    PubMed Central

    2013-01-01

    At scales below micrometers, Brownian motion dictates most of the behaviors. The simple observation of a colloid is striking: a permanent and random motion is seen, whereas inertial forces play a negligible role. This Physics, where velocity is proportional to force, has opened new horizons in biology. The random feature is challenged in living systems where some proteins - molecular motors - have a directed motion whereas their passive behaviors of colloid should lead to a Brownian motion. Individual proteins, polymers of living matter such as DNA, RNA, actin or microtubules, molecular motors, all these objects can be viewed as chains of colloids. They are submitted to shocks from molecules of the solvent. Shapes taken by these biopolymers or dynamics imposed by motors can be measured and modeled from single molecules to their collective effects. Thanks to the development of experimental methods such as optical tweezers, Atomic Force Microscope (AFM), micropipettes, and quantitative fluorescence (such as Förster Resonance Energy Transfer, FRET), it is possible to manipulate these individual biomolecules in an unprecedented manner: experiments allow to probe the validity of models; and a new Physics has thereby emerged with original biological insights. Theories based on statistical mechanics are needed to explain behaviors of these systems. When force-extension curves of these molecules are extracted, the curves need to be fitted with models that predict the deformation of free objects or submitted to a force. When velocity of motors is altered, a quantitative analysis is required to explain the motions of individual molecules under external forces. This lecture will give some elements of introduction to the lectures of the session 'Nanophysics for Molecular Biology'. PMID:24565227

  16. Container molecules based on imine type ligands.

    PubMed

    Schulze, A Carina; Oppel, Iris M

    2012-01-01

    This chapter will give a short overview about container molecules, their synthesis and possible applications. The main focus is on those which are based on imine type ligands. These containers can be used for example for guest exchange, gas separation, as chemical sensors or for the stabilisation of white phosphorus under water. The described cages have wide openings or tightly closed ones. For one cage the reversible opening and closing is also described.

  17. Novel Small-Molecule Antibacterial Agents

    DTIC Science & Technology

    2014-07-01

    Molecules, Reversible Inhibitors, Irreversible Inhibitors, Therapeutics, Antidotes, Countermeasures, Botulism , and Neurotoxins. REPORT DOCUMENTATION...Standard Form 298 (Rev 8/98) Prescribed by ANSI Std. Z39.18 W911NF-09-1-0095 507-266-7991 Final Report 56085-LS.6 a. REPORT 14. ABSTRACT 16...8,404,728 B2) is 71 ± 26 nM (2 independent experiments with chi square 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13. SUPPLEMENTARY NOTES

  18. Potential energy landscapes of tetragonal pyramid molecules

    NASA Astrophysics Data System (ADS)

    Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.

    2016-11-01

    Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.

  19. Soliton molecules for advanced optical telecommunications

    NASA Astrophysics Data System (ADS)

    Mitschke, Fedor; Hause, Alexander; Mahnke, Christoph

    2016-11-01

    Recent developments in the technology of optical telecommunications are pushed forward by the rapidly growing demand for data-carrying capacity. Current approaches are discussed; most lines of investigation are limited to the linear (i.e. low power) regime. It is shown how this restriction poses a limit for further evolution. If, on the other hand, the nonlinear regime is entered, recent developments about soliton molecules offer a possibility to advance further.

  20. Circular Intensity Differential Scattering of chiral molecules

    SciTech Connect

    Bustamante, C.J.

    1980-12-01

    In this thesis a theory of the Circular Intensity Differential Scattering (CIDS) of chiral molecules as modelled by a helix oriented with respect to the direction of incidence of light is presented. It is shown that a necessary condition for the existence of CIDS is the presence of an asymmetric polarizability in the scatterer. The polarizability of the scatterer is assumed generally complex, so that both refractive and absorptive phenomena are taken into account.

  1. Sensor Materials - Detecting Molecules, Mixtures and Microorganisms -

    DTIC Science & Technology

    2002-04-05

    1090 Vienna, Austria ABSTRACT Sensor materials based on molecularly imprinted organic and inorganic polymers were designed and characterized according...both organic and inorganic polymers , able to selectively re-include the template species. Imprinting was performed both on the molecular and the...for the specific detection of small organic molecules, major improvements in sensor layer design can be achieved by molecular imprinting methods [3,4

  2. Model systems for single molecule polymer dynamics.

    PubMed

    Latinwo, Folarin; Schroeder, Charles M

    2011-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of "ideal" and "real" chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force-extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer-monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of "real" polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.

  3. (Aerodynamic focusing of particles and heavy molecules)

    SciTech Connect

    de la Mora, J.F.

    1990-01-08

    By accelerating a gas containing suspended particles or large molecules through a converging nozzle, the suspended species may be focused and therefore used to write fine lines on a surface. Our objective was to study the limits on how narrow this focal region could be as a function of particle size. We find that, for monodisperse particles with masses m{sub p} some 3.6 {times} 10{sup 5} times larger than the molecular mass m of the carrier gas (diameters above some 100{angstrom}), there is no fundamental obstacle to directly write submicron features. However, this conclusion has been verified experimentally only with particles larger than 0.1 {mu}m. Experimental, theoretical and numerical studies on the defocusing role of Brownian motion for very small particles or heavy molecules have shown that high resolution (purely aerodynamic) focusing is impossible with volatile molecules whose masses are typically smaller than 1000 Dalton. For these, the minimal focal diameter after optimization appears to be 5{radical}(m/m{sub p}) times the nozzle diameter d{sub n}. But combinations of focused lasers and aerodynamic focusing appear as promising for direct writing with molecular precursors. Theoretical and numerical schemes capable of predicting the evolution of the focusing beam, including Brownian motion effects, have been developed, although further numerical work would be desirable. 11 refs.

  4. Signaling Molecules: Hydrogen Sulfide and Polysulfide

    PubMed Central

    2015-01-01

    Abstract Significance: Hydrogen sulfide (H2S) has been recognized as a signaling molecule as well as a cytoprotectant. It modulates neurotransmission, regulates vascular tone, and protects various tissues and organs, including neurons, the heart, and kidneys, from oxidative stress and ischemia-reperfusion injury. H2S is produced from l-cysteine by cystathionine β-synthase (CBS), cystathionine γ-lyase (CSE), and 3-mercaptopyruvate sulfurtransferase (3MST) along with cysteine aminotransferase. Recent Advances: In addition to these enzymes, we recently identified a novel pathway to produce H2S from d-cysteine, which involves d-amino acid oxidase (DAO) along with 3MST. These enzymes are localized in the cytoplasm, mitochondria, and peroxisomes. However, some enzymes translocate to organelles under specific conditions. Moreover, H2S-derived potential signaling molecules such as polysulfides and HSNO have been identified. Critical Issues: The physiological stimulations, which trigger the production of H2S and its derivatives and maintain their local levels, remain unclear. Future Directions: Understanding the regulation of the H2S production and H2S-derived signaling molecules and the specific stimuli that induce their release will provide new insights into the biology of H2S and therapeutic development in diseases involving these substances. Antioxid. Redox Signal. 22, 362–376. PMID:24800864

  5. Toward Single-Molecule Nanomechanical Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Roukes, Michael

    2009-03-01

    Mass spectrometry (MS) has become a preeminent methodology of proteomics since it provides rapid and quantitative identification of protein species with relatively low sample consumption. Yet with the trend toward biological analysis at increasingly smaller scales, ultimately down to the volume of an individual cell, MS with few-to-single molecule resolution will be required. We report the first realization of MS based on single-biological-molecule detection with nanoelectromechanical systems (NEMS). NEMS provide unparalleled mass resolution, now sufficient for detection of individual molecular species in real time. However, high sensitivity is only one of several components required for MS. We demonstrate a first complete prototype NEMS-MS system for single-molecule mass spectrometry providing proof-of-principle for this new technique. Nanoparticles and protein species are introduced by electrospray injection from the fluid phase in ambient conditions into vacuum and subsequently delivered to the NEMS detector by hexapole ion optics . Mass measurements are then recorded in real-time as analytes adsorb, one-by-one, onto a phase-locked, ultrahigh frequency (UHF) NEMS resonator. These first NEMS-MS spectra, obtained with modest resolution from only several hundred mass adsorption events, presage the future capabilities of this methodology. We outline the substantial improvements feasible in near term, through recent advances and technological avenues that are unique to NEMS-MS.

  6. Rotational isomerism of molecules in condensed phases

    NASA Astrophysics Data System (ADS)

    Sakka, Tetsuo; Iwasaki, Matae; Ogata, Yukio

    1991-08-01

    A statistical mechanical model is developed for the description of the conformational distribution of organic molecules in the liquid and solid phases. In the model, they are assumed to have one internal freedom of rotation. The molecules are fixed to lattice sites and have two types of ordering, conformational and distributional. The latter is supposed to represent an ordering typical of solid state. The model is compared with the experimental results of the rotational-isomeric ratio of 1,2-dichloro-1,1-difluoroethane, in the temperature range from 77 to 300 K. It explains successfully the experimental results, especially the behavior near the melting point. From the point of view of melting, the present model is an extension of the Lennard-Jones and Devonshire model, because, when the distinctions between the two conformers are neglected, the parameter representing the distributional ordering of the molecules results in the same equation as that derived from the Lennard-Jones and Devonshire model.

  7. Atoms and Molecules in Strong Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Schmelcher, P.; Cederbaum, L. S.

    Selected topics on atoms and molecules in strong magnetic fields are reviewed. The enormous progress made for the hydrogen atom in a magnetic field and its impact on different areas like, for example, modern semi-classics and dynamics of non-integrable systems as well as laser spectroscopy are outlined. Due to the non-separability of the centre of mass and electronic motion of atoms/molecules in magnetic fields a variety of two-body phenomena can be observed in highly excited systems. Examples are the classical diffusion of the centre of mass and the giant dipole states for crossed fields. For ions energy transfer processes lead to the so-called self-ionisation process. Magnetically induced crossovers for the ground states of atoms are investigated. The increasing complexity of the ground state behaviour of magnetically dressed multi-electron atoms due to changes of the spin polarisation as well as spatial orbitals is demonstrated. For molecules, both fundamental aspects as well as the electronic structure of few-electron diatomics are reviewed.

  8. Partially dark optical molecule via phase control

    NASA Astrophysics Data System (ADS)

    Wang, Z. H.; Xu, Xun-Wei; Li, Yong

    2017-01-01

    We study the tunable photonic distribution in an optical molecule consisting of two linearly coupled single-mode cavities. With the intercavity coupling and two driving fields, the energy levels of the optical-molecule system form a closed cyclic energy-level diagram, and the phase difference between the driving fields serves as a sensitive controller on the dynamics of the system. Due to the quantum interference effect, we can realize a partially dark optical molecule, where the steady-state mean photon number in one of the cavities achieves zero even under the external driving. And the dark cavity can be changed from one of the cavities to the other by only adjusting the phase difference. We also show that our proposal is robust to the noise at zero temperature. Furthermore, we show that when one of the cavities couples with an atomic ensemble, it will be dark under the same condition as that in the case without atoms, but the condition for the other cavity to be dark is modified.

  9. Designing a small molecule erythropoietin mimetic.

    PubMed

    Guarnieri, Frank

    2015-01-01

    Erythropoietin (EPO) is a protein made by the kidneys in response to low red blood cell count that is secreted into the bloodstream and binds to a receptor on hematopoietic stem cells in the bone marrow inducing them to become new red blood cells. EPO made with recombinant DNA technology was brought to market in the 1980s to treat anemia caused by kidney disease and cancer chemotherapy. Because EPO infusion was able to replace blood transfusions in many cases, it rapidly became a multibillion dollar per year drug and as the first biologic created with recombinant technology it launched the biotech industry. For many years intense research was focused on creating a small molecule orally available EPO mimetic. The Robert Wood Johnson (RWJ) group seemed to definitively establish that only large peptides with a minimum of 60 residues could replace EPO, as anything less was not a full agonist. An intense study of the published work led me to hypothesize that the size of the mimetic is not the real issue, but the symmetry making and breaking of the EPO receptor induced by the ligand is the key to activating the stem cells. This analysis meant that residues in the binding site of the receptor deemed absolutely essential for ligand binding and activation from mutagenesis experiments, were probably not really that important. My fundamental hypotheses were: (a) the symmetric state of the homodimeric receptor is the most stable state and thus must be the off-state, (b) a highly localized binding site exists at a pivot point where the two halves of the receptor meet, (c) small molecules can be created that have high potency for this site that will be competitive with EPO and thus can displace the protein-protein interaction, (d) small symmetric molecules will stabilize the symmetric off-state of the receptor, and (e) a key asymmetry in the small molecule will stabilize a mirror image asymmetry in the receptor resulting in the stabilization of the on-state and proliferation of

  10. Fixman compensating potential for general branched molecules

    NASA Astrophysics Data System (ADS)

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-12-01

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

  11. Fixman compensating potential for general branched molecules

    PubMed Central

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-01-01

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules. PMID:24387353

  12. MONA – Interactive manipulation of molecule collections

    PubMed Central

    2013-01-01

    Working with small‐molecule datasets is a routine task for cheminformaticians and chemists. The analysis and comparison of vendor catalogues and the compilation of promising candidates as starting points for screening campaigns are but a few very common applications. The workflows applied for this purpose usually consist of multiple basic cheminformatics tasks such as checking for duplicates or filtering by physico‐chemical properties. Pipelining tools allow to create and change such workflows without much effort, but usually do not support interventions once the pipeline has been started. In many contexts, however, the best suited workflow is not known in advance, thus making it necessary to take the results of the previous steps into consideration before proceeding. To support intuition‐driven processing of compound collections, we developed MONA, an interactive tool that has been designed to prepare and visualize large small‐molecule datasets. Using an SQL database common cheminformatics tasks such as analysis and filtering can be performed interactively with various methods for visual support. Great care was taken in creating a simple, intuitive user interface which can be instantly used without any setup steps. MONA combines the interactivity of molecule database systems with the simplicity of pipelining tools, thus enabling the case‐to‐case application of chemistry expert knowledge. The current version is available free of charge for academic use and can be downloaded at http://www.zbh.uni‐hamburg.de/mona. PMID:23985157

  13. Driving Organic Molecule Crystalliztion with Surface Reconstructions

    NASA Astrophysics Data System (ADS)

    Bickel, Jessica; Trovato, Gianfranco

    This work examines how surface reconstructions can drive crystallization of organic molecules via self-assembly. Organic electronic molecules have low conductivities compared to inorganic materials, but crystallizing these polymers increases their conductivity. This project uses surface reconstructions with periodically repeating topographies to drive the crystallization process. The samples are grown by placing a drop of a dilute PEDOT solution on the clean Si(001)-(2x1) or Si(111)-(7x7) surface reconstruction and heating the surface up to both evaporate the solvent and promote diffusion of the polymer to the thermodynamically defined lowest energy position. The resulting samples are characterized by scanning tunneling microscopy (STM) with respect to their crystallinity and electronic properties. Of particular interest is whether there is a preferential location for the PEDOT molecule to adsorb and whether there are any conformational changes upon adsorption that modify the HOMO-LUMO gap. This work is being done in a new pan-style RHK-STM enclosed in a glovebox at Cleveland State University. The glovebox has O2 and H2O levels of less than 1ppm. This allows for sample preparation and imaging in a controlled environment that is free from contamination.

  14. Electron Correlation Effects in Biological Molecules

    NASA Astrophysics Data System (ADS)

    Cox, D. L.; Endres, R.; Kulkarni, R. V.; Labute, M.; Singh, R. R. P.

    2002-07-01

    Allosteric (conformation changing) proteins with transition metal atoms are at the heart of much important biological function (e.g., myoglobin hemoglobin used for storing and transporting oxygen in the bloodstream). In the case of myoglobin and hemoglobin, oxygen ligation to the iron center induces a spin crossover (high to low) coupled to a structural change; apart from the role of Hunds' exchange in the spin crossover, electron interaction effects have been ignored. We argue that the spin crossover/structure change observed in the similarly structured but far simpler cobalt valence tautomer molecules1 necessitates an inclusion of underscreened Kondo like correlations for a complete description of the energetics of the transition and dynamics, e.g., for x-ray absorption data. We carry this study out with Varma-Yafet-Gunnarsson-Schonhammer wave functions, which, in chemistry language, are basis set restricted configuration interaction in character. We briefly review the applicability of such wave functions to the description of the putative Kondo molecules cerocene (Ce[(CH)5]2) and ytterbocene bipyridine (Yb[(CH)5]2(bipy)) and to the problem of electron transfer in biological molecules and organic conductors, where anomalous long range tunneling may occur.

  15. Electron Correlation Effects in Biological Molecules

    NASA Astrophysics Data System (ADS)

    Cox, D. L.; Endres, R.; Kulkarni, R. V.; Labute, M.; Singh, R. R. P.

    Allosteric (conformation changing) proteins with transition metal atoms are at the heart of much important biological function (e.g., myoglobin hemoglobin used for storing and transporting oxygen in the bloodstream). In the case of myoglobin and hemoglobin, oxygen ligation to the iron center induces a spin crossover (high to low) coupled to a structural change; apart from the role of Hunds' exchange in the spin crossover, electron interaction effects have been ignored. We argue that the spin crossover/structure change observed in the similarly structured but far simpler cobalt valence tautomer molecules1 necessitates an inclusion of underscreened Kondo like correlations for a complete description of the energetics of the transition and dynamics, e.g., for x-ray absorption data. We carry this study out with Varma-Yafet-Gunnarsson-Schonhammer wave functions, which, in chemistry language, are basis set restricted configuration interaction in character. We briefly review the applicability of such wave functions to the description of the putative Kondo molecules cerocene (Ce[(CH)5]2) and ytterbocene bipyridine (Yb[(CH)5]2(bipy)) and to the problem of electron transfer in biological molecules and organic conductors, where anomalous long range tunneling may occur. Research supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Division of Materials Research.

  16. Anion binding to the ubiquitin molecule.

    PubMed Central

    Makhatadze, G. I.; Lopez, M. M.; Richardson, J. M.; Thomas, S. T.

    1998-01-01

    Effects of different salts (NaCl, MgCl2, CaCl2, GdmCl, NaBr, NaClO4, NaH2PO4, Na2SO4) on the stability of the ubiquitin molecule at pH 2.0 have been studied by differential scanning calorimetry, circular dichroism, and Tyr fluorescence spectroscopies. It is shown that all of the salts studied significantly increase the thermostability of the ubiquitin molecule, and that this stabilization can be interpreted in terms of anion binding. Estimated thermodynamic parameters of binding for Cl- show that this binding is relatively weak (Kd = 0.15 M) and is characterized by a negative enthalpy of -15 kJ/mol per site. Particularly surprising was the observed stabilizing effect of GdmCl through the entire concentration range studied (0.01-2 M), however, to a lesser extent than stabilization by NaCl. This stabilizing effect of GdmCl appears to arise from the binding of Cl- ions. Analysis of the observed changes in the stability of the ubiquitin molecule in the presence of GdmCl can be adequately described by combining the thermodynamic model of denaturant binding with Cl- binding effects. PMID:9541401

  17. Sorption of small molecules in polymeric media

    NASA Astrophysics Data System (ADS)

    Camboni, Federico; Sokolov, Igor M.

    2016-12-01

    We discuss the sorption of penetrant molecules from the gas phase by a polymeric medium within a model which is very close in spirit to the dual sorption mode model: the penetrant molecules are partly dissolved within the polymeric matrix, partly fill the preexisting voids. The only difference with the initial dual sorption mode situation is the assumption that the two populations of molecules are in equilibrium with each other. Applying basic thermodynamics principles we obtain the dependence of the penetrant concentration on the pressure in the gas phase and find that this is expressed via the Lambert W-function, a different functional form than the one proposed by dual sorption mode model. The Lambert-like isotherms appear universally at low and moderate pressures and originate from the assumption that the internal energy in a polymer-penetrant-void ternary mixture is (in the lowest order) a bilinear form in the concentrations of the three components. Fitting the existing data shows that in the domain of parameters where the dual sorption mode model is typically applied, the Lambert function, which describes the same behavior as the one proposed by the gas-polymer matrix model, fits the data equally well.

  18. The missing organic molecules on Mars

    NASA Technical Reports Server (NTRS)

    Benner, S. A.; Devine, K. G.; Matveeva, L. N.; Powell, D. H.

    2000-01-01

    GC-MS on the Viking 1976 Mars missions did not detect organic molecules on the Martian surface, even those expected from meteorite bombardment. This result suggested that the Martian regolith might hold a potent oxidant that converts all organic molecules to carbon dioxide rapidly relative to the rate at which they arrive. This conclusion is influencing the design of Mars missions. We reexamine this conclusion in light of what is known about the oxidation of organic compounds generally and the nature of organics likely to come to Mars via meteorite. We conclude that nonvolatile salts of benzenecarboxylic acids, and perhaps oxalic and acetic acid, should be metastable intermediates of meteoritic organics under oxidizing conditions. Salts of these organic acids would have been largely invisible to GC-MS. Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Approximately 2 kg of meteorite-derived mellitic acid may have been generated per m(2) of Martian surface over 3 billion years. How much remains depends on decomposition rates under Martian conditions. As available data do not require that the surface of Mars be very strongly oxidizing, some organic molecules might be found near the surface of Mars, perhaps in amounts sufficient to be a resource. Missions should seek these and recognize that these complicate the search for organics from entirely hypothetical Martian life.

  19. Self and directed assembly: people and molecules

    PubMed Central

    2016-01-01

    Summary Self-assembly and directed-assembly are two very important aspects of supramolecular chemistry. As a young postgraduate student working in Canada with Tom Fyles my introduction to Supramolecular Chemistry was through the self-assembly of phospholipid membranes to form vesicles for which we were developing unimolecular and self-assembling transporter molecules. The next stage of my development as a scientist was in Japan with Seiji Shinkai where in a “Eureka” moment, the boronic acid templating unit (directed-assembly) of Wulff was combined with photoinduced electron transfer systems pioneered by De Silva. The result was a turn-on fluorescence sensor for saccharides; this simple result has continued to fuel my research to the present day. Throughout my career as well as assembling molecules, I have enjoyed bringing together researchers in order to develop collaborative networks. This is where molecules meet people resulting in assemblies worth more than the individual “molecule” or “researcher”. My role in developing networks with Japan was rewarded by the award of a Daiwa-Adrian Prize in 2013 and I was recently rewarded for developing networks with China with an Inaugural CASE Prize in 2015. PMID:27340435

  20. Electron attachment to the phthalide molecule

    SciTech Connect

    Asfandiarov, N. L.; Pshenichnyuk, S. A.; Vorob’ev, A. S.; Nafikova, E. P.; Lachinov, A. N.; Kraikin, V. A.; Modelli, A.

    2015-05-07

    Phthalide, the simplest chain of conductive polymer thin film, was investigated by means of Electron Transmission Spectroscopy, Negative Ion Mass Spectrometry, and density functional theory quantum chemistry. It has been found that formation of gas-phase long-lived molecular anions of phthalide around 0.7 eV takes place through cleavage of a C–O bond of the pentacyclic ring of the parent molecular anion to give a vibrationally excited (electronically more stable) open-ring molecular anion. The energy of the transition state for ring opening of the parent negative ion is calculated to be 0.65 eV above the neutral ground state of the molecule. The energy (2.64 eV) evaluated for the corresponding transition state in the neutral molecule is much higher, so that the process of electron detachment from the anion must lead to a neutral molecule with its initial pentacyclic structure. The average lifetime of the molecular negative ions formed at an electron energy of 0.75 eV and 80 °C is measured to be about 100 μs. The known switching effect of thin phthalide films could stem from the presence of a similar open/closed transition state also in the polymer.

  1. Single molecule thermodynamics in biological motors.

    PubMed

    Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

    2007-04-01

    Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

  2. Model systems for single molecule polymer dynamics

    PubMed Central

    Latinwo, Folarin

    2012-01-01

    Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of “ideal” and “real” chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force–extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer–monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of “real” polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena. PMID:22956980

  3. Rydberg States of Atoms and Molecules

    NASA Astrophysics Data System (ADS)

    Stebbings, R. F.; Dunning, F. B.

    2011-03-01

    List of contributors; Preface; 1. Rydberg atoms in astrophysics A. Dalgarno; 2. Theoretical studies of hydrogen Rydberg atoms in electric fields R. J. Damburg and V. V. Kolosov; 3. Rydberg atoms in strong fields D. Kleppner, Michael G. Littman and Myron L. Zimmerman; 4. Spectroscopy of one- and two-electron Rydberg atoms C. Fabre and S. Haroche; 5. Interaction of Rydberg atoms with blackbody radiation T. F. Gallagher; 6. Theoretical approaches to low-energy collisions of Rydberg atoms with atoms and ions A. P. Hickman, R. E. Olson and J. Pascale; 7. Experimental studies of the interaction of Rydberg atoms with atomic species at thermal energies F. Gounand and J. Berlande; 8. Theoretical studies of collisions of Rydberg atoms with molecules Michio Matsuzawa; 9. Experimental studies of thermal-energy collisions of Rydberg atoms with molecules F. B. Dunning and R. F. Stebbings; 10. High-Rydberg molecules Robert S. Freund; 11. Theory of Rydberg collisions with electrons, ions and neutrals M. R. Flannery; 12. Experimental studies of the interactions of Rydberg atoms with charged particles J. -F. Delpech; 13. Rydberg studies using fast beams Peter M. Koch; Index.

  4. Crystal structure prediction of rigid molecules.

    PubMed

    Elking, Dennis M; Fusti-Molnar, Laszlo; Nichols, Anthony

    2016-08-01

    A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r(6) dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.

  5. Fixman compensating potential for general branched molecules

    SciTech Connect

    Jain, Abhinandan; Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan

    2013-12-28

    The technique of constraining high frequency modes of molecular motion is an effective way to increase simulation time scale and improve conformational sampling in molecular dynamics simulations. However, it has been shown that constraints on higher frequency modes such as bond lengths and bond angles stiffen the molecular model, thereby introducing systematic biases in the statistical behavior of the simulations. Fixman proposed a compensating potential to remove such biases in the thermodynamic and kinetic properties calculated from dynamics simulations. Previous implementations of the Fixman potential have been limited to only short serial chain systems. In this paper, we present a spatial operator algebra based algorithm to calculate the Fixman potential and its gradient within constrained dynamics simulations for branched topology molecules of any size. Our numerical studies on molecules of increasing complexity validate our algorithm by demonstrating recovery of the dihedral angle probability distribution function for systems that range in complexity from serial chains to protein molecules. We observe that the Fixman compensating potential recovers the free energy surface of a serial chain polymer, thus annulling the biases caused by constraining the bond lengths and bond angles. The inclusion of Fixman potential entails only a modest increase in the computational cost in these simulations. We believe that this work represents the first instance where the Fixman potential has been used for general branched systems, and establishes the viability for its use in constrained dynamics simulations of proteins and other macromolecules.

  6. Heavy exotic molecules with charm and bottom

    NASA Astrophysics Data System (ADS)

    Liu, Yizhuang; Zahed, Ismail

    2016-11-01

    We revisit the formation of pion-mediated heavy-light exotic molecules with both charm and bottom and their chiral partners under the general strictures of both heavy-quark and chiral symmetry. The chiral exotic partners with good parity formed using the (0+ ,1+) multiplet are about twice more bound than their primary exotic partners formed using the (0- ,1-) multiplet. The chiral couplings across the multiplets (0± ,1±) cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for J ≤ 1. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with JPC =1++ bind, which we identify as the reported neutral X (3872). Also, the bottom isotriplet exotic with JPC =1+- binds, which we identify as a mixture of the reported charged exotics Zb+ (10610) and Zb+ (10650). The bound isosinglet with JPC =1++ is suggested as a possible neutral Xb (10532) not yet reported.

  7. Physiological roles of small RNA molecules.

    PubMed

    Michaux, Charlotte; Verneuil, Nicolas; Hartke, Axel; Giard, Jean-Christophe

    2014-06-01

    Unlike proteins, RNA molecules have emerged lately as key players in regulation in bacteria. Most reviews hitherto focused on the experimental and/or in silico methods used to identify genes encoding small RNAs (sRNAs) or on the diverse mechanisms of these RNA regulators to modulate expression of their targets. However, less is known about their biological functions and their implications in various physiological responses. This review aims to compile what is known presently about the diverse roles of sRNA transcripts in the regulation of metabolic processes, in different growth conditions, in adaptation to stress and in microbial pathogenesis. Several recent studies revealed that sRNA molecules are implicated in carbon metabolism and transport, amino acid metabolism or metal sensing. Moreover, regulatory RNAs participate in cellular adaptation to environmental changes, e.g. through quorum sensing systems or development of biofilms, and analyses of several sRNAs under various physiological stresses and culture conditions have already been performed. In addition, recent experiments performed with Gram-positive and Gram-negative pathogens showed that regulatory RNAs play important roles in microbial virulence and during infection. The combined results show the diversity of regulation mechanisms and physiological processes in which sRNA molecules are key actors.

  8. Single-molecule force spectroscopy of the Aplysia cell adhesion molecule reveals two homophilic bonds.

    PubMed

    Martines, E; Zhong, J; Muzard, J; Lee, A C; Akhremitchev, B B; Suter, D M; Lee, G U

    2012-08-22

    Aplysia californica neurons comprise a powerful model system for quantitative analysis of cellular and biophysical properties that are essential for neuronal development and function. The Aplysia cell adhesion molecule (apCAM), a member of the immunoglobulin superfamily of cell adhesion molecules, is present in the growth cone plasma membrane and involved in neurite growth, synapse formation, and synaptic plasticity. apCAM has been considered to be the Aplysia homolog of the vertebrate neural cell adhesion molecule (NCAM); however, whether apCAM exhibits similar binding properties and neuronal functions has not been fully established because of the lack of detailed binding data for the extracellular portion of apCAM. In this work, we used the atomic force microscope to perform single-molecule force spectroscopy of the extracellular region of apCAM and show for the first time (to our knowledge) that apCAM, like NCAM, is indeed a homophilic cell adhesion molecule. Furthermore, like NCAM, apCAM exhibits two distinct bonds in the trans configuration, although the kinetic and structural parameters of the apCAM bonds are quite different from those of NCAM. In summary, these single-molecule analyses further indicate that apCAM and NCAM are species homologs likely performing similar functions.

  9. Complex molecules in galactic dust cores: Biologically interesting molecules and dust chemistry

    NASA Astrophysics Data System (ADS)

    Liu, Shen-Yuan

    2000-06-01

    The astronomical study of molecules has been an essential research field since the development of radio astronomy. Presently nearly 120 molecules have been identified in interstellar and circumstellar environments. The complexity of molecular species, and particularly organic molecules, that can be synthesized in the interstellar medium (ISM) leads to one interesting and important subfield in interstellar molecular studies, namely, the search and study for molecules of possible biological interest. Observationally, complex and most saturated molecules are observed exclusively toward compact hot, dense regions, often called ``hot cores'', in molecular clouds. To account for the observed amount of saturated organic molecules, interstellar dust particles play an important role. It has often been suggested that solid state reactions on grain surfaces provide an efficient way to synthesis saturated organic molecules. The objective of this study is to obtain observational data on biologically interesting molecules and to study important complex interstellar molecules. Since hot molecular cores are inherently compact, interferometric observations are therefore an ideal approach to study these sources. All our observations were all made with the Berkeley-Illinois-Maryland-Association (BIMA) Array. We conducted the first survey of formic acid (HCOOH) with an interferometric array, and identified at least three sources. HCOOH is found with column densities above 1015 cm-2 in these sources. The correlation between HCOOH and HCOOCH3 emission implies a surface chemistry origin of HCOOH. Details of the results are given in Chapter 2. Meanwhile, we continued to search for molecules of biological interest, namely urea, acetic acid, and glycine. In Chapter 3, the results of column density limits set by our observations are discussed. We have also investigated properties of individual hot molecular cores. It is very important to obtain the physical and chemical properties of these

  10. Current status of single-molecule spectroscopy: Theoretical aspects

    NASA Astrophysics Data System (ADS)

    Jung, YounJoon; Barkai, Eli; Silbey, Robert J.

    2002-12-01

    We survey the current status of single-molecule spectroscopy in the view point of theoretical aspects. After an explanation of basic concepts in single-molecule spectroscopy, we focus on the following topics: (1) line shape phenomena in disordered media, (2) photon counting statistics for time-dependent fluctuations in single-molecule spectroscopy, (3) fluorescence intensity fluctuations for nonergodic systems, (4) time-resolved single-molecule fluorescence for conformational dynamics of single biomolecules, (5) single-molecule reaction dynamics at room temperature, and (6) quantum jump method of single quantum system. We conclude this paper with some open questions and perspectives of single-molecule spectroscopy.

  11. Phase Transitions in a Model of Y-Molecules Abstract

    NASA Astrophysics Data System (ADS)

    Holz, Danielle; Ruth, Donovan; Toral, Raul; Gunton, James

    Immunoglobulin is a Y-shaped molecule that functions as an antibody to neutralize pathogens. In special cases where there is a high concentration of immunoglobulin molecules, self-aggregation can occur and the molecules undergo phase transitions. This prevents the molecules from completing their function. We used a simplified model of 2-Dimensional Y-molecules with three identical arms on a triangular lattice with 2-dimensional Grand Canonical Ensemble. The molecules were permitted to be placed, removed, rotated or moved on the lattice. Once phase coexistence was found, we used histogram reweighting and multicanonical sampling to calculate our phase diagram.

  12. Single Molecule Studies on Dynamics in Liquid Crystals

    PubMed Central

    Täuber, Daniela; von Borczyskowski, Christian

    2013-01-01

    Single molecule (SM) methods are able to resolve structure related dynamics of guest molecules in liquid crystals (LC). Highly diluted small dye molecules on the one hand explore structure formation and LC dynamics, on the other hand they report about a distortion caused by the guest molecules. The anisotropic structure of LC materials is used to retrieve specific conformation related properties of larger guest molecules like conjugated polymers. This in particular sheds light on organization mechanisms within biological cells, where large molecules are found in nematic LC surroundings. This review gives a short overview related to the application of highly sensitive SM detection schemes in LC. PMID:24077123

  13. Strongly enhanced field-dependent single-molecule electroluminescence

    NASA Astrophysics Data System (ADS)

    Lee, Tae-Hee; Gonzalez, Jose I.; Dickson, Robert M.

    2002-08-01

    Individual, strongly electroluminescent Agn molecules (n = 28 atoms) have been electrically written within otherwise nonemissive silver oxide films. Exhibiting characteristic single-molecule behavior, these individual room-temperature molecules exhibit extreme electroluminescence enhancements (>104 vs. bulk and dc excitation on a per molecule basis) when excited with specific ac frequencies. Occurring through field extraction of electrons with subsequent reinjection and radiative recombination, single-molecule electroluminescence is enhanced by a general mechanism that avoids slow bulk material response. Thus, while we detail strong electroluminescence from single, highly fluorescent Agn molecules, this mechanism also yields strong ac-excited electroluminescence from similarly prepared, but otherwise nonemissive, individual Cu nanoclusters.

  14. Single-molecule detection: applications to ultrasensitive biochemical analysis

    NASA Astrophysics Data System (ADS)

    Castro, Alonso; Shera, E. Brooks

    1995-06-01

    Recent developments in laser-based detection of fluorescent molecules have made possible the implementation of very sensitive techniques for biochemical analysis. We present and discuss our experiments on the applications of our recently developed technique of single-molecule detection to the analysis of molecules of biological interest. These newly developed methods are capable of detecting and identifying biomolecules at the single-molecule level of sensitivity. In one case, identification is based on measuring fluorescence brightness from single molecules. In another, molecules are classified by determining their electrophoretic velocities.

  15. Oligomer Molecules for Efficient Organic Photovoltaics.

    PubMed

    Lin, Yuze; Zhan, Xiaowei

    2016-02-16

    Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability

  16. Contacting organic molecules by soft methods: towards molecule-based electronic devices.

    PubMed

    Haick, Hossam; Cahen, David

    2008-03-01

    Can we put organic molecules to use as electronic components? The answer to this question is to no small degree limited by the ability to contact them electrically without damaging the molecules. In this Account, we present some of the methods for contacting molecules that do not or minimally damage them and that allow formation of electronic junctions that can become compatible with electronics from the submicrometer to the macroscale. In "Linnaean" fashion, we have grouped contacting methods according to the following main criteria: (a) is a chemical bond is required between contact and molecule, and (b) is the contact "ready-made", that is, preformed, or prepared in situ? Contacting methods that, so far, seem to require a chemical bond include spin-coating a conductive polymer and transfer printing. In the latter, a metallic pattern on an elastomeric polymer is mechanically transferred to molecules with an exposed terminal group that can react chemically with the metal. These methods allow one to define structures from several tens of nanometers size upwards and to fabricate devices on flexible substrates, which is very difficult by conventional techniques. However, the requirement for bifunctionality severely restricts the type of molecules that can be used and can complicate their self-assembly into monolayers. Methods that rely on prior formation of the contact pad are represented by two approaches: (a) use of a liquid metal as electrode (e.g., Hg, Ga, various alloys), where molecules can be adsorbed on the liquid metal and the molecularly modified drop is brought into contact with the second electrode, the molecules can be adsorbed on the second electrode and then the liquid metal brought into contact with them, or bilayers are used, with a layer on both the metal and the second electrode and (b) use of preformed metal pads from a solid substrate and subsequent pad deposition on the molecules with the help of a liquid. These methods allow formation of

  17. Observation of ultralong range Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Shaffer, James

    2009-05-01

    In 1934, Enrico Fermi described the scattering of a low energy electron from a neutral atom by using the ideas of scattering length and pseudopotential. Although the long range potential for an electron-atom interaction is always attractive, Fermi realized that the s-wave scattering length that characterizes the low energy collision can be either positive or negative. For a positive scattering length, the wavefunction of the electron is shifted away from the atom, the electron is repelled; whereas for a negative scattering length, the wavefunction of the electron is shifted to the atom, the electron is attracted. Based on Fermi's approach, Greene and co-workers predicted a novel molecular binding mechanism where a low energy Rydberg electron is scattered from a ground state atom in the case of negative scattering length. In this situation, the interaction between the electron and ground state atom is attractive and results in the formation of bound states of the ground state atom and the Rydberg atom. Molecules bound by electron scattering can have an internuclear separation of several thousand Bohr radii and are very different from molecules formed by 2 Rydberg atoms where the binding is the result of multipolar forces between the atoms alone. In this talk, we present experimental data on the observation of these exotic molecular states for Rb Rydberg atoms in S states for principal quantum numbers n between 34 and 40. The spectroscopic results for the vibrational ground and first excited state of the dimer Rb(5S)-Rb(nS) are presented and the s-wave scattering length for electron-Rb(5S) scattering in the low energy regime where the kinetic energy is less than 100 meV. Finally, we discuss and present data on the lifetimes and decay mechanisms of these molecules in a magnetic trap.

  18. Effect of lysosomotropic molecules on cellular homeostasis.

    PubMed

    Kuzu, Omer F; Toprak, Mesut; Noory, M Anwar; Robertson, Gavin P

    2017-03-01

    Weak bases that readily penetrate through the lipid bilayer and accumulate inside the acidic organelles are known as lysosomotropic molecules. Many lysosomotropic compounds exhibit therapeutic activity and are commonly used as antidepressant, antipsychotic, antihistamine, or antimalarial agents. Interestingly, studies also have shown increased sensitivity of cancer cells to certain lysosomotropic agents and suggested their mechanism of action as a promising approach for selective destruction of cancer cells. However, their chemotherapeutic utility may be limited due to various side effects. Hence, understanding the homeostatic alterations mediated by lysosomotropic compounds has significant importance for revealing their true therapeutic potential as well as toxicity. In this review, after briefly introducing the concept of lysosomotropism and classifying the lysosomotropic compounds into two major groups according to their cytotoxicity on cancer cells, we focused on the subcellular alterations mediated by class-II lysosomotropic compounds. Briefly, their effect on intracellular cholesterol homeostasis, autophagy and lysosomal sphingolipid metabolism was discussed. Accordingly, class-II lysosomotropic molecules inhibit intracellular cholesterol transport, leading to the accumulation of cholesterol inside the late endosomal-lysosomal cell compartments. However, the accumulated lysosomal cholesterol is invisible to the cellular homeostatic circuits, hence class-II lysosomotropic molecules also upregulate cholesterol synthesis pathway as a downstream event. Considering the fact that Niemann-Pick disease, a lysosomal cholesterol storage disorder, also triggers similar pathologic abnormalities, this review combines the knowledge obtained from the Niemann-Pick studies and lysosomotropic compounds. Taken together, this review is aimed at allowing readers a better understanding of subcellular alterations mediated by lysosomotropic drugs, as well as their potential

  19. Single-molecule visualization of ROS-induced DNA damage in large DNA molecules.

    PubMed

    Lee, Jinyong; Kim, Yongkyun; Lim, Sangyong; Jo, Kyubong

    2016-02-07

    We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent labeling on damaged lesions via nick translation. This single molecule analytical platform provided the capability to count one or two damaged sites per λ DNA molecule (48.5 kb), which were reliably dependent on the concentrations of hydrogen peroxide and ferrous ion at the micromolar level. More importantly, the labeled damaged sites that were visualized under a microscope provided positional information, which offered the capability of comparing DNA damaged sites with the in silico genomic map to reveal sequence specificity that GTGR is more sensitive to oxidative damage. Consequently, single DNA molecule analysis provides a sensitive analytical platform for ROS-induced DNA damage and suggests an interesting biochemical insight that the genome primarily active during the lysogenic cycle may have less probability for oxidative DNA damage.

  20. Single-Molecule Enzymatic Conformational Dynamics: Spilling Out the Product Molecules

    PubMed Central

    2015-01-01

    Product releasing is an essential step of an enzymatic reaction, and a mechanistic understanding primarily depends on the active-site conformational changes and molecular interactions that are involved in this step of the enzymatic reaction. Here we report our work on the enzymatic product releasing dynamics and mechanism of an enzyme, horseradish peroxidase (HRP), using combined single-molecule time-resolved fluorescence intensity, anisotropy, and lifetime measurements. Our results have shown a wide distribution of the multiple conformational states involved in active-site interacting with the product molecules during the product releasing. We have identified that there is a significant pathway in which the product molecules are spilled out from the enzymatic active site, driven by a squeezing effect from a tight active-site conformational state, although the conventional pathway of releasing a product molecule from an open active-site conformational state is still a primary pathway. Our study provides new insight into the enzymatic reaction dynamics and mechanism, and the information is uniquely obtainable from our combined time-resolved single-molecule spectroscopic measurements and analyses. PMID:25025461

  1. Photoisomerization Dyanamics of the Sunscreen Molecule Avobenzone

    NASA Astrophysics Data System (ADS)

    Dunkelberger, Adam D.; Kieda, Ryan D.; Crim, F. Fleming

    2013-06-01

    We report the photoisomerization dynamics of the widely utilized sunscreen molecule avobenzone after near UV excitation at 350 nm. Probing with 266 nm light was utilized to elucidate isomerization dynamics producing what appears to be a twisted form of the initial enol state. Probing with broadband continuum light from 350-600 nm provides a picture of the ground state bleach, excited state dynamics, and subsequent relaxation on the ground state. The combination of these probing techniques provides a comprehensive view of the ultrafast dynamics initiated by absorption at 350 nm.

  2. Molecular-beam spectroscopy of interhalogen molecules

    SciTech Connect

    Sherrow, S.A.

    1983-08-01

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of /sup 79/Br/sup 35/Cl. Analyses of these spectra and of microwave spectra published by other authors have yielded new values for the electric dipole moment and for the nuclear quadrupole coupling constants in this molecule. The new constants are significantly different from the currently accepted values. Van der Waals clusters containing chlorine monofluoride have been studied under various expansion conditions by the molecular-beam electric-deflection method. The structural possibilities indicated by the results are discussed, and cluster geometries are proposed.

  3. Kondo Tunneling through Real and Artificial Molecules

    NASA Astrophysics Data System (ADS)

    Kikoin, Konstantin; Avishai, Yshai

    2001-03-01

    When an asymmetric double dot is hybridized with itinerant electrons, its singlet ground state and lowly excited triplet state cross, leading to a competition between the Zhang-Rice mechanism of singlet-triplet splitting in a confined cluster and the Kondo effect (which accompanies the tunneling through quantum dot under a Coulomb blockade restriction). The rich physics of an underscreened S = 1 Kondo impurity in the presence of low-lying triplet-singlet excitations is exposed and estimates of the magnetic susceptibility and the electric conductance are presented, together with applications for molecule chemisorption on metallic substrates.

  4. Configurations of the amphiphilic molecules in micelles

    SciTech Connect

    Dill, K.A.

    1982-04-29

    Several theoretic models aim to account for the properties of micelles in terms of the configurations of the constituent amphiphilic chain molecules. Recent /sup 13/C NMR measurement of one property of the configuration distribution of the the hydrocarbon chain segments allows critical evaluation of these theories. It is concluded that the interphase and singly-bent chain theories, which fully account for chain continuity and for intermolecular constraints imposed by hydrophobic and steric forces, give a more satisfactory description of micellar molecular organization than models in which chains are ordered and radially aligned, or in which they have the complete disorder characteristic of an amorphous hydrocarbon liquid.

  5. New Band Systems of the YBr Molecule

    PubMed

    Gopal

    1997-11-01

    The thermal emission spectrum of the YBr molecule has been photographed in the region 4130-4750 A at a temperature about 2300degreesC using Saha's vacuum furnace at a dispersion of 3.5 A/mm on the C. Z. Ebert plane grating spectrograph. A total of 123 red-degraded bands have been recorded and assigned to two new systems, namely F-X and G-X, and one previously reported system, viz. E-X. The vibrational constants have been evaluated for these systems. Copyright 1997 Academic Press. Copyright 1997Academic Press

  6. Carrier molecules for use in veterinary vaccines.

    PubMed

    Gerdts, Volker; Mutwiri, George; Richards, James; van Drunen Littel-van den Hurk, Sylvia; Potter, Andrew A

    2013-01-11

    The practice of immunization of animals and humans has been carried out for centuries and is generally accepted as the most cost effective and sustainable method of infectious disease control. Over the past 20 years there have been significant changes in our ability to produce antigens by conventional extraction and purification, recombinant DNA and synthesis. However, many of these products need to be combined with carrier molecules to generate optimal immune responses. This review covers selected topics in the development of carrier technologies for use in the veterinary vaccine field, including glycoconjugate and peptide vaccines, microparticle and nanoparticle formulations, and finally virus-like particles.

  7. Reactive collisions of atoms with diatomic molecules

    NASA Astrophysics Data System (ADS)

    Wolniewicz, L.; Hinze, Juergen; Alijah, Alexander

    1993-08-01

    The theory of the reactive collision of an atom with a diatomic molecule is formulated in 'democratic' hyperspherical coordinates. An adiabatic ansatz is used to separate the distance coordinate from the angular coordinates. The angular eigenvalue problem is solved, using the hyperspherical harmonics as basis functions, while the R-matrix propagation method is used to integrate the resulting coupled equations along the distance coordinate. As an example, reactive collision probabilities for H + H2 are computed, using the Porter-Karplus surface. The symmetry requirements, when dealing with three identical Fermions in the collision, are considered explicitly.

  8. Long-range interactions between chiral molecules

    SciTech Connect

    Salam, A.

    2015-01-22

    Results of molecular quantum electrodynamics calculations of discriminatory interactions between two chiral molecules undergoing resonance energy transfer, van der Waals dispersion, and optical binding are presented. A characteristic feature of the theory is that the radiation field is quantized with signals consequently propagating between centres at the speed of light. In order to correctly describe optically active chromophores, it is necessary to include magnetic as well as electric dipole coupling terms in the time-dependent perturbation theory computations. Recent work investigating the effect of an absorptive and dispersive chiral medium on the rate of migration of energy will also be discussed.

  9. Indirect observation of unobservable interstellar molecules

    NASA Technical Reports Server (NTRS)

    Herbst, E.; Green, S.; Thaddeus, P.; Klemperer, W.

    1977-01-01

    It is suggested that the abundances of neutral non-polar interstellar molecules unobservable by radio astronomy can be systematically determined by radio observation of the protonated ions. As an example, observed N2H(+) column densities are analyzed to infer molecular nitrogen abundances in dense interstellar clouds. The chemistries and expected densities of the protonated ions of O2, C2, CO2, C2H2 and CH4 are then discussed. Microwave transition frequencies fo HCO2(+) and C2H3(+) are estimated, and a preliminary astronomical search for HCO2(+) is described.

  10. Nonrelativistic Lamb shift for muonic molecules

    NASA Astrophysics Data System (ADS)

    Bukowski, Robert; Jeziorski, Bogumil

    1993-03-01

    A recently developed formula [R. Bukowski and B. Jeziorski, Phys. Rev. A46 (1992) 5437]. has been applied to estimate the soft-photon Lamb shift contribution to the energies of the muonic molecules ppμ, ddμ, ttμ, pdμ, ptμ and dtμ. The corresponding corrections to the dissociation energies for the excited P states of ddμ and dtμ have been found to be almost identical and equal to 0.048 meV. The magnitude of this stabilizing effect is too small to affect seriously the formation rates predictions.

  11. Non-equilibrium processes in interstellar molecules

    NASA Technical Reports Server (NTRS)

    Strelnitskiy, V. S.

    1979-01-01

    The types of nonequilibrium emission and absorption by interstellar molecules are summarized. The observed brightness emission temperatures of compact OH and H2O sources are discussed using the concept of maser amplification. A single thermodynamic approach was used in which masers and anti-masers are considered as heat engines for the theoretical interpretation of the cosmic maser and anti-maser phenomena. The requirements for different models of pumping are formulated and a classification is suggested for the mechanisms of pumping, according to the source and discharge of energy.

  12. Identification of cell density signal molecule

    DOEpatents

    Schwarz, R.I.

    1998-04-21

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS) between 25 and 35 kD, which is secreted by fibroblastic primary avian tendon cells in culture, and causes the cells to self-regulate their proliferation and the expression of differentiated function. It effects an increase of procollagen production in avian tendon cell cultures of ten fold while proliferation rates are decreased. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use. 2 figs.

  13. Identification of cell density signal molecule

    DOEpatents

    Schwarz, Richard I.

    1998-01-01

    Disclosed herein is a novel proteinaceous cell density signal molecule (CDS) between 25 and 35 kD, which is secreted by fibroblastic primary avian tendon cells in culture, and causes the cells to self-regulate their proliferation and the expression of differentiated function. It effects an increase of procollagen production in avian tendon cell cultures of ten fold while proliferation rates are decreased. CDS, and the antibodies which recognize them, are important for the development of diagnostics and treatments for injuries and diseases involving connective tissues, particularly tendon. Also disclosed are methods of production and use.

  14. Kondo tunneling through real and artificial molecules.

    PubMed

    Kikoin, K; Avishai, Y

    2001-03-05

    When an asymmetric double dot is hybridized with itinerant electrons, its singlet ground state and lowly excited triplet state cross, leading to a competition between the Zhang-Rice mechanism of singlet-triplet splitting in a confined cluster and the Kondo effect (which accompanies the tunneling through quantum dot under a Coulomb blockade restriction). The rich physics of an underscreened S = 1 Kondo impurity in the presence of low-lying triplet-singlet excitations is exposed and estimates of the magnetic susceptibility and the electric conductance are presented, together with applications for molecule chemisorption on metallic substrates.

  15. EDITORIAL: Focus on Cold and Ultracold Molecules FOCUS ON COLD AND ULTRACOLD MOLECULES

    NASA Astrophysics Data System (ADS)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    Cold and ultracold molecules are the next wave of ultracold physics, giving rise to an exciting array of scientific opportunities, including many body physics for novel quantum phase transitions, new states of matter, and quantum information processing. Precision tests of fundamental physical laws benefit from the existence of molecular internal structure with exquisite control. The study of novel collision and reaction dynamics will open a new chapter of quantum chemistry. Cold molecules bring together researchers from a variety of fields, including atomic, molecular, and optical physics, chemistry and chemical physics, quantum information science and quantum simulations, condensed matter physics, nuclear physics, and astrophysics, a truly remarkable synergy of scientific explorations. For the past decade there have been steady advances in direct cooling techniques, from buffer-gas cooling to cold molecular beams to electro- and magneto-molecular decelerators. These techniques have allowed a large variety of molecules to be cooled for pioneering studies. Recent amazing advances in experimental techniques combining the ultracold and the ultraprecise have furthermore brought molecules to the point of quantum degeneracy. These latter indirect cooling techniques magnetically associate atoms from a Bose-Einstein condensate and/or a quantum degenerate Fermi gas, transferring at 90% efficiency highly excited Fano-Feshbach molecules, which are on the order of 10 000 Bohr radii in size, to absolute ground state molecules just a few Bohr across. It was this latter advance, together with significant breakthroughs in internal state manipulations, which inspired us to coordinate this focus issue now, and is the reason why we say the next wave of ultracold physics has now arrived. Whether directly or indirectly cooled, heteronuclear polar molecules offer distinct new features in comparison to cold atoms, while sharing all of their advantages (purity, high coherence

  16. Investigation of picosecond blue laser emission from chlorophyll molecules

    SciTech Connect

    Liu Yixian; Wang Yagang; Zhu Wei; Li Fuming; Yang Shanyuan; Zhou Peilin

    1988-03-01

    Results on picosecond blue laser emission from a chlorophyll (chl) dye laser with an ultrashort cavity are reported. The laser mechanism involves intermolecular energy transfer from excited coumarin (co) molecules to chlorophyll a and b pigment molecules.

  17. Nanodevices for generating power from molecules and batteryless sensing

    DOEpatents

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

    2014-07-15

    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.

  18. Nanodevices for generating power from molecules and batteryless sensing

    DOEpatents

    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.

  19. Nanodevices for generating power from molecules and batteryless sensing

    DOEpatents

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

    2015-06-09

    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.

  20. Nanoconstructions Based on Spatially Ordered Nucleic Acid Molecules

    NASA Astrophysics Data System (ADS)

    Yevdokimov, Yu. M.

    Different strategies for the design of nanoconstructions whose building blocks are both linear molecules of double-stranded nucleic acids and nucleic acid molecules fixed in the spatial structure of particles of liquid-crystalline dispersions are described.

  1. A Simplified Quantum Mechanical Model of Diatomic Molecules

    ERIC Educational Resources Information Center

    Nielsen, Lars Drud

    1978-01-01

    Introduces a simple one-dimensional model of a diatomic molecule that can explain all the essential features of a real two particle quantum mechanical system and gives quantitative results in fair agreement with those of a hydrogen molecule. (GA)

  2. Roles of water molecules in trapping carbon dioxide molecules inside the interlayer space of graphene oxides.

    PubMed

    Yumura, Takashi; Yamasaki, Ayumi

    2014-05-28

    Density functional theory (DFT) calculations were employed to investigate the energetics of carbon dioxide migration within hydrated or anhydrous graphene oxides (GOs). When anhydrous GO structures contain a carbon dioxide molecule, the carbon dioxide interacts repulsively with the GO layers to increase the interlayer spacing. The repulsive electrostatic interactions are reduced by the insertion of water molecules into CO2-containing GO structures due to the occurrence of attractive water-layer interactions through hydrogen bonding. Consequently, the interlayer spacings in CO2-containing hydrated structures are shortened compared with those in the anhydrous structures. The results indicate that the intercalated water molecules have the ability to connect the GO layers in the presence of carbon dioxide. Furthermore, the DFT calculations indicated that the GO interlayer spacings, which are influenced by the intercalation of water molecules, control carbon dioxide migration within the GO layers. The importance of the interlayer spacings on the migration of carbon dioxide arises from the occurrence of repulsive interactions between CO2 and oxygen-containing groups attached on the graphene sheets. When the GO interlayer spacings are short due to the presence of intercalated water molecules, the repulsive interactions between carbon dioxide and the GO layers are strong enough to prevent CO2 from migrating from its original position. Such repulsive interactions do not occur during the migration of CO2 within anhydrous GO structures because of the relatively longer interlayer spacing. Accordingly, CO2 migrates within anhydrous GO with a less significant barrier, indicating that carbon dioxide molecules are easily released from the GO.

  3. Resonances in Positron-molecule Interactions

    NASA Astrophysics Data System (ADS)

    Surko, C. M.

    2006-05-01

    The development of cold, trap-based beams has enabled high-resolution, energy-resolved studies of positron scattering and annihilation processes [1]. This talk focuses on three topics in this area. For hydrocarbon molecules such as alkanes (CnH2n+2), giant enhancements in annihilation rates are observed due to vibrational Feshbach resonances. The dependence of the rates on positron energy provides evidence that positrons bind to these molecules and a measure of the binding energies [1]. Recent results include evidence for a second, ``positronically excited'' bound state and new data for the methane series, CH3X, where X is a halogen. Other ``resonance-like features'' are sharp increases in the near-threshold electronic excitation cross sections for CO and N2 [2], and in the vibrational excitation cross sections for CO, CO2 and CH4 [3, 4]. Outstanding questions and the relationship of these observations to available theoretical predictions will be discussed.1. C. M. Surko, G. F. Gribakin, and S. J. Buckman, J. Phys. B 38, R57 (2005).2. J. P. Marler and C. M. Surko, Phys. Rev. A 72, 062713 (2005).3. J. P. Marler and C. M. Surko, Phys. Rev. A 72, 062702 (2005).4. J. P. Marler, G. F. Gribakin and C. M. Surko, Nuclear Instrum. and Meth. B, in press (2006).

  4. Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions

    PubMed Central

    Ruiz, Lorena; Delgado, Susana; Ruas-Madiedo, Patricia; Margolles, Abelardo; Sánchez, Borja

    2016-01-01

    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. PMID:27536282

  5. Single molecule and single cell epigenomics.

    PubMed

    Hyun, Byung-Ryool; McElwee, John L; Soloway, Paul D

    2015-01-15

    Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications. Though very powerful, these methods are not without limitations. Notably, they are best at characterizing one chromatin feature at a time, yet chromatin features arise and function in combination. Investigators commonly superimpose separate ChIP-seq or BS-seq datasets, and then infer where chromatin features are found together. While these inferences might be correct, they can be misleading when the chromatin source has distinct cell types, or when a given cell type exhibits any cell to cell variation in chromatin state. These ambiguities can be eliminated by robust methods that directly characterize the existence and genomic locations of combinations of chromatin features in very small inputs of cells or ideally, single cells. Here we review single molecule epigenomic methods under development to overcome these limitations, the technical challenges associated with single molecule methods and their potential application to single cells.

  6. Small Molecule Docking from Theoretical Structural Models

    NASA Astrophysics Data System (ADS)

    Novoa, Eva Maria; de Pouplana, Lluis Ribas; Orozco, Modesto

    Structural approaches to rational drug design rely on the basic assumption that pharmacological activity requires, as necessary but not sufficient condition, the binding of a drug to one or several cellular targets, proteins in most cases. The traditional paradigm assumes that drugs that interact only with a single cellular target are specific and accordingly have little secondary effects, while promiscuous molecules are more likely to generate undesirable side effects. However, current examples indicate that often efficient drugs are able to interact with several biological targets [1] and in fact some dirty drugs, such as chlorpromazine, dextromethorphan, and ibogaine exhibit desired pharmacological properties [2]. These considerations highlight the tremendous difficulty of designing small molecules that both have satisfactory ADME properties and the ability of interacting with a limited set of target proteins with a high affinity, avoiding at the same time undesirable interactions with other proteins. In this complex and challenging scenario, computer simulations emerge as the basic tool to guide medicinal chemists during the drug discovery process.

  7. Half collision resonance phenomena in molecules

    SciTech Connect

    Maximo Garcia-Sucre ); Raseev, G. ); Ross, S.C. )

    1991-01-01

    The Escuela Latinoamericana de Fisica (ELAF) is a series of meeting s that for 28 years has played an important role in research-level teaching of physics in Latin America. This book contains the proceedings of ELAF 90 which was held at the Instituto Venezolano de Investigaciones Cientificas (IVIC) in Caracas, Venezuela from July 23 to August 3, 1990, as part of the commemoration of the 30th anniversary of IVIC. In contrast to previous ELAF's that were of general scope, ELAF 90 centered on a particular subject matter: Half Collisional Resonance Phenomena in Molecules, Experimental and Theoretical Approaches. The term Half Collision'' refers to the fragmentation of a molecular system following is excitation by light. The lack of an incident fragmentation of a molecular system following is excitation by light. The lack of an incident particle (other than the photon) in the fragmentation process is what leads to the term. The purpose of this volume is to present current results in the experimental and theoretical study of half collisions and also to include pedagogical papers at an introductory or intermediate level. The contributions are grouped into several sections; light sources; ionization; dissociation-experimental; dissociation-theory; competition between ionization and dissociation; and particle-molecule collisions.

  8. Floppy Molecules with Internal Rotation and Inversion

    NASA Astrophysics Data System (ADS)

    Kreglewski, Marek

    2016-06-01

    There are different ways to analyze rovibrational structure of molecules having several large amplitude motions of different type, like internal rotation and inversion or ring-puckering. In my research group we have developed and used methods starting from potential surfaces for large amplitude motions but also applied purely effective Hamiltonians, where tunneling splittings were key parameters. Whatever is the method the following problems must be solved when addressing a rovibrational problem with large amplitude vibrations: 1) a definition of the permutation-inversion molecular symmetry group, 2) a choice of the internal coordinates and their transformation in the symmetry group, 3) derivation of the Hamiltonian in chosen coordinates, 4) calculation of the Hamiltonian matrix elements in a symmetrized basis set. These points will be discussed. The advantage of methods which start from the geometry and potential surface for large amplitude vibrations give much clearer picture of internal dynamics of molecules but generally the fit to experimental data is much poorer. The fitting procedure is strongly non-linear and the iteration procedure much longer. The effective Hamiltonians the fit is generally much better since almost all optimized parameters are linear but the parameters have no clear physical meaning. This method is very useful in the assignment of experimental spectra. Results of the application of both method to methylamine and hydrazine will be presented.

  9. Entanglement of polar molecules in pendular states

    NASA Astrophysics Data System (ADS)

    Wei, Qi; Kais, Sabre; Friedrich, Bretislav; Herschbach, Dudley

    2011-03-01

    In proposals for quantum computers using arrays of trapped ultracold polar molecules as qubits, a strong external field with appreciable gradient is imposed in order to prevent quenching of the dipole moments by rotation and to distinguish among the qubit sites. That field induces the molecular dipoles to undergo pendular oscillations, which markedly affect the qubit states and the dipole-dipole interaction. We evaluate entanglement of the pendular qubit states for two linear dipoles, characterized by pairwise concurrence, as a function of the molecular dipole moment and rotational constant, strengths of the external field and the dipole-dipole coupling, and ambient temperature. We also evaluate a key frequency shift, △ω, produced by the dipole-dipole interaction. Under conditions envisioned for the proposed quantum computers, both the concurrence and △ω become very small for the ground eigenstate. In principle, such weak entanglement can be sufficient for operation of logic gates, provided the resolution is high enough to detect the △ω shift unambiguously. In practice, however, for many candidate polar molecules it appears a challenging task to attain adequate resolution. Simple approximate formulas fitted to our numerical results are provided from which the concurrence and △ω shift can be obtained in terms of unitless reduced variables.

  10. Single molecule force spectroscopy of asphaltene aggregates.

    PubMed

    Long, Jun; Xu, Zhenghe; Masliyah, Jacob H

    2007-05-22

    Asphaltene aggregation and deposition cause severe problems in nearly all phases of petroleum processing. To resolve those problems, understanding the aggregation mechanisms is a prerequisite and has attracted the interest of a great number of investigators. However, to date, the nature and extent of asphaltene aggregation remain widely debated. In the present study, we attempt to investigate asphaltene aggregation from a completely new perspective. The technique of single molecule force spectroscopy (SMFS) was used to investigate the response of single asphaltene aggregates under an external pulling force. Force curves representing the stretching of single asphaltene aggregates were obtained in simple electrolyte solutions (KCl and calcium) and organic solvents (toluene and heptane). These force curves were well-fitted by the modified worm-like chain model, indicating that those asphaltene aggregates acted like long-chain polymers under pulling by an external force. It was found that lower solution pH values and the presence of divalent cations resulted in a lower bending rigidity of the formed aggregates. The information retrieved from the force curves suggests that asphaltene molecules with a structure featuring small aromatic clusters connected by aliphatic chains do exist and that asphaltene aggregation could occur through a linear polymerization mechanism. The current study extends the application scope of SMFS.

  11. Size selective hydrophobic adsorbent for organic molecules

    NASA Technical Reports Server (NTRS)

    Sharma, Pramod K. (Inventor); Hickey, Gregory S. (Inventor)

    1997-01-01

    The present invention relates to an adsorbent formed by the pyrolysis of a hydrophobic silica with a pore size greater than 5 .ANG., such as SILICALITE.TM., with a molecular sieving polymer precursor such as polyfurfuryl alcohol, polyacrylonitrile, polyvinylidene chloride, phenol-formaldehyde resin, polyvinylidene difluoride and mixtures thereof. Polyfurfuryl alcohol is the most preferred. The adsorbent produced by the pyrolysis has a silicon to carbon mole ratio of between about 10:1 and 1:3, and preferably about 2:1 to 1:2, most preferably 1:1. The pyrolysis is performed as a ramped temperature program between about 100.degree. and 800.degree. C., and preferably between about 100.degree. and 600.degree. C. The present invention also relates to a method for selectively adsorbing organic molecules having a molecular size (mean molecular diameter) of between about 3 and 6 .ANG. comprising contacting a vapor containing the small organic molecules to be adsorbed with the adsorbent composition of the present invention.

  12. The Bichromatic Force on Small Molecules

    NASA Astrophysics Data System (ADS)

    Aldridge, Leland M.; Galica, Scott E.; Sheets, Donal; Eyler, Edward E.

    2016-06-01

    The bichromatic force is a coherent optical force that has been demonstrated to exceed the saturated radiative force from a monochromatic cw laser by orders of magnitude in atomic systems. By stimulating photon emission between two states, the bichromatic force allows us to increase the photon scattering rate beyond the spontaneous emission rate while also suppressing decays into dark states. We present studies of the efficacy of the bichromatic force on molecular systems using the test cases of B-X (0,0), P11(1.5)/^PQ12(0.5) in CaF and tilde{A}(000)-tilde{X}(000), P11(1.5)/^PQ12(0.5) in the linear triatomic molecule SrOH. Computational results from detailed multilevel models indicate that both of these molecular systems are suitable for the use of the bichromatic force, with neither repumping nor magnetic destabilization of dark states interrupting the coherent cycling at the heart of the force. We comment on the applicability of the bichromatic force to arbitrary polyatomic molecules, and present our experimental progress in demonstrating the bichromatic force on CaF and possibly on SrOH. Supported by the National Science Foundation.

  13. Small molecule phagocytosis inhibitors for immune cytopenias.

    PubMed

    Neschadim, Anton; Kotra, Lakshmi P; Branch, Donald R

    2016-08-01

    Immune cytopenias are conditions characterized by low blood cell counts, such as platelets in immune thrombocytopenia (ITP) and red blood cells in autoimmune hemolytic anemia (AIHA). Chronic ITP affects approximately 4 in 100,000 adults annually while AIHA is much less common. Extravascular phagocytosis and massive destruction of autoantibody-opsonized blood cells by macrophages in the spleen and liver are the hallmark of these conditions. Current treatment modalities for ITP and AIHA include the first-line use of corticosteroids; whereas, IVIg shows efficacy in ITP but not AIHA. One main mechanism of action by which IVIg treatment leads to the reduction in platelet destruction rates in ITP is thought to involve Fcγ receptor (FcγR) blockade, ultimately leading to the inhibition of extravascular platelet phagocytosis. IVIg, which is manufactured from the human plasma of thousands of donors, is a limited resource, and alternative treatments, particularly those based on bioavailable small molecules, are needed. In this review, we overview the pathophysiology of ITP, the role of Fcγ receptors, and the mechanisms of action of IVIg in treating ITP, and outline the efforts and progress towards developing novel, first-in-class inhibitors of phagocytosis as synthetic, small molecule substitutes for IVIg in ITP and other conditions where the pathobiology of the disease involves phagocytosis.

  14. Singlet fission in linear chains of molecules

    SciTech Connect

    Ambrosio, Francesco E-mail: A.Troisi@warwick.ac.uk; Troisi, Alessandro E-mail: A.Troisi@warwick.ac.uk

    2014-11-28

    We develop a model configuration interaction Hamiltonian to study the electronic structure of a chain of molecules undergoing singlet fission. We first consider models for dimer and trimer and then we use a matrix partitioning technique to build models of arbitrary size able to describe the relevant electronic structure for singlet fission in linear aggregates. We find that the multi-excitonic state (ME) is stabilized at short inter-monomer distance and the extent of this stabilization depends upon the size of orbital coupling between neighboring monomers. We also find that the coupling between ME states located on different molecules is extremely small leading to bandwidths in the order of ∼10 meV. This observation suggests that multi-exciton states are extremely localized by electron-phonon coupling and that singlet fission involves the transition between a relatively delocalized Frenkel exciton and a strongly localized multi-exciton state. We adopt the methodology commonly used to study non-radiative transitions to describe the singlet fission dynamics in these aggregates and we discuss the limit of validity of the approach. The results indicate that the phenomenology of singlet fission in molecular crystals is different in many important ways from what is observed in isolated dimers.

  15. Triton - Stratospheric molecules and organic sediments

    NASA Technical Reports Server (NTRS)

    Thompson, W. Reid; Singh, Sushil K.; Khare, B. N.; Sagan, Carl

    1989-01-01

    Continuous-flow plasma discharge techniques show production rates of hydrocarbons and nitriles in N2 + CH4 atmospheres appropriate to the stratosphere of Titan, and indicate that a simple eddy diffusion model together with the observed electron flux quantitatively matches the Voyager IRIS observations for all the hydrocarbons, except for the simplest ones. Charged particle chemistry is very important in Triton's stratosphere. In the more CH4-rich case of Titan, many hydrocarbons and nitriles are produced in high yield. If N2 is present, the CH4 fraction is low, but hydrocarbons and nitriles are produced in fair yield, abundances of HCN and C2H2 in Triton's stratosphere exceed 10 to the 19th molecules/sq cm per sec, and NCCN, C3H4, and other species are predicted to be present. These molecules may be detected by IRIS if the stratosphere is as warm as expected. Both organic haze and condensed gases will provide a substantial UV and visible opacity in Triton's atmosphere.

  16. Electron Impact Fragmentation of CH4 Molecules

    NASA Astrophysics Data System (ADS)

    Suzuki, Ryoji; Oguri, Kazuhiro; Makochekanwa, Casten; Kitajima, Masashi; Tanaka, Hiroshi

    2004-09-01

    Absolute electron-molecule impact dissociation cross sections are of interest in many fields of physics and chemistry, plasma etching of microelectronic devices and other industrial applications. However, experimental data on these cross sections is scarce mainly because of the difficulties involved in measuring neutral fragments [1]. Electron impact dissociation of CH4 molecules into the CH3 radicals have been investigated over the energy range 15.0 to 37.0 eV. The experimental procedure involves a dual-electron-beam in a two-stage collision system in conjunction with a quadrupole mass spectrometer (QMS). This is similar to the threshold-ionization mass spectrometry method [2]. Significant differences, in magnitude up to four times at 100 eV, exist between the only available absolute measurements by Sugai et al. [2] and Moore et al. [3]. Our data shows very close agreement with the Moore et al. data, which which show reasonable consistency with the available CH4 total dissociation data by Winters [3]. [1] L. S. Polak and D. I. Slovetsky, Int. J. Rad. Phys. Chem. 8, 257 (1976). [2] H. Sugai, H. Toyoda and T. Nakano, Jpn. J. Appl. Phys. 30, 2912 (1991). [3] H. F. Winters, J. Chem. Phys. 63, 3462 (1975).

  17. Electroluminescence from completely horizontally oriented dye molecules

    NASA Astrophysics Data System (ADS)

    Komino, Takeshi; Sagara, Yuta; Tanaka, Hiroyuki; Oki, Yuji; Nakamura, Nozomi; Fujimoto, Hiroshi; Adachi, Chihaya

    2016-06-01

    A complete horizontal molecular orientation of a linear-shaped thermally activated delayed fluorescent guest emitter 2,6-bis(4-(10Hphenoxazin-10-yl)phenyl)benzo[1,2-d:5,4-d'] bis(oxazole) (cis-BOX2) was obtained in a glassy host matrix by vapor deposition. The orientational order of cis-BOX2 depended on the combination of deposition temperature and the type of host matrix. Complete horizontal orientation was obtained when a thin film with cis-BOX2 doped in a 4,4'-bis(N-carbazolyl)-1,1'-biphenyl (CBP) host matrix was fabricated at 200 K. The ultimate orientation of guest molecules originates from not only the kinetic relaxation but also the kinetic stability of the deposited guest molecules on the film surface during film growth. Utilizing the ultimate orientation, a highly efficient organic light-emitting diode with the external quantum efficiency of 33.4 ± 2.0% was realized. The thermal stability of the horizontal orientation of cis-BOX2 was governed by the glass transition temperature (Tg) of the CBP host matrix; the horizontal orientation was stable unless the film was annealed above Tg.

  18. Spin-crossover molecule based thermoelectric junction

    SciTech Connect

    Ghosh, Dibyajyoti; Parida, Prakash; Pati, Swapan K.

    2015-05-11

    Using ab-initio numerical methods, we explore the spin-dependent transport and thermoelectric properties of a spin-crossover molecule (i.e., iron complex of 2-(1H-pyrazol-1-yl)-6-(1H-tetrazole-5-yl)pyridine) based nano-junction. We demonstrate a large magnetoresistance, efficient conductance-switching, and spin-filter activity in this molecule-based two-terminal device. The spin-crossover process also modulates the thermoelectric entities. It can efficiently switch the magnitude as well as spin-polarization of the thermocurrent. We find that thermocurrent is changed by ∼4 orders of magnitude upon spin-crossover. Moreover, it also substantially affects the thermopower and consequently, the device shows extremely efficient spin-crossover magnetothermopower generation. Furthermore, by tuning the chemical potential of electrodes into a certain range, a pure spin-thermopower can be achieved for the high-spin state. Finally, the reasonably large values of figure-of-merit in the presence and absence of phonon demonstrate a large heat-to-voltage conversion efficiency of the device. We believe that our study will pave an alternative way of tuning the transport and thermoelectric properties through the spin-crossover process and can have potential applications in generation of spin-dependent current, information storage, and processing.

  19. Towards ultracold RbCa molecules

    NASA Astrophysics Data System (ADS)

    Kleinert, Michaela

    2011-10-01

    Ultracold heteronuclear molecules have received much attention lately because of their potential applications in high-precision spectroscopy, studies of fundamental symmetries and quantum information processing. So far the focus has been on alkaline/alkaline dimers since their constituent atoms have been studied extensively. Recently, several groups have begun work on more challenging alkaline/alkaline-earth or alkaline/rare-earth combinations. In addition to a permanent electric dipole moment, which makes the alkaline/alkaline dimers such an intriguing system, alkaline/alkaline-earth molecules also possess a permanent magnetic dipole moment, thus allowing the manipulation with electric and magnetic fields. In addition, the molecular ground state of an alkaline/alkaline-earth dimer has a non-vanishing spin. Interesting collision dynamics, for example the suppression of collisions in carefully tailored external fields, have been predicted. At Willamette University, we will trap ultracold gases of rubidium and calcium together to form the molecular dimer RbCa via photoassociation of the constituent atoms. In this talk we will discuss the current state of the experiment and our future plans.[4pt] In collaboration with Hayley Whitson, Garrett Potter, and Kristen Norton, Willamette University.

  20. Subdiffusion in Membrane Permeation of Small Molecules

    PubMed Central

    Chipot, Christophe; Comer, Jeffrey

    2016-01-01

    Within the solubility–diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t0.7, in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids. PMID:27805049

  1. Toroidal nanotraps for cold polar molecules

    DOE PAGES

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, andmore » polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.« less

  2. Metal‐Catalysed Azidation of Organic Molecules

    PubMed Central

    Goswami, Monalisa

    2016-01-01

    The azide moiety is a desirable functionality in organic molecules, useful in a variety of transformations such as olefin aziridination, C–H bond amination, isocyanate synthesis, the Staudinger reaction and the formation of azo compounds. To harness the versatility of the azide functionality fully it is important that these compounds be easy to prepare, in a clean and cost‐effective manner. Conventional (non‐catalysed) methods to synthesise azides generally require quite harsh reaction conditions that are often not tolerant of functional groups. In the last decade, several metal‐catalysed azidations have been developed in attempts to circumvent this problem. These methods are generally faster, cleaner and more functional‐group‐tolerant than conventional methods to prepare azides, and can sometimes even be conveniently combined with one‐pot follow‐up transformations of the installed azide moiety. This review highlights metal‐catalysed approaches to azide synthesis, with a focus on the substrate scopes and mechanisms, as well as on advantages and disadvantages of the methods. Overall, metal‐catalysed azidation reactions provide shorter routes to a variety of potentially useful organic molecules containing the azide moiety. PMID:28344503

  3. Subdiffusion in Membrane Permeation of Small Molecules.

    PubMed

    Chipot, Christophe; Comer, Jeffrey

    2016-11-02

    Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t(0.7), in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.

  4. Injectable controlled release depots for large molecules

    PubMed Central

    Schwendeman, Steven P.; Shah, Ronak B.; Bailey, Brittany A.; Schwendeman, Anna S.

    2014-01-01

    Biodegradable, injectable depot formulations for long-term controlled drug release have improved therapy for a number of drug molecules and led to over a dozen highly successful pharmaceutical products. Until now, success has been limited to several small molecules and peptides, although remarkable improvements have been accomplished in some of these cases. For example, twice-a-year depot injections with leuprolide are available compared to the once-a-day injection of the solution dosage form. Injectable depots are typically prepared by encapsulation of the drug in poly(lactic-co-glycolic acid) (PLGA), a polymer that is used in children every day as a resorbable suture material, and therefore, highly biocompatible. PLGAs remain today as one of the few “real world” biodegradable synthetic biomaterials used in US FDA-approved parenteral long-acting-release (LAR) products. Despite their success, there remain critical barriers to the more widespread use of PLGA LAR products, particularly for delivery of more peptides and other large molecular drugs, namely proteins. In this review, we describe key concepts in the development of injectable PLGA controlled-release depots for peptides and proteins, and then use this information to identify key issues impeding greater widespread use of PLGA depots for this class of drugs. Finally, we examine important approaches, particularly those developed in our research laboratory, toward overcoming these barriers to advance commercial LAR development. PMID:24929039

  5. Transport mirages in single-molecule devices

    NASA Astrophysics Data System (ADS)

    Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

    2017-03-01

    Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

  6. Carbon Monoxide: An Essential Signalling Molecule

    NASA Astrophysics Data System (ADS)

    Mann, Brian E.

    Carbon monoxide (CO), like nitric oxide (NO), is an essential signalling molecule in humans. It is active in the cardiovascular system as a vasodilator. In addition, CO possesses anti-inflammatory, anti-apoptotic and anti-proliferative properties and protects tissues from hypoxia and reperfusion injury. Some of its applications in animal models include suppression of organ graft rejection and safeguarding the heart during reperfusion after cardiopulmonary bypass surgery. CO also suppresses arteriosclerotic lesions following angioplasty, reverses established pulmonary hypertension and mitigates the development of post-operative ileus in the murine small intestine and the development of cerebral malaria in mice as well as graft-induced intimal hyperplasia in pigs. There have been several clinical trials using air-CO mixtures for the treatment of lung-, heart-, kidney- and abdominal-related diseases. This review examines the research involving the development of classes of compounds (with particular emphasis on metal carbonyls) that release CO, which could be used in clinically relevant conditions. The review is drawn not only from published papers in the chemical literature but also from the extensive biological literature and patents on CO-releasing molecules (CO-RMs).

  7. Internal Dynamics of Supercoiled DNA Molecules

    PubMed Central

    Kalkbrenner, Thomas; Arnold, Axel; Tans, Sander J.

    2009-01-01

    Abstract The intramolecular diffusive motion within supercoiled DNA molecules is of central importance for a wide array of gene regulation processes. It has recently been shown, using fluorescence correlation spectroscopy, that plasmid DNA exhibits unexpected acceleration of its internal diffusive motion upon supercoiling to intermediate density. Here, we present an independent study that shows a similar acceleration for fully supercoiled plasmid DNA. We have developed a method that allows fluorescent labeling of a 200-bp region, as well as efficient supercoiling by Escherichia coli gyrase. Compared to plain circular or linear DNA, the submicrosecond motion within the supercoiled molecules appears faster by up to an order of magnitude. The mean-square displacement as a function of time reveals an additional intermediate regime with a lowered scaling exponent compared to that of circular DNA. Although this unexpected behavior is not fully understood, it could be explained by conformational constraints of the DNA strand within the supercoiled topology in combination with an increased apparent persistence length. PMID:19527654

  8. Toroidal nanotraps for cold polar molecules

    SciTech Connect

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-14

    Electronic excitations in metallic nanoparticles in the optical regime that have been of great importance in surface-enhanced spectroscopy and emerging applications of molecular plasmonics, due to control and confinement of electromagnetic energy, may also be of potential to control the motion of nanoparticles and molecules. Here, we propose a concept for trapping polarizable particles and molecules using toroidal metallic nanoparticles. Specifically, gold nanorings are investigated for their scattering properties and field distribution to computationally show that the response of these optically resonant particles to incident photons permit the formation of a nanoscale trap when proper aspect ratio, photon wavelength, and polarization are considered. However, interestingly the resonant plasmonic response of the nanoring is shown to be detrimental to the trap formation. The results are in good agreement with analytic calculations in the quasistatic limit within the first-order perturbation of the scalar electric potential. The possibility of extending the single nanoring trapping properties to two-dimensional arrays of nanorings is suggested by obtaining the field distribution of nanoring dimers and trimers.

  9. Injectable controlled release depots for large molecules.

    PubMed

    Schwendeman, Steven P; Shah, Ronak B; Bailey, Brittany A; Schwendeman, Anna S

    2014-09-28

    Biodegradable, injectable depot formulations for long-term controlled drug release have improved therapy for a number of drug molecules and led to over a dozen highly successful pharmaceutical products. Until now, success has been limited to several small molecules and peptides, although remarkable improvements have been accomplished in some of these cases. For example, twice-a-year depot injections with leuprolide are available compared to the once-a-day injection of the solution dosage form. Injectable depots are typically prepared by encapsulation of the drug in poly(lactic-co-glycolic acid) (PLGA), a polymer that is used in children every day as a resorbable suture material, and therefore, highly biocompatible. PLGAs remain today as one of the few "real world" biodegradable synthetic biomaterials used in US FDA-approved parenteral long-acting-release (LAR) products. Despite their success, there remain critical barriers to the more widespread use of PLGA LARproducts, particularly for delivery of more peptides and other large molecular drugs, namely proteins. In this review, we describe key concepts in the development of injectable PLGA controlled-release depots for peptides and proteins, and then use this information to identify key issues impeding greater widespread use of PLGA depots for this class of drugs. Finally, we examine important approaches, particularly those developed in our research laboratory, toward overcoming these barriers to advance commercial LAR development.

  10. Grafting single molecule magnets on gold nanoparticles.

    PubMed

    Perfetti, Mauro; Pineider, Francesco; Poggini, Lorenzo; Otero, Edwige; Mannini, Matteo; Sorace, Lorenzo; Sangregorio, Claudio; Cornia, Andrea; Sessoli, Roberta

    2014-01-29

    The chemical synthesis and characterization of the first hybrid material composed by gold nanoparticles and single molecule magnets (SMMs) are described. Gold nanoparticles are functionalized via ligand exchange using a tetrairon(III) SMM containing two 1,2-dithiolane end groups. The grafting is evidenced by the shift of the plasmon resonance peak recorded with a UV-vis spectrometer, by the suppression of nuclear magnetic resonance signals, by X-ray photoemission spectroscopy peaks, and by transmission electron microscopy images. The latter evidence the formation of aggregates of nanoparticles as a consequence of the cross-linking ability of Fe4 through the two 1,2-dithiolane rings located on opposite sides of the metal core. The presence of intact Fe4 molecules is directly proven by synchrotron-based X-ray absorption spectroscopy and X-ray magnetic circular dichroism spectroscopy, while a detailed magnetic characterization, obtained using electron paramagnetic resonance and alternating-current susceptibility, confirms the persistence of SMM behavior in this new hybrid nanostructure.

  11. Imaging the wave functions of adsorbed molecules.

    PubMed

    Lüftner, Daniel; Ules, Thomas; Reinisch, Eva Maria; Koller, Georg; Soubatch, Serguei; Tautz, F Stefan; Ramsey, Michael G; Puschnig, Peter

    2014-01-14

    The basis for a quantum-mechanical description of matter is electron wave functions. For atoms and molecules, their spatial distributions and phases are known as orbitals. Although orbitals are very powerful concepts, experimentally only the electron densities and -energy levels are directly observable. Regardless whether orbitals are observed in real space with scanning probe experiments, or in reciprocal space by photoemission, the phase information of the orbital is lost. Here, we show that the experimental momentum maps of angle-resolved photoemission from molecular orbitals can be transformed to real-space orbitals via an iterative procedure which also retrieves the lost phase information. This is demonstrated with images obtained of a number of orbitals of the molecules pentacene (C22H14) and perylene-3,4,9,10-tetracarboxylic dianhydride (C24H8O6), adsorbed on silver, which are in excellent agreement with ab initio calculations. The procedure requires no a priori knowledge of the orbitals and is shown to be simple and robust.

  12. Interstellar grain chemistry and organic molecules

    NASA Technical Reports Server (NTRS)

    Allamandola, L. J.; Sandford, S. A.

    1990-01-01

    The detection of prominant infrared absorption bands at 3250, 2170, 2138, 1670 and 1470 cm(-1) (3.08, 4.61, 4.677, 5.99 and 6.80 micron m) associated with molecular clouds show that mixed molecular (icy) grain mantles are an important component of the interstellar dust in the dense interstellar medium. These ices, which contain many organic molecules, may also be the production site of the more complex organic grain mantles detected in the diffuse interstellar medium. Theoretical calculations employing gas phase as well as grain surface reactions predict that the ices should be dominated only by the simple molecules H2O, H2CO, N2, CO, O2, NH3, CH4, possibly CH3OH, and their deuterated counterparts. However, spectroscopic observations in the 2500 to 1250 cm(-1)(4 to 8 micron m) range show substantial variation from source reactions alone. By comparing these astronomical spectra with the spectra of laboratory-produced analogs of interstellar ices, one can determine the composition and abundance of the materials frozen on the grains in dense clouds. Experiments are described in which the chemical evolution of an interstellar ice analog is determined during irradiation and subsequent warm-up. Particular attention is paid to the types of moderately complex organic materials produced during these experiments which are likely to be present in interstellar grains and cometary ices.

  13. Techniques for visualization of carbohydrate molecules.

    PubMed

    Kuttel, Michelle; Gain, James; Burger, Anton; Eborn, Ian

    2006-11-01

    Standard molecular visualizations, such as the classic ball-and-stick model, are not suitable for large, complex molecules because the overall molecular structure is obscured by the atomic detail. For proteins, the more abstract ribbon and cartoon representations are instead used to reveal large scale molecular conformation and connectivity. However, there is currently no accepted convention for simplifying oligo- and polysaccharide structures. We introduce two novel visualization algorithms for carbohydrates, incorporated into a visualization package, CarboHydra. Both algorithms highlight the sugar rings and backbone conformation of the carbohydrate chain, ignoring ring substituents. The first algorithm, termed PaperChain, emphasizes the type and conformation of the carbohydrate rings. The second, Twister, emphasizes the relative orientation of the rings. We further include two rendering enhancements to augment these visualizations: silhouettes edges and a translucent overlay of the ball-and-stick atomic representation. To demonstrate their utility, the algorithms and visualization enhancements are here applied to a variety of carbohydrate molecules. User evaluations indicate that they present a more useful view of carbohydrate structure than the standard ball-and-stick representation. The algorithms were found to be complementary, with PaperChain particularly effective for smaller carbohydrates and Twister useful at larger scales for highlighting the backbone twist of polysaccharides.

  14. Co-conspirators: Space, Molecules and Life

    NASA Astrophysics Data System (ADS)

    Jheeta, Sohan

    2012-07-01

    The field of astrobiology is rapidly becoming a discipline in its own right as it seeks to answer the following questions: What are the conditions under which life can develop?; How widespread are these conditions in the Universe?; and What are the mechanisms by which life evolves from basic `building blocks' into self replicating systems? It is believed that some of the necessary organic molecules may have been formed in the specialised areas of space (namely dark molecular clouds, eg Horsehead nebula) and delivered on to the Earth during the early period of its history, approximately 4.0 x 109 years ago. These organic molecules may have played a pivotal role in the formation of life on Earth. In addition it is believed that life on Earth was formed within a very short geological time frame of only 200-300 million years. So it is not unreasonable to suppose that these molecules were initially made in space as this could be, metaphorically speaking a huge laboratory when compared to the Earth. Currently we have very little definite knowledge of `how life began on Earth?' or whether `there is life elsewhere in the Universe?' These two questions are inextricably interlinked in that, as life exists on Earth, it is quite feasible that it should also flourish elsewhere in the Universe. To answer these questions, mechanisms have to be found whereby `non-living chemicals' could be transformed into 3-dimensional `first' living organisms. This process is often termed `chemical evolution.'~ The research being presented at this conference focuses on the formation of molecules under a variety of simulated space conditions (eg different temperatures, levels of radiation energies and different types of impinging radiations). Results pertaining to irradiation of methyl cyanide ice at 15 K with 200 keV protons and 1:1 mixture of NH _{3}:CO _{2} ice at 30 K with 1 keV electrons, and 1:1 mixture of NH _{3}:CH _{3}OH ice also at 30 K with 1 keV electrons will be presented. These

  15. Redox-gated electron transport in electrically wired ferrocene molecules

    NASA Astrophysics Data System (ADS)

    Xiao, Xiaoyin; Brune, Daniel; He, Jin; Lindsay, Stuart; Gorman, Christopher B.; Tao, Nongjian

    2006-07-01

    We have synthesized cysteamine-terminated ferrocene molecules and determined the dependence of the electron transport properties of the molecules on their redox states by measuring the current through the molecules as a function of the electrode potential. The current fluctuates over a large range, but its average value increases with the potential. We attribute the current fluctuation and its increase with the potential to the switching of the molecules from low-conductance reduced state to high-conductance oxidized state.

  16. Recent advances in developing small molecules targeting RNA.

    PubMed

    Guan, Lirui; Disney, Matthew D

    2012-01-20

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

  17. Development of Lattice Trapped Paramagnetic Polar Molecules for Quantum Simulation

    DTIC Science & Technology

    2015-06-23

    pancake traps. We have also produced heteronuclear molecules of ytterbium-lithium for the first time, using the technique of photoassociation. We...molecular state using a Raman technique . 15. SUBJECT TERMS Molecules, Paramagnetic 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18...Distribution approved for public release. Subhadeep Gupta 3 We also produced heteronuclear molecules of ytterbium-lithium using the technique of

  18. Conductance and Geometry of Pyridine-Linked Single Molecule Junctions

    SciTech Connect

    Kamenetska, M.; Hybertsen, M.; Quek, S.Y.; Whalley, A.C.; Steigerwald, M.L.; Choi, H.J.; Louie, S.G.; Nuckolls, C.; Neaton, J.B.; Venkataraman, L.

    2010-05-19

    We have measured the conductance and characterized molecule-electrode binding geometries of four pyridine-terminated molecules by elongating and then compressing gold point contacts in a solution of molecules. We have found that all pyridine-terminated molecules exhibit bistable conductance signatures, signifying that the nature of the pyridine-gold bond allows two distinct conductance states that are accessed as the gold-molecule-gold junction is elongated. We have identified the low-conductance state as corresponding to a molecule fully stretched out between the gold electrodes, where the distance between contacts correlates with the length of the molecule; the high-conductance state is due to a molecule bound at an angle. For all molecules, we have found that the distribution of junction elongations in the low-conductance state is the same, while in the high-conductance state, the most likely elongation length increases linearly with molecule length. The results of first-principles conductance calculations for the four molecules in the low-conductance geometry agree well with the experimental results and show that the dominant conducting channel in the conjugated pyridine-linked molecules is through the {pi}* orbital.

  19. Single-Molecule Electronic Measurements with Metal Electrodes

    ERIC Educational Resources Information Center

    Lindsay, Stuart

    2005-01-01

    A review of concepts like tunneling through a metal-molecule-metal-junction, contrast with electrochemical and optical-charge injection, strong-coupling limit, calculations of tunnel transport, electron transfer through Redox-active molecules is presented. This is followed by a discussion of experimental approaches for single-molecule measurements.

  20. The Stereochemistry of Biochemical Molecules: A Subject to Revisit

    ERIC Educational Resources Information Center

    Centelles, Josep J.; Imperial, Santiago

    2005-01-01

    Although Fischer's convention for stereoisomers is useful for simple molecules, the stereochemistry of complex biochemical molecules is often poorly indicated in textbooks. This article reports on errors in stereochemistry of complex hydrosoluble vitamin B12 molecule. Twenty-five popular biochemistry textbooks were examined for their treatment of…

  1. New frontiers for quantum gases of polar molecules

    NASA Astrophysics Data System (ADS)

    Moses, Steven A.; Covey, Jacob P.; Miecnikowski, Matthew T.; Jin, Deborah S.; Ye, Jun

    2017-01-01

    Compared to atoms, molecules possess additional degrees of freedom that can be exploited in fundamental tests, ultracold chemistry, and engineering new quantum phases in many-body systems. Here, we review the recent progress in creating and manipulating ultracold bialkali molecules to study quantum gases of polar molecules.

  2. Decoding the photochemistry of simple astrophysical molecules

    NASA Astrophysics Data System (ADS)

    Jackson, William M.; Ng, Cheuk Y; Lu, Zhou; Chang, Yih C

    2014-06-01

    An experimental apparatus with two tunable vacuum ultraviolet (VUV) lasers in a windowless pump-probe configuration with slice imaging detection has been used to study the photochemistry of simple astrophysical molecules such as N2, NO, CO, and CO2. The VUV pump laser is set at the desired photodissociation wavelength and the VUV probe laser is set detect the atom by setting it to excite a one-photon transition in the VUV region and then using a visible photon to ionize the excited atoms. The photodissociation of CO2 in the energy region between 94,000.3 and 98,496.4 cm-1 (11.655-12.212eV) is studied and we have been able to show that all of the energetically accessible photochemical channels occur.CO2+ hν → O(3P”J”) + CO(X1Σ+) hν ≥ 5.45 eV→ O(1D) + CO(X1Σ+) hν ≥ 7.42 eV→ O(1S) + CO(X1Σ+) hν ≥ 9.64 eV→ O(3PJ) + CO(a3Π) hν ≥ 11.46 eV→ C(3PJ) + O2 (X3ΣJ-) hν ≥ 11.44 eVThis is the first time that all of these channels in CO2 have been determined by the direct detection of the atomic fragments. It shows that even simple molecules made up of first row atoms that do not contain H atoms can dissociate into spin forbidden products. We have also been able to use this apparatus to systematically determine the branching ratios between the 4S, 2D, and 2P states of N atoms produced in the photolysis of N2 in the wavelength range from 100,819.7 to 121,870.1 cm-1(12.500-15.110 eV). These examples show that the photodissociation of the major molecules that occur in the atmospheres of planets, comets, moons and the interstellar medium can be studied in the windowless region of the VUV spectrum. Acknowledgements:William M. Jackson and Zhou Lu gratefully acknowledge the support of the National Science Foundation (NSF) under Grant No. CHE-1301501. Cheuk Y. Ng acknowledges the support by the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, (U.S.) Department of Energy (DOE) under Contract No

  3. New observations of interstellar organic molecules

    NASA Technical Reports Server (NTRS)

    Irvine, W. M.; Friberg, P.; Matthews, H. E.; Minh, Y. C.; Ziurys, L. M.

    1990-01-01

    Discussed here are new observations of 3-carbon-containing interstellar molecules which play an important role in the chemistry of dense molecular clouds: protonated carbon dioxide, formic acid, and propynal. In 1984 a new oxide of carbon, C3O, was discovered in the interstellar medium (Matthews et al. 1984; Brown et al. 1985). Theoretical models suggest that C3O is produced by dissociative electron recombination with the ion H3C3O+. Although no laboratory data for the branching ratios of such a recombination exist, it seemed to us likely that additional products would include H2C3O. This molecule has more than one isomeric form, but one stable species is propynal (HC2CHO), which had been suggested as a possible interstellar molecule by Winnewisser (1973). In observations at the National Radio Astronomy Observatory 43 m telescope in Green Bank earlier this year, researchers detected a line in the cold cloud TMC-1 which they assign to the 2(0,2)-1(0,1) transition of propynal. The observed line agrees with the laboratory frequency to well within the experimental uncertainty a few parts in 10 to the 7th power. Researchers sought and failed to detect the corresponding 2(1,1)-1(1,0) line, which is understandable given the presence of both a and b components of the electric dipole moment in propynal. The b type transitions will drain population from energy levels with K(sub p) does not equal 0 into the K(sub p) equal 0 stack. If the researchers' assignment is correct, this is the first interstellar detection of propynal. Assuming typical rotational temperatures for TMC-1 and that the line is optically thin, the column density determined is about 5 times 10 to the 12th power cm to the -2nd power, or about three times that for C3O. Formic acid (HCOOH) was the first organic acid to be observed in the interstellar medium, in the Galactic center source Sgr B2. The only other interstellar detection has been recently made in the giant molecular cloud in Orion. As part of the

  4. Imaging biological molecules with single molecule sensitivity using near-field scanning optical microscopy

    SciTech Connect

    Ambrose, W.P.; Affleck, R.L.; Goodwin, P.M.; Keller, R.A.; Martin, J.C.; Petty, J.T.; Schecker, J.A.; Wu, Ming

    1995-12-01

    We have developed a near-field scanning optical microscope with the sensitivity to detect single fluorescent molecules. Our microscope is based on scanning a sample under a tapered and metal coated fiber optic probe and has an illumination-aperture diameter as small as 100 nm. The microscope simultaneously acquires a shear force image with a height noise of {approximately} 1 nm. We have used this system to demonstrate the detection of single molecules of Rhodamine-6G on silica. In this paper, we explore the use of NSOM for investigations of biological molecules. We have prepared and imaged double-stranded DNA intercalated with thiazole orange homodimer (TOTO); single chromosomes stained with propidium iodide; and {beta}-phycoerythrin proteins on dry, borosilicate-glass surfaces. At very dilute coverages, isolated fluorescent spots are observed for the un-intercalated TOTO dye and for {beta}-phycoerythrin. These fluorescent spots exhibit-emission intensity fluctuations and abrupt bleaching transitions, similar to the intensity behavior observed previously for single Rhodamine 6G molecules on silica.

  5. Aptamer-based Nanosensors: Juglone as an Attached-Redox Molecule for Detection of Small Molecules

    PubMed Central

    Saberian, Mehdi; Hamzeiy, Hossein; Aghanejad, Ayuob; Asgari, Davoud

    2011-01-01

    Introduction Among several biosensing approaches, electrochemical-based procedures have been described as one of the most common and useful methods for sensing because of their simplicity, sensitivity, accuracy, and low cost. The electroactive species, which called redox, play a main role in the electrochemical-based approaches. Among several redox molecules used for electrochemical experiments, ferrocene is one of the commonly used redox molecules. However, instability of ferrocenium ion in the chloride containing solutions appeared to be weakness of this redox molecule limiting its utilization. Methods In the current study, Juglone was attached (using EDC/NHS coupling method) to the 3'-amino-modified terminus of the immobilized specific aptamer of codeine, which was successfully used in a cyclic electrochemical voltammetry procedure. Results The cyclic voltammogram peak of aptamer-attached Juglone was observed in the potential range of +0.4 to +0.9 V and the fabricated aptamer-based sensor was used for detection of different concentrations of codeine in the phosphate buffer 0.1 M solution containing 2 M NaCl. Conclusion Based on these findings, it can be suggested that the new aptamer-attached Juglone could be considered as an effective alternative redox molecule in particular with oligonucleotide-based sensing systems. PMID:23678405

  6. Covalent small-molecule-RNA complex formation enables cellular profiling of small-molecule-RNA interactions.

    PubMed

    Guan, Lirui; Disney, Matthew D

    2013-09-16

    Won't let you go! A strategy is described to design small molecules that react with their cellular RNA targets. This approach not only improves the activity of compounds targeting RNA in cell culture by a factor of about 2500 but also enables cell-wide profiling of its RNA targets.

  7. Low energy ion-molecule reactions

    SciTech Connect

    Farrar, J.M.

    1993-12-01

    This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.

  8. Dissociative Electron Attachment of Water Molecules

    NASA Astrophysics Data System (ADS)

    Belkacem, Ali; Adaniya, Hidehito; Osipov, Timur; Weber, Thorsten; Lee, Sun Y.; Hertlein, Marcus; Rudek, Benedikt

    2008-05-01

    A Coltrims method is developed to measure the kinetic energy and angular distribution of fragment negative ions arising from dissociative electron attachment of molecules. A low energy pulsed electron gun is used in combination with pulsing the extraction plates of the Coltrims spectrometer. This technique is applied to study the negative oxygen anion channel for the three resonances, ^2B1, ^2A1, and ^2B2 resonances of water. The measured kinetic energy of the O- fragment gives a good measure of the two-body channel versus three-body channel for each resonance. The angular distribution of the O- fragments with respect tom the electron beam direction is found reflect well the symmetry of the resonance state. The experimental results are compared to the theoretical predictions.

  9. Molecule concept nanocars: chassis, wheels, and motors?

    PubMed

    Joachim, Christian; Rapenne, Gwénael

    2013-01-22

    The design, synthesis, and running of a molecular nanovehicle on a surface assisted by proper nanocommunication channels for feeding and guiding the vehicle now constitute an active field of research and are no longer a nano-joke. In this Perspective, we describe how this field began, its growth, and problems to be solved. Better molecular wheels, a molecular motor with its own gears assembling for torque transmission must be mounted on (i.e., chemically bonded to) a good molecular chassis for the resulting covalently constructed molecular nanovehicle to run on a surface in a controlled manner at the atomic scale. We propose a yearly molecule concept nanocar contest to boost molecular nanovehicle research.

  10. Evolutionary game theory: molecules as players.

    PubMed

    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.

  11. Discrete energy transport in collagen molecules

    NASA Astrophysics Data System (ADS)

    Alain, Mvogo; Germain, H. Ben-Bolie; Timoléon, C. Kofané

    2014-09-01

    The modulational instability in the three coupled α-polypeptide chains of a collagen molecule is investigated. Choosing symmetric and asymmetric solutions, and applying the so-called rotating-wave approximation, we describe the dynamics of the system by the discrete nonlinear Schrödinger (DNLS) equation. The linear stability analysis of the continuous wave solution is performed. The numerical simulations show the generation of trains of solitonic structures in the lattice with increasing amplitude as time progresses. The effect of damping and noise forces of the physiological temperature (T = 300 K) introduces an erratic behavior to the formed patterns, reinforcing the idea that the energy used in metabolic processes is confined to specific regions for efficiency.

  12. Single-molecule optomechanics in "picocavities".

    PubMed

    Benz, Felix; Schmidt, Mikolaj K; Dreismann, Alexander; Chikkaraddy, Rohit; Zhang, Yao; Demetriadou, Angela; Carnegie, Cloudy; Ohadi, Hamid; de Nijs, Bart; Esteban, Ruben; Aizpurua, Javier; Baumberg, Jeremy J

    2016-11-11

    Trapping light with noble metal nanostructures overcomes the diffraction limit and can confine light to volumes typically on the order of 30 cubic nanometers. We found that individual atomic features inside the gap of a plasmonic nanoassembly can localize light to volumes well below 1 cubic nanometer ("picocavities"), enabling optical experiments on the atomic scale. These atomic features are dynamically formed and disassembled by laser irradiation. Although unstable at room temperature, picocavities can be stabilized at cryogenic temperatures, allowing single atomic cavities to be probed for many minutes. Unlike traditional optomechanical resonators, such extreme optical confinement yields a factor of 10(6) enhancement of optomechanical coupling between the picocavity field and vibrations of individual molecular bonds. This work sets the basis for developing nanoscale nonlinear quantum optics on the single-molecule level.

  13. Forces from periodic charging of adsorbed molecules

    NASA Astrophysics Data System (ADS)

    Kocić, N.; Decurtins, S.; Liu, S.-X.; Repp, J.

    2017-03-01

    In a recent publication [Kocić et al., Nano Lett. 15, 4406 (2015)], it was shown that gating of molecular levels in the field of an oscillating tip of an atomic force microscope can enable a periodic charging of individual molecules synchronized to the tip's oscillatory motion. Here we discuss further implications of such measurements, namely, how the force difference associated with the single-electron charging manifests itself in atomic force microscopy images and how it can be detected as a function of tip-sample distance. Moreover, we discuss how the critical voltage for the charge-state transition depends on distance and how that relates to the local contact potential difference. These measurements allow also for an estimate of the absolute tip-sample distance.

  14. Single molecule magnets from magnetic building blocks

    NASA Astrophysics Data System (ADS)

    Kroener, W.; Paretzki, A.; Cervetti, C.; Hohloch, S.; Rauschenbach, S.; Kern, K.; Dressel, M.; Bogani, L.; M&üLler, P.

    2013-03-01

    We provide a basic set of magnetic building blocks that can be rationally assembled, similar to magnetic LEGO bricks, in order to create a huge variety of magnetic behavior. Using rare-earth centers and multipyridine ligands, fine-tuning of intra and intermolecular exchange interaction is demonstrated. We have investigated a series of molecules with monomeric, dimeric and trimeric lanthanide centers using SQUID susceptometry and Hall bar magnetometry. A home-made micro-Hall-probe magnetometer was used to measure magnetic hysteresis loops at mK temperatures and fields up to 17 T. All compounds show hysteresis below blocking temperatures of 3 to 4 K. The correlation of the assembly of the building blocks with the magnetic properties will be discussed.

  15. Increased throughput single molecule detection of DNA

    NASA Astrophysics Data System (ADS)

    Gurjar, Rajan; Seetamraju, Madhavi; Kolodziejski, Noah; Myers, Richard; Staples, Christopher; Christian, James; Squillante, Michael R.; Entine, Gerald

    2007-09-01

    In this work, we present research in using confocal optical techniques with femtolitre focal volumes and obtain very high signal-to-noise and signal-to-background ratios for single molecule detection (SMD). We were able to achieve improved signal strength by using highly fluorescent quantum dots and nanopatterned substrates to obtain plasmon induced resonant fluorescence enhancement. A method to simultaneously using multiple excitation spots without the use of confocal apertures and an array of single photon sensitive Geiger mode avalanche photodiodes was used to increase the throughput of the detection system. Using this highly sensitive SMD system, we detect small quantities of synthetic DNA through hybridization eliminating the need of polymerase chain reaction.

  16. Structure determination of molecules of biochemical interest

    NASA Astrophysics Data System (ADS)

    Honzatko, R. B.

    1985-10-01

    In the past year we have established a new laboratory for the determination of macromolecular structure. Currently, facilities are in place for data collection, data processing, molecular modeling and X-ray refinement of structures of up to 100,000 molecular weight in their crystallographic asymmetric unit. In parallel with establishing a new laboratory, we have pursued structure investigations of hemoglobin from the sea lamprey, aspartate carbamoyltransferase from Escherichia coli and p-nitrobenzylidine aminoguanidine, a small molecule which is an acceptor of the adenosine diphosphate ribosyl group in an enzyme mediated reaction. In addition to the structural studies above we have made a theoretical study by techniques of energy minimization of possible modes of aggregation of lamprey hemoglobin and the relationship between aggregate formation and cooperativity expressed in solutions by lamprey hemoglobin.

  17. Spin doping using transition metal phthalocyanine molecules

    NASA Astrophysics Data System (ADS)

    Atxabal, A.; Ribeiro, M.; Parui, S.; Urreta, L.; Sagasta, E.; Sun, X.; Llopis, R.; Casanova, F.; Hueso, L. E.

    2016-12-01

    Molecular spins have become key enablers for exploring magnetic interactions, quantum information processes and many-body effects in metals. Metal-organic molecules, in particular, let the spin state of the core metal ion to be modified according to its organic environment, allowing localized magnetic moments to emerge as functional entities with radically different properties from its simple atomic counterparts. Here, using and preserving the integrity of transition metal phthalocyanine high-spin complexes, we demonstrate the magnetic doping of gold thin films, effectively creating a new ground state. We demonstrate it by electrical transport measurements that are sensitive to the scattering of itinerant electrons with magnetic impurities, such as Kondo effect and weak antilocalization. Our work expands in a simple and powerful way the classes of materials that can be used as magnetic dopants, opening a new channel to couple the wide range of molecular properties with spin phenomena at a functional scale.

  18. Small molecule regulators of protein arginine methyltransferases.

    PubMed

    Cheng, Donghang; Yadav, Neelu; King, Randall W; Swanson, Maurice S; Weinstein, Edward J; Bedford, Mark T

    2004-06-04

    Here we report the identification of small molecules that specifically inhibit protein arginine N-methyltransferase (PRMT) activity. PRMTs are a family of proteins that either monomethylate or dimethylate the guanidino nitrogen atoms of arginine side chains. This common post-translational modification is implicated in protein trafficking, signal transduction, and transcriptional regulation. Most methyltransferases use the methyl donor, S-adenosyl-L-methionine (AdoMet), as a cofactor. Current methyltransferase inhibitors display limited specificity, indiscriminately targeting all enzymes that use AdoMet. In this screen we have identified a primary compound, AMI-1, that specifically inhibits arginine, but not lysine, methyltransferase activity in vitro and does not compete for the AdoMet binding site. Furthermore, AMI-1 prevents in vivo arginine methylation of cellular proteins and can modulate nuclear receptor-regulated transcription from estrogen and androgen response elements, thus operating as a brake on certain hormone actions.

  19. On the conformation of the propranolol molecule

    NASA Astrophysics Data System (ADS)

    Sadlej-Sosnowska, N.; Dobrowolski, J. Cz; Mazurek, A. P.

    2000-03-01

    The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G ∗ refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.

  20. Spin doping using transition metal phthalocyanine molecules

    PubMed Central

    Atxabal, A.; Ribeiro, M.; Parui, S.; Urreta, L.; Sagasta, E.; Sun, X.; Llopis, R.; Casanova, F.; Hueso, L. E.

    2016-01-01

    Molecular spins have become key enablers for exploring magnetic interactions, quantum information processes and many-body effects in metals. Metal-organic molecules, in particular, let the spin state of the core metal ion to be modified according to its organic environment, allowing localized magnetic moments to emerge as functional entities with radically different properties from its simple atomic counterparts. Here, using and preserving the integrity of transition metal phthalocyanine high-spin complexes, we demonstrate the magnetic doping of gold thin films, effectively creating a new ground state. We demonstrate it by electrical transport measurements that are sensitive to the scattering of itinerant electrons with magnetic impurities, such as Kondo effect and weak antilocalization. Our work expands in a simple and powerful way the classes of materials that can be used as magnetic dopants, opening a new channel to couple the wide range of molecular properties with spin phenomena at a functional scale. PMID:27941810

  1. Hard molecule-based magnet of Fe

    NASA Astrophysics Data System (ADS)

    Vaz, M. G. F.; Ardisson, J. D.; Stumpf, H. O.; Macedo, W. A. A.

    2001-05-01

    A new molecule-based magnet containing Fe 2+, Fe 3+, Cu(opba) 2- and Bu 4N +, with opba=ortho-phenylenebis(oxamato) and Bu 4N +=tetra-n-butylammonium, was synthesized. The samples were characterized by infrared spectroscopy, elemental analysis, atomic absorption, vibrating sample magnetometry and 57Fe Mössbauer spectroscopy. The magnetic measurements show that the compound presents a magnetic transition around 25 K and a high coercivity, around 1.3 T. Above the transition temperature, the Mössbauer spectrum is dominated by a broad doublet characteristic of Fe 2+. At 20 K, the spectrum shows clear magnetic splitting and at least two non-equivalent Fe sites can be identified. To the best of our knowledge, this compound presents the highest coercive field observed for an iron-based molecular magnetic system.

  2. Alkaline pH sensor molecules.

    PubMed

    Murayama, Takashi; Maruyama, Ichiro N

    2015-11-01

    Animals can survive only within a narrow pH range. This requires continual monitoring of environmental and body-fluid pH. Although a variety of acidic pH sensor molecules have been reported, alkaline pH sensor function is not well understood. This Review describes neuronal alkaline pH sensors, grouped according to whether they monitor extracellular or intracellular alkaline pH. Extracellular sensors include the receptor-type guanylyl cyclase, the insulin receptor-related receptor, ligand-gated Cl- channels, connexin hemichannels, two-pore-domain K+ channels, and transient receptor potential (TRP) channels. Intracellular sensors include TRP channels and gap junction channels. Identification of molecular mechanisms underlying alkaline pH sensing is crucial for understanding how animals respond to environmental alkaline pH and how body-fluid pH is maintained within a narrow range.

  3. Fragmentation of methane molecules by antiproton impact

    NASA Astrophysics Data System (ADS)

    Salehzadeh, Arash; Kirchner, Tom

    2016-09-01

    Extending previous work for proton impact, we have investigated the fragmentation of methane molecules due to collisions with antiprotons in the 25 keV to 5 MeV impact energy range. The multi-center nature of the problem is addressed by using a spectral representation of the molecular Hartree-Fock-level Hamiltonian and a single-center expansion of the initially populated molecular orbitals. The two-center basis generator method (TC-BGM) is used for orbital propagation. Electron-removal cross sections obtained from the TC-BGM solutions are complemented with a dynamical decay-route fragmentation model to calculate cross sections for the production of fragment ions. Good agreement with the available experimental data is observed for CH4+,CH3+,CH2+and CH+. Work supported by NSERC, Canada.

  4. Dynamics of DNA molecules under gel electrophoresis

    SciTech Connect

    Kotaka, Tadao, Adachi, Shiro; Shikata, Toshiyuki

    1993-12-31

    Electrophoretic mobilities {mu} of double stranded linear DNAs were examined in agarose gels subjected to a biased sinusoidal field (BSF) that utilizes a sinusoidal field of strength E{sub s} and frequency f superposed on a steady bias field of strength E{sub b}. Under BSF with E{sub s} {much_gt} E{sub b}. DNA fragments with the size M > 20 kbp exhibited peculiar behavior which the authors called a pin down phenomenon in that the {mu} shows a minimum {mu}{sub p} at a particular f{sub p} (pin down frequency) specific to M, C{sub gel} and the field strengths. The dynamics of DNA molecules under such pin-down conditions were examined by direct observation via fluorescence microscopy as well as dynamic electric birefringence.

  5. Adiabatic theory for anisotropic cold molecule collisions

    SciTech Connect

    Pawlak, Mariusz; Shagam, Yuval; Narevicius, Edvardas; Moiseyev, Nimrod

    2015-08-21

    We developed an adiabatic theory for cold anisotropic collisions between slow atoms and cold molecules. It enables us to investigate the importance of the couplings between the projection states of the rotational motion of the atom about the molecular axis of the diatom. We tested our theory using the recent results from the Penning ionization reaction experiment {sup 4}He(1s2s {sup 3}S) + HD(1s{sup 2}) → {sup 4}He(1s{sup 2}) + HD{sup +}(1s) + e{sup −} [Lavert-Ofir et al., Nat. Chem. 6, 332 (2014)] and demonstrated that the couplings have strong effect on positions of shape resonances. The theory we derived provides cross sections which are in a very good agreement with the experimental findings.

  6. Monitoring Molecules in Neuroscience Then and Now.

    PubMed

    Rice, Margaret E

    2017-02-15

    The 16th International Conference on Monitoring Molecules in Neuroscience (MMiN) was held in Gothenburg, Sweden in late spring 2016. This conference originated as a methods meeting focused on in vivo voltammetric techniques and microdialysis. Over time, however, the scope has evolved to include a number of other methods for neurochemical detection that range from single-cell fluorescence in vitro and in vivo in animal models to whole-brain imaging in humans. Overall, MMiN provides a unique forum for introducing new developments in neurochemical detection, as well as for reporting exciting neurobiological insights provided by established and novel methods. This Viewpoint includes a brief history of the meeting, factors that have contributed its evolution, and some highlights of MMiN 2016.

  7. Spin doping using transition metal phthalocyanine molecules.

    PubMed

    Atxabal, A; Ribeiro, M; Parui, S; Urreta, L; Sagasta, E; Sun, X; Llopis, R; Casanova, F; Hueso, L E

    2016-12-12

    Molecular spins have become key enablers for exploring magnetic interactions, quantum information processes and many-body effects in metals. Metal-organic molecules, in particular, let the spin state of the core metal ion to be modified according to its organic environment, allowing localized magnetic moments to emerge as functional entities with radically different properties from its simple atomic counterparts. Here, using and preserving the integrity of transition metal phthalocyanine high-spin complexes, we demonstrate the magnetic doping of gold thin films, effectively creating a new ground state. We demonstrate it by electrical transport measurements that are sensitive to the scattering of itinerant electrons with magnetic impurities, such as Kondo effect and weak antilocalization. Our work expands in a simple and powerful way the classes of materials that can be used as magnetic dopants, opening a new channel to couple the wide range of molecular properties with spin phenomena at a functional scale.

  8. Nanostructuring discotic molecules on ITO support

    NASA Astrophysics Data System (ADS)

    Hesse, H. C.; Lembke, D.; Dössel, L.; Feng, X.; Müllen, K.; Schmidt-Mende, L.

    2011-02-01

    Patterning of organic compounds on a nanometer length scale is of great interest for solar applications: defined control over the donor-acceptor interface will allow design of an optimized nano-morphology promoting exciton separation and reducing charge recombination. Herein we present an imprinting technique using anodized alumina oxide (AAO) hard templates as stamps. We show an exact pattern transfer of the AAO structures into a solution processable hexa-peri-hexabenzocoronene (HBC), a discotic small molecule with acrylate moieties which is polymerized in situ. Film fabrication is realized for a variety of nanowire dimensions on square centimeter areas. The fabrication directly on conductive glass support and control over the formation of a dense barrier layer render this approach appealing for the fabrication of fully organic nanostructured photovoltaic devices.

  9. Ultracold Heteronuclear Molecules in a 3D Optical Lattice

    SciTech Connect

    Ospelkaus, C.; Ospelkaus, S.; Humbert, L.; Ernst, P.; Sengstock, K.; Bongs, K.

    2006-09-22

    We report on the creation of ultracold heteronuclear molecules assembled from fermionic {sup 40}K and bosonic {sup 87}Rb atoms in a 3D optical lattice. Molecules are produced at a heteronuclear Feshbach resonance on both the attractive and the repulsive sides of the resonance. We precisely determine the binding energy of the heteronuclear molecules from rf spectroscopy across the Feshbach resonance. We characterize the lifetime of the molecular sample as a function of magnetic field and measure lifetimes between 20 and 120 ms. The efficiency of molecule creation via rf association is measured and is found to decrease as expected for more deeply bound molecules.

  10. Spectroscopic characterization of Venus at the single molecule level.

    PubMed

    David, Charlotte C; Dedecker, Peter; De Cremer, Gert; Verstraeten, Natalie; Kint, Cyrielle; Michiels, Jan; Hofkens, Johan

    2012-02-01

    Venus is a recently developed, fast maturating, yellow fluorescent protein that has been used as a probe for in vivo applications. In the present work the photophysical characteristics of Venus were analyzed spectroscopically at the bulk and single molecule level. Through time-resolved single molecule measurements we found that single molecules of Venus display pronounced fluctuations in fluorescence emission, with clear fluorescence on- and off-times. These fluorescence intermittencies were found to occupy a broad range of time scales, ranging from milliseconds to several seconds. Such long off-times can complicate the analysis of single molecule counting experiments or single-molecule FRET experiments.

  11. Computing Fluxes Of Molecules On And Near A Spacecraft

    NASA Technical Reports Server (NTRS)

    Ehlers, H. K.; Rios, E. R.; Hakes, C. L.; Bui, B. D.

    1996-01-01

    Molecular Flux (MOLFLUX) computer code is versatile program used to compute following conditions on and near spacecraft: fluxes of molecules to, and deposition of molecules on, surfaces; densities and column densities of molecules in surrounding space, and return fluxes of molecules to surfaces caused by both collisions of molecules with ambient atmosphere and by self-scattering. User has option to modify spacecraft configurations and sources of contamination and to choose which critical surfaces to examine. Written in FORTRAN and C language. Three machine versions available: VAX version (MSC-22260), HP version (MSC-22565), and Cray version (MSC-22566).

  12. Theoretical investigation on single-molecule chiroptical spectroscopy

    SciTech Connect

    Wakabayashi, M.; Yokojima, S.; Fukaminato, T.; Ogata, K.; Nakamura, S.

    2013-12-10

    Some experimental results of chiroptical response of single molecule have already reported. In those experiments, dissymmetry parameter, g was used as an indicator of the relative circular dichroism intensity. The parameter for individual molecules was measured. For the purpose of giving an interpretation or explanation to the experimental result, the dissymmetry parameter is formulated on the basis of Fermi’s golden rule. Subsequently, the value of individual molecules is evaluated as a function of the direction of light propagation to the orientationary fixed molecules. The ground and excited wavefunction of electrons in the molecule and transition moments needed are culculated using the density functional theory.

  13. Microfluidics for biological measurements with single-molecule resolution.

    PubMed

    Streets, Aaron M; Huang, Yanyi

    2014-02-01

    Single-molecule approaches in biology have been critical in studies ranging from the examination of physical properties of biological macromolecules to the extraction of genetic information from DNA. The variation intrinsic to many biological processes necessitates measurements with single-molecule resolution in order to accurately recapitulate population distributions. Microfluidic technology has proven to be useful in the facilitation and even enhancement of single-molecule studies because of the precise liquid handling, small volume manipulation, and high throughput capabilities of microfluidic devices. In this review we survey the microfluidic "toolbox" available to the single-molecule specialist and summarize some recent biological applications of single-molecule detection on chip.

  14. Reversible Aptamer-Au Plasmon Rulers for Secreted Single Molecules

    DOE PAGES

    Lee, Somin Eunice; Chen, Qian; Bhat, Ramray; ...

    2015-06-03

    Plasmon rulers, consisting of pairs of gold nanoparticles, allow single-molecule analysis without photobleaching or blinking; however, current plasmon rulers are irreversible, restricting detection to only single events. Here, we present a reversible plasmon ruler, comprised of coupled gold nanoparticles linked by a single aptamer, capable of binding individual secreted molecules with high specificity. We show that the binding of target secreted molecules to the reversible plasmon ruler is characterized by single-molecule sensitivity, high specificity, and reversibility. Lastly, such reversible plasmon rulers should enable dynamic and adaptive live-cell measurement of secreted single molecules in their local microenvironment.

  15. Molecules in Laboratory and in Interstellar Space?

    NASA Astrophysics Data System (ADS)

    Thimmakondu, Venkatesan S.

    2016-06-01

    In this talk, the quantum chemistry of astronomically relevant molecules will be outlined with an emphasis on the structures and energetics of C_7H_2 isomers, which are yet to be identified in space. Although more than 100's of isomers are possible for C_7H_2, to date only 6 isomers had been identified in the laboratory. The equilibrium geometries of heptatriynylidene (1), cyclohepta-1,2,3,4-tetraen-6-yne (2), and heptahexaenylidene (3), which we had investigated theoretically will be discussed briefly. While 1 and 3 are observed in the laboratory, 2 is a hypothetical molecule. The theoretical data may be useful for the laboratory detection of 2 and astronomical detection of 2 and 3. THIS WORK IS SUPPORTED BY A RESEARCH GRANT (YSS/2015/00099) FROM SERB, DST, GOVERNMENT OF INDIA. Apponi, A. P.; McCarthy, M. C.; Gottlieb, C. A.; Thaddeus, P. Laboratory Detection of Four New Cumulene Carbenes: H_2C_7, H_2C_8, H_2C_9, and D_2C10, Astrophys. J. 2000, 530, 357-361 Ball, C. D; McCarthy, M. C.; Thaddeus, P. Cavity Ringdown Spectroscopy of the Linear Carbon Chains HC_7H, HC_9H, HC11H, and HC13H. J. Chem. Phys. 2000, 112, 10149-10155 Dua, S.; Blanksby, S. J.; Bowie, J. H. Formation of Neutral C_7H_2 Isomers from Four Isomeric C_7H_2 Radical Anion Precursors in the Gas Phase. J. Phys. Chem. A, 2000, 104, 77-85. Thimmakondu, V. S. The equilibrium geometries of heptatriynylidene, cyclohepta-1,2,3,4-tetraen-6-yne, and heptahexaenylidene, Comput. Theoret. Chem. 2016, 1079, 1-10

  16. Kidney Injury Molecule-1: A Translational Journey

    PubMed Central

    Bonventre, Joseph V.

    2014-01-01

    Kidney injury molecule-1 (KIM-1, also named TIM-1 and HAVCR-1) was identified as the most highly upregulated protein in the proximal tubule of the kidney after injury. This protein is present with injury in multiple species including man, and also after a large number of acute and chronic insults to the kidney. It is a type-1 membrane protein whose ectodomain is released into the lumen of the tubule. The ectodomain is heavily glycosylated and stable and appears in the urine after injury. It has been qualified by the United States Food and Drug Administration and the European Medicines Agency for preclinical assessment of nephrotoxicity and on a case-by-case basis for clinical evaluation. As a biomarker in humans, its utility has been demonstrated in acute and chronic injury and in renal cell carcinoma, a condition similar to injury, where there is dedifferentiation of the epithelial cell. KIM-1 is a phosphatidylserine receptor which recognizes apoptotic cells directing them to lysosomes. It also serves as a receptor for oxidized lipoproteins and hence is important for uptake of components of the tubular lumen which may be immunomodulatory and/or toxic to the cell. KIM-1 is unique in being the first molecule, not also present on myeloid cells, that transforms kidney proximal epithelial cells into semi-professional phagocytes. Data suggest that KIM-1 expression is protective during early injury, whereas in chronic disease states, prolonged KIM-1 expression may be maladaptive and may represent a target for therapy of chronic kidney disease. PMID:25125746

  17. Keystone predation and molecules of keystone significance.

    PubMed

    Zimmer, Richard K; Ferrier, Graham A; Kim, Steven J; Ogorzalek Loo, Rachel R; Zimmer, Cheryl Ann; Loo, Joseph A

    2017-04-04

    Keystone species structure ecological communities and are major determinants of biodiversity. A synthesis of research on keystone species is nonetheless missing a critical component -NDASH- the sensory mechanisms for behavioral interactions that determine population- and community-wide attributes. Here, we establish the chemosensory basis for keystone predation by sea stars (Pisaster ochraceus) on mussels. This consumer-resource interaction is prototypic of top-down driven trophic cascades. Each mussel species (Mytilus californianus and M. galloprovincialis) secretes a glycoprotein orthologue (29.6 and 28.1 kDa, respectively) that acts, singularly, to evoke the sea star predatory response. The orthologues (named 'KEYSTONEin') are localized in the epidermis, extrapallial fluid, and organic shell coating (periostracum) of live, intact mussels. Thus, KEYSTONEin contacts chemosensory receptors on tube feet as sea stars crawl over rocky surfaces in search of prey. The complete nucleotide sequences reveal that KEYSTONEin shares 87% (M. californianus) or 98% (M. galloprovincialis) homology with a calcium-binding protein in the shell matrix of a closely related congener, M. edulis. All three molecules cluster tightly within the Complement Component 1 Domain Containing (C1qDC) protein family; each exhibits a large globular domain, low complexity region(s), coiled coil, and at least four of five histidine-aspartic acid tandem motifs. Collective results support the hypothesis that KEYSTONEin evolved ancestrally in immunological, and later, in biomineralization roles. More recently, the substance has become exploited by sea stars as a contact cue for prey recognition. As the first identified compound to evoke keystone predation, KEYSTONEin provides valuable sensory information, promotes biodiversity, and shapes community structure and function. Without this molecule, there would be no predation by sea stars on mussels. This article is protected by copyright. All rights

  18. Studies of atmospheric molecules by multiphoton spectroscopy

    SciTech Connect

    Johnson, P.M.

    1991-10-01

    Carbon dioxide presents a great challenge to spectroscopy because of its propensity toward dissociation in all of its excited states. Multiphoton ionization spectroscopy is usually not applicable to the study of dissociating molecules because the dissociation competes effectively with ionization, resulting in no signal. We reasoned, however, that with high enough laser fluence, ionization could compete with dissociation in the longer lived states, exposing them for study from the continuous spectral background resulting from rapidly dissociating states. We describe the various spectroscopic and photophysical effects found through the multiphoton ionization and multiphoton photoelectron spectra. A recently developed variant of threshold ionization spectroscopy, usually called ZEKE, has shown a great deal of usefulness in providing the same information as traditional photoelectron spectroscopy but with higher resolution and much better signal-to-noise when using standard laboratory lasers. Threshold ionization techniques locate the states of an ion by scanning a light source across the ionization continuum of a neutral and somehow detecting when electrons are produced with no kinetic energy. We chose to develop our capabilities in threshold ionization spectroscopy using aromatic molecules because of their importance and because their electronic structure allows a pump-probe type of excitation scheme which avoids the use of vacuum ultraviolet laser beams. Among aromatics, the azines are noted for their small S{sub 1}-T{sub 1} energy gap which give them unique and interesting photophysical properties. We have continued our work on the multiphoton spectrum of metastable nitrogen produced by an electric discharge in supersonic beam. We have been able to assign more of the lines and simulated their rotational structure but many peaks remain unassigned.

  19. Quantum Monte Carlo for vibrating molecules

    SciTech Connect

    Brown, W.R. |

    1996-08-01

    Quantum Monte Carlo (QMC) has successfully computed the total electronic energies of atoms and molecules. The main goal of this work is to use correlation function quantum Monte Carlo (CFQMC) to compute the vibrational state energies of molecules given a potential energy surface (PES). In CFQMC, an ensemble of random walkers simulate the diffusion and branching processes of the imaginary-time time dependent Schroedinger equation in order to evaluate the matrix elements. The program QMCVIB was written to perform multi-state VMC and CFQMC calculations and employed for several calculations of the H{sub 2}O and C{sub 3} vibrational states, using 7 PES`s, 3 trial wavefunction forms, two methods of non-linear basis function parameter optimization, and on both serial and parallel computers. In order to construct accurate trial wavefunctions different wavefunctions forms were required for H{sub 2}O and C{sub 3}. In order to construct accurate trial wavefunctions for C{sub 3}, the non-linear parameters were optimized with respect to the sum of the energies of several low-lying vibrational states. In order to stabilize the statistical error estimates for C{sub 3} the Monte Carlo data was collected into blocks. Accurate vibrational state energies were computed using both serial and parallel QMCVIB programs. Comparison of vibrational state energies computed from the three C{sub 3} PES`s suggested that a non-linear equilibrium geometry PES is the most accurate and that discrete potential representations may be used to conveniently determine vibrational state energies.

  20. Photophysics of thermally activated delayed fluorescence molecules

    NASA Astrophysics Data System (ADS)

    Dias, Fernando B.; Penfold, Thomas J.; Monkman, Andrew P.

    2017-03-01

    Thermally activated delayed fluorescence (TADF) has recently emerged as one of the most attractive methods for harvesting triplet states in metal-free organic materials for application in organic light emitting diodes (OLEDs). A large number of TADF molecules have been reported in the literature with the purpose of enhancing the efficiency of OLEDs by converting non-emissive triplet states into emissive singlet states. TADF emitters are able to harvest both singlets and triplet states through fluorescence (prompt and delayed), the latter due to the thermally activated reverse intersystem crossing mechanism that allows up-conversion of low energy triplet states to the emissive singlet level. This allows otherwise pure fluorescent OLEDs to overcome their intrinsic limit of 25% internal quantum efficiency (IQE), which is imposed by the 1:3 singlet–triplet ratio arising from the recombination of charges (electrons and holes). TADF based OLEDS with IQEs close to 100% are now routinely fabricated in the green spectral region. There is also significant progress for blue emitters. However, red emitters still show relatively low efficiencies. Despite the significant progress that has been made in recent years, still significant challenges persist to achieve full understanding of the TADF mechanism and improve the stability of these materials. These questions need to be solved in order to fully implement TADF in OLEDs and expand their application to other areas. To date, TADF has been exploited mainly in the field of OLEDs, but applications in other areas, such as sensing and fluorescence microscopies, are envisaged. In this review, the photophysics of TADF molecules is discussed, summarising current methods to characterise these materials and the current understanding of the TADF mechanism in various molecular systems.

  1. From single molecule to single tubules

    NASA Astrophysics Data System (ADS)

    Guo, Chin-Lin

    2012-02-01

    Biological systems often make decisions upon conformational changes and assembly of single molecules. In vivo, epithelial cells (such as the mammary gland cells) can respond to extracellular matrix (ECM) molecules, type I collagen (COL), and switch their morphology from a lobular lumen (100-200 micron) to a tubular lumen (1mm-1cm). However, how cells make such a morphogenetic decision through interactions with each other and with COL is unclear. Using a temporal control of cell-ECM interaction, we find that epithelial cells, in response to a fine-tuned percentage of type I collagen (COL) in ECM, develop various linear patterns. Remarkably, these patterns allow cells to self-assemble into a tubule of length ˜ 1cm and diameter ˜ 400 micron in the liquid phase (i.e., scaffold-free conditions). In contrast with conventional thought, the linear patterns arise through bi-directional transmission of traction force, but not through diffusible biochemical factors secreted by cells. In turn, the transmission of force evokes a long-range (˜ 600 micron) intercellular mechanical interaction. A feedback effect is encountered when the mechanical interaction modifies cell positioning and COL alignment. Micro-patterning experiments further reveal that such a feedback is a novel cell-number-dependent, rich-get-richer process, which allows cells to integrate mechanical interactions into long-range (> 1mm) linear coordination. Our results suggest a mechanism cells can use to form and coordinate long-range tubular patterns, independent of those controlled by diffusible biochemical factors, and provide a new strategy to engineer/regenerate epithelial organs using scaffold-free self-assembly methods.

  2. Single molecule measurements and biological motors.

    PubMed

    Knight, Alex E; Mashanov, Gregory; Molloy, Justin E

    2005-12-01

    Recent technological advances in lasers and optical detectors have enabled a variety of new, single molecule technologies to be developed. Using intense and highly collimated laser light sources in addition to super-sensitive cameras, the fluorescence of single fluorophores can now be imaged in aqueous solution. Also, laser optical tweezers have enabled the piconewton forces produced by pair of interacting biomolecules to be measured directly. However, for a researcher new to the field to begin to use such techniques in their own research might seem a daunting prospect. Most of the equipment that is in use is custom-built. However, most of the equipment is essence fairly simple and the aim of this article is to provide an entry point to the field for a newcomer. It focuses mainly on those practical aspects which are not particularly well covered in the literature, and aims to provide an overview of the field as a whole with references and web links to more detailed sources elsewhere. Indeed, the opportunity to publish an article such as this on the Internet affords many new opportunities (and more space!) for presenting scientific ideas and information. For example, we have illustrated the nature of optical trap data with an interactive Java simulation; provided links to relevant web sites and technical documents, and included a large number of colour figures and plots. Our group's research focuses on molecular motors, and the bias of this article reflects this. It turns out that molecular motors have been a paradigm (or prototype) for single molecule research and the field has seen a rapid development in the techniques. It is hoped that the methods described here will be broadly applicable to other biological systems.

  3. Decomposition of Chemical Chain Molecules with Atmospheric Pressure Plasma

    NASA Astrophysics Data System (ADS)

    Tansli, Murat; Tasal, Erol

    2016-10-01

    Chemical chain molecules' decomposition is an interesting subject area for the atmospheric pressure plasma applications. The effects of the atmospheric pressure argon plasma on 4-((2-methoxyphenyl)Diazenyl)Benzene-1,3,-Diol molecule at room temperature are investigated. This molecule is one of the industrial dye molecules used widely. When considering the ecological life, this molecule will be very harmful and danger. We suggest a different, easy and useful decomposing method for such molecules. Atmospheric pressure plasma jet was principally treated for this decomposing of the molecule. Fourier transform infrared spectrometry (FT-IR) was used to characterization of the molecule after the plasma application to molecule in liquid phase with ethanol and methanol solvents. The atmospheric-pressure plasma jet of argon (Ar) as non-equilibrium has been formed by ac-power generator with frequency - 24 kHz and voltage - 12 kV. Characterizations for solutions prepared with ethanol and methanol solvents of molecule have been examined after applying (duration: 3 minutes) the atmospheric pressure plasma jet. The molecule was broken at 6C-7N =8N-9C stretching peak after the plasma treatment. The new plasma photo-products for ethanol and methanol solutions were produced as 6C-7N-8N =9C (strong, varying) and 12C =17O (strong, wide) stretching peaks.

  4. Rotational motion of a single water molecule in a buckyball.

    PubMed

    Farimani, A Barati; Wu, Yanbin; Aluru, N R

    2013-11-07

    Encapsulation of a single water molecule in a buckyball (C60) can provide fundamental insights into the properties of water. Investigation of a single water molecule is feasible through its solitary confinement in C60. In this paper, we performed a detailed study of the properties and dynamics of a single water molecule in a buckyball using DFT and MD simulations. We report on the enhancement of rotational diffusion and entropy of a water molecule in C60, compared to a bulk water molecule. H2O@C60 has zero translational diffusion and terahertz revolution frequency. The harmonic, high amplitude rotation of a single water molecule in C60 is compared to stochastic behavior of bulk water molecules. The combination of large rotational and negligible translational motion of water in C60 creates new opportunities in nanotechnology applications.

  5. Long-range effects in electron scattering by polar molecules

    NASA Astrophysics Data System (ADS)

    Fabrikant, Ilya I.

    2016-11-01

    We review long-range effects in electron collisions with polar molecules, starting with elastic scattering. We then go to rotationally and vibrationally inelastic processes and dissociative electron attachment. The last two are strongly affected by vibrational Feshbach resonances which have been observed and described theoretically in many systems from simple diatomic molecules to more complex polyatomics, biologically relevant molecules, and van der Waals clusters. We then review environmental effects which include electron interaction with molecules adsorbed on surfaces and molecules in cluster environments. We concentrate on physics rather than on listing results of ab initio calculations. With increasing complexity of targets and processes model approaches become more relevant. We demonstrate their success in the theoretical description of electron attachment to polyatomic molecules and to molecules in complex environments.

  6. Cooling molecules in a cell for FTMW spectroscopy

    NASA Astrophysics Data System (ADS)

    Patterson, David; Doyle, John M.

    2012-08-01

    Gas phase benzonitrile, acetone, 1-2 propanediol, fluorobenzene, and anisole molecules are produced in a cell at a temperature of 8 K, and detected via Fourier transform microwave spectroscopy (FTMW). Helium buffer gas is used to cool the molecules originating from a high flux room temperature beam. This general, continuous source of cold molecules offers comparable spectral resolution to existing seeded pulsed supersonic beam/FTMW spectroscopy experiments but with higher number sensitivity. It is also an attractive tool for quantitative studies of cold molecule-helium and molecule-molecule elastic and inelastic collisions. Preliminary data on helium-molecule low temperature rotational and vibrational relaxation cross-sections are presented. Applications of the technique as a sensitive broad spectrum mixture analyser and a high resolution slow-beam spectrometer are discussed.

  7. Atoms and Molecules Interacting with Light

    NASA Astrophysics Data System (ADS)

    van der Straten, Peter; Metcalf, Harold

    2016-02-01

    ; 15. The periodic system of the elements; Appendix 15. A paramagnetism; Appendix 15.B. The color of gold; 16. Molecules; Appendix 16.A. Morse potential; 17. Binding in the hydrogen molecule; Appendix 17.A. Confocal elliptical coordinates; Appendix 17.B. One-electron two-center integrals; Appendix 17.C. Electron-electron interaction in molecular hydrogen; 18. Ultra-cold chemistry; Part III. Applications: 19. Optical forces and laser cooling; 20. Confinement of neutral atoms; 21. Bose-Einstein condensation; Appendix 21.A. Distribution functions; Appendix 21.B. Density of states; 22. Cold molecules; 23. Three level systems; Appendix 23.A. General Case for _1 , _2; 24. Fundamental physics; Part IV. Appendices: Appendix A. Notation and definitions; Appendix B. Units and notation; Appendix C. Angular momentum in quantum mechanics; Appendix D. Transition strengths; References; Index.

  8. Dissociative Ionization of Aromatic and Heterocyclic Molecules

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    2003-01-01

    Space radiation poses a major health hazard to humans in space flight. The high-energy charged particles in space radiation ranging from protons to high atomic number, high-energy (HZE) particles, and the secondary species they produce, attack DNA, cells, and tissues. Of the potential hazards, long-term health effects such as carcinogenesis are likely linked to the DNA lesions caused by secondary electrons in the 1 - 30 eV range. Dissociative ionization (DI) is one of the electron collision processes that can damage the DNA, either directly by causing a DNA lesion, or indirectly by producing radicals and cations that attack the DNA. To understand this process, we have developed a theoretical model for DI. Our model makes use of the fact that electron motion is much faster than nuclear motion and assumes DI proceeds through a two-step process. The first step is electron-impact ionization resulting in a particular state of the molecular ion in the geometry of the neutral molecule. In the second step the ion undergoes unimolecular dissociation. Thus the DI cross section sigma(sup DI)(sub a) for channel a is given by sigma(sup DI)(sub a) = sigma(sup I)(sub a) P(sub D) with sigma(sup I)(sub a) the ionization cross section of channel a and P(sub D) the dissociation probability. This model has been applied to study the DI of H2O, NH3, and CH4, with results in good agreement with experiment. The ionization cross section sigma(sup I)(sub a) was calculated using the improved binary encounter-dipole model and the unimolecular dissociation probability P(sub D) obtained by following the minimum energy path determined by the gradients and Hessians of the electronic energy with respect to the nuclear coordinates of the ion. This model is used to study the DI from the low-lying channels of benzene and pyridine to understand the different product formation in aromatic and heterocyclic molecules. DI study of the DNA base thymine is underway. Solvent effects will also be discussed.

  9. Detection of Steps in Single Molecule Data

    PubMed Central

    Aggarwal, Tanuj; Materassi, Donatello; Davison, Robert; Hays, Thomas; Salapaka, Murti

    2013-01-01

    Over the past few decades, single molecule investigations employing optical tweezers, AFM and TIRF microscopy have revealed that molecular behaviors are typically characterized by discrete steps or events that follow changes in protein conformation. These events, that manifest as steps or jumps, are short-lived transitions between otherwise more stable molecular states. A major limiting factor in determining the size and timing of the steps is the noise introduced by the measurement system. To address this impediment to the analysis of single molecule behaviors, step detection algorithms incorporate large records of data and provide objective analysis. However, existing algorithms are mostly based on heuristics that are not reliable and lack objectivity. Most of these step detection methods require the user to supply parameters that inform the search for steps. They work well, only when the signal to noise ratio (SNR) is high and stepping speed is low. In this report, we have developed a novel step detection method that performs an objective analysis on the data without input parameters, and based only on the noise statistics. The noise levels and characteristics can be estimated from the data providing reliable results for much smaller SNR and higher stepping speeds. An iterative learning process drives the optimization of step-size distributions for data that has unimodal step-size distribution, and produces extremely low false positive outcomes and high accuracy in finding true steps. Our novel methodology, also uniquely incorporates compensation for the smoothing affects of probe dynamics. A mechanical measurement probe typically takes a finite time to respond to step changes, and when steps occur faster than the probe response time, the sharp step transitions are smoothed out and can obscure the step events. To address probe dynamics we accept a model for the dynamic behavior of the probe and invert it to reveal the steps. No other existing method addresses

  10. Searching for line active molecules on biphasic lipid monolayers.

    PubMed

    Bischof, Andrea Alejandra; Mangiarotti, Agustín; Wilke, Natalia

    2015-03-21

    In membranes with phase coexistence, line tension appears as an important parameter for the determination of the amount of domains, as well as their size and their shape, thus defining the membrane texture. Different molecules have been proposed as "linactants" (i.e. molecules that reduce the line tension, thereby modulating the membrane texture). In this work, we explore the efficiency of different molecules as linactants in monolayers with two coexisting phases of different thicknesses. We tested the linactant ability of a molecule with chains of different saturation degrees, another molecule with different chain lengths and a bulky molecule. In this way, we show in the same system the effect of molecules with chains of different rigidities, with an intrinsic thickness mismatch and with a bulky moiety, thereby analyzing different hypotheses of how a molecule may change the line tension in a monolayer system. Both lipids with different hydrocarbon chains did not act as linactants, while only one of the bulky molecules tested decreased the line tension in the monolayer studied. We conclude that there are no universal rules for the structure of a molecule that enable us to predict that it will behave as a linactant and thus, designing linactants appears to be a difficult task and a challenge for future studies. Furthermore, in regard to the membrane texture, there was no direct influence of the line tension in the distribution of domain sizes.

  11. Small molecule screening at Helmholtz Zentrum München - from biology to molecules.

    PubMed

    Schorpp, Kenji; Hadian, Kamyar

    2014-03-01

    Within the last few years the Helmholtz Zentrum München has established several initiatives enabling the translation of basic research results into discovery of novel small molecules that affect pathomechanisms of chronic and complex diseases. Here, one of the main operations is the Assay Development and Screening Platform (ADSP) that has state-of-the-art equipment for compound screening and provides knowledge in a variety of biochemical or cell-based phenotypic assays. In particular, ADSP has a strong focus on complex assays such as high-content screening in stem cells that are likely to provide an innovative approach complementary to biochemical assays for the discovery of novel small molecules modulating key biological processes.

  12. How surface interactions freeze polymer molecules at room temperature: a single molecule approach

    NASA Astrophysics Data System (ADS)

    Araújo, F. L.; Valente, G. T.; Faria, R. M.; Guimarães, F. E. G.

    2015-11-01

    The planar conformation assumed by polyfluorenes is used as a model system to investigate how solid surfaces interact with an individual polymer chain as well as to access the effects of substrates and interchain interactions on the polymer conformation. We demonstrate that confocal fluorescence microscopy is very sensitive to characterize photophysical processes associated to conformation assumed by a single conjugated unit of poly (9,9 dioctylfluorene) or PFO. Emissions from interacting molecules have been resolved for the first time between the energies of the planar (β phase) and the non-planar (amorphous) phase that were associated to perturbations of the primary chain conformation. But we have found the planar conformation is assumed by single PFO molecules due to strong interactions with the hydrophilic quartz surfaces. This PFO conformation persists frozen even at room temperature, although emission lines are significantly broadened due to interactions with vibrating substrate atoms.

  13. Quantum chemical predictions of the vibrational spectra of polyatomic molecules. The uracil molecule and two derivatives.

    PubMed

    Palafox, Mauricio Alcolea; Rastogi, V K

    2002-02-01

    This work describes the different scaling procedures used to correct the quantum-chemical theoretical predictions of the IR and Raman vibrational wavenumbers. Examples of each case are shown, with special attention to the uracil molecule and some derivatives. The results obtained with different semiempirical and ab initio methods, and basis sets, are compared and discussed. A comprehensive compendium of the main scale factors and scaling equations available to obtain the scaled wavenumbers is also shown.

  14. Single-Molecule Analysis of Chromatin: Changing the View of Genomes One Molecule at a Time

    PubMed Central

    Pondugula, Santhi; Kladde, Michael P.

    2010-01-01

    Wrapping DNA into chromatin provides a wealth of regulatory mechanisms that ensure normal growth and development in eukaryotes. Our understanding of chromatin structure, including nucleosomes and non-histone protein-DNA interactions, has benefited immensely from nuclease and chemical digestion techniques. DNA-bound proteins, such as histones or site-specific factors, protect DNA against nuclease cleavage and generate large nucleosomal or small regulatory factor footprints. Chromatin subject to distinct modes of regulation often coincides with sites of nuclease hypersensitivity or nucleosome positioning. An inherent limitation of cleavage-based analyses has been the inability to reliably analyze regions of interest when levels of digestion depart from single-hit kinetics. Moreover, cleavage-based techniques provide views that are averaged over all the molecules in a sample population. Therefore, in cases of occupancy of multiple regulatory elements by factors, one cannot define whether the factors are bound to the same or different molecules in the population. The recent development of DNA methyltransferase-based, single-molecule MAP-IT technology overcomes limitations of ensemble approaches and has opened numerous new avenues in chromatin research. Here, we review the strengths, limitations, applications and future prospects of MAP-IT ranging from structural issues to mechanistic questions in eukaryotic chromatin regulation. PMID:18615586

  15. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering

    NASA Astrophysics Data System (ADS)

    Kim, Jae-Yeol; Kim, Cheolhee; Lee, Nam Ki

    2015-04-01

    Single-molecule fluorescence resonance energy transfer (smFRET) is one of the powerful techniques for deciphering the dynamics of unsynchronized biomolecules. However, smFRET is limited in its temporal resolution for observing dynamics. Here, we report a novel method for observing real-time dynamics with submillisecond resolution by tethering molecules to freely diffusing 100-nm-sized liposomes. The observation time for a diffusing molecule is extended to 100 ms with a submillisecond resolution, which allows for direct analysis of the transition states from the FRET time trace using hidden Markov modelling. We measure transition rates of up to 1,500 s-1 between two conformers of a Holliday junction. The rapid diffusional migration of Deinococcus radiodurans single-stranded DNA-binding protein (SSB) on single-stranded DNA is resolved by FRET, faster than that of Escherichia coli SSB by an order of magnitude. Our approach is a powerful method for studying the dynamics and movements of biomolecules at submillisecond resolution.

  16. Direct visualization of single-molecule translocations through synthetic nanopores comparable in size to a molecule.

    PubMed

    Kurz, Volker; Nelson, Edward M; Shim, Jiwook; Timp, Gregory

    2013-05-28

    A nanopore is the ultimate analytical tool. It can be used to detect DNA, RNA, oligonucleotides, and proteins with submolecular sensitivity. This extreme sensitivity is derived from the electric signal associated with the occlusion that develops during the translocation of the analyte across a membrane through a pore immersed in electrolyte. A larger occluded volume results in an improvement in the signal-to-noise ratio, and so the pore geometry should be made comparable to the size of the target molecule. However, the pore geometry also affects the electric field, the charge density, the electro-osmotic flow, the capture volume, and the response time. Seeking an optimal pore geometry, we tracked the molecular motion in three dimensions with high resolution, visualizing with confocal microscopy the fluorescence associated with DNA translocating through nanopores with diameters comparable to the double helix, while simultaneously measuring the pore current. Measurements reveal single molecules translocating across the membrane through the pore commensurate with the observation of a current blockade. To explain the motion of the molecule near the pore, finite-element simulations were employed that account for diffusion, electrophoresis, and the electro-osmotic flow. According to this analysis, detection using a nanopore comparable in diameter to the double helix represents a compromise between sensitivity, capture volume, the minimum detectable concentration, and response time.

  17. Model-independent counting of molecules in single-molecule localization microscopy

    PubMed Central

    Hummer, Gerhard; Fricke, Franziska; Heilemann, Mike

    2016-01-01

    Most biomolecular processes rely on tightly controlled stoichiometries, from the formation of molecular assemblies to cellular signaling. Single-molecule localization micro­scopy studies of fluorophore blinking offer a promising route to probe oligomeric states. Here we show that the distribution of the number of blinking events assumes a universal functional form, independent of photophysics, under relatively mild assumptions. The number of photophysical states, the kinetics of interconversion, and the fraction of active fluorophores enter as two or three constants. This essentially model-independent formulation allows us to determine molecule counts from fluorophore blinking statistics. The formulas hold even if the fluorophores have many different yet unresolved dark states, as long as there is only a single fluorescent state, or if there are different yet unresolvable fluorescent states, as long as there is only a single dark state. We demonstrate the practical applicability of this approach by quantifying the oligomerization states of membrane proteins tagged with the mEos2 fluorescent protein. We find that the model parameters, obtained by likelihood maximization, are transferable. With the counting statistics being independent of the detailed photophysics and its parameters being transferable, the method should be robust and broadly applicable to counting colocalized molecules in vivo and in vitro. PMID:27466316

  18. Aurora kinase inhibitors as anticancer molecules.

    PubMed

    Katayama, Hiroshi; Sen, Subrata

    2010-01-01

    Aurora kinase family of serine/threonine kinases are important regulators of mitosis that are frequently over expressed in human cancers and have been implicated in oncogenic transformation including development of chromosomal instability in cancer cells. In humans, among the three members of the kinase family, Aurora-A, -B and -C, only Aurora-A and -B are expressed at detectable levels in all somatic cells undergoing mitotic cell division and have been characterized in greater detail for their involvement in cellular pathways relevant to the development of cancer associated phenotypes. Aurora-A and -B are being investigated as potential targets for anticancer therapy. Development of inhibitors against Aurora kinases as anticancer molecules gained attention because of the facts that aberrant expression of these kinases leads to chromosomal instability and derangement of multiple tumor suppressor and oncoprotein regulated pathways. Preclinical studies and early phase I and II clinical trials of multiple Aurora kinase inhibitors as targeted anticancer drugs have provided encouraging results. This article discusses functional involvement of Aurora kinase-A and -B in the regulation of cancer relevant cellular phenotypes together with findings on some of the better characterized Aurora kinase inhibitors in modulating the functional interactions of Aurora kinases. Future possibilities about developing next generation Aurora kinase inhibitors and their clinical utility as anticancer therapeutic drugs are also discussed.

  19. Transition metal catalyzed transformations of unsaturated molecules

    SciTech Connect

    Not Available

    1989-01-01

    In this proposal, research in three areas of transition metal catalyzed transformations of small molecules is proposed. The first encompasses metal catalyzed processes for the synthesis of several classes of carbon monoxide containing polymers. This section describes plans for metal catalyzed synthesis of (a) new alternating copolymers of carbon monoxide and olefins, (b) block copolymers consisting of segments of the olefin homopolymer and the olefin- carbon monoxide alternating copolymer, and (c) polycarbonates, polyesters and polyamides. The second section involves the examination of the chemistry of metal complexes incorporating oxo and hydrocarbyl ligands as a model for the heterogeneous oxidation of olefins and alkanes by meal oxides. Specific plans are to mimic in solution two proposed key steps in the heterogeneous oxidations. These are (a) the heterolytic cleavage of an alkyl (or allyl) C-H bond that is assisted by an oxo group, and (a) the transfer of an oxo group to the resultant metal bound alkyl (or allyl) ligand. The third section concerned with the development of a hybrid catalyst system involving both homogeneous and heterogeneous components for the oxidative functionalization of alkanes. The basic idea is to employ a transition metal in the elemental state to activate C-H bonds of alkanes and form surface alkyl groups. An additional transition metal species will be present in solution which will serve to oxidize these surface alkyl groups to ultimately yield oxidatively functionalized organic products. 57 refs.

  20. Perspective: Mechanochemistry of biological and synthetic molecules

    SciTech Connect

    Makarov, Dmitrii E.

    2016-01-21

    Coupling of mechanical forces and chemical transformations is central to the biophysics of molecular machines, polymer chemistry, fracture mechanics, tribology, and other disciplines. As a consequence, the same physical principles and theoretical models should be applicable in all of those fields; in fact, similar models have been invoked (and often repeatedly reinvented) to describe, for example, cell adhesion, dry and wet friction, propagation of cracks, and action of molecular motors. This perspective offers a unified view of these phenomena, described in terms of chemical kinetics with rates of elementary steps that are force dependent. The central question is then to describe how the rate of a chemical transformation (and its other measurable properties such as the transition path) depends on the applied force. I will describe physical models used to answer this question and compare them with experimental measurements, which employ single-molecule force spectroscopy and which become increasingly common. Multidimensionality of the underlying molecular energy landscapes and the ensuing frequent misalignment between chemical and mechanical coordinates result in a number of distinct scenarios, each showing a nontrivial force dependence of the reaction rate. I will discuss these scenarios, their commonness (or its lack), and the prospects for their experimental validation. Finally, I will discuss open issues in the field.

  1. Indexing molecules with chemical graph identifiers.

    PubMed

    Gregori-Puigjané, Elisabet; Garriga-Sust, Rut; Mestres, Jordi

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used.

  2. Hydrogen Molecules in SN 1987A

    NASA Technical Reports Server (NTRS)

    Culhane, Michael; McCray, Richard

    1995-01-01

    The observations of CO and SiO in the infrared spectrum of SN 1987A clearly indicate that molecules can form in the debris of a supernova explosion. Since H2 is not easily observable we compute its abundance theoretically. For conditions typical of the inner (v less than 2500 km/s) envelope of SN 1987A, the fraction of H that is in molecular form rises to approx. 1% by t approx. 800 days. For t less than 500 days the formation is dominated by the gas-phase reactions H + H(+) yields H2(+) + hv; H2(+) + H yields H2 + H(+). Thereafter, the formation is dominated by the reactions H + e yields H(-) + hv; H(-) + H yields H2 + e. At early times the H(-) may absorb approx. 10%-30% of visible photons, contributing to the apparent paucity of H alpha emission. For t greater than 1000 days the abundance of H2 'freezes out' due to the slowing of all reactions. The opacity of the supernova envelope in the range 912 less than lambda less than or approx. equal to 1400 A (the upper limit depending on temperature) is dominated by resonance scattering in the Lyman and Werner bands of H2. The resulting fluorescence emission bands of H2 in the range 1150 less than lambda less than 1650 A may be observable in the UV spectra of supernovae at late times.

  3. Database of small molecule thermochemistry for combustion.

    PubMed

    Goldsmith, C Franklin; Magoon, Gregory R; Green, William H

    2012-09-13

    High-accuracy ab initio thermochemistry is presented for 219 small molecules relevant in combustion chemistry, including many radical, biradical, and triplet species. These values are critical for accurate kinetic modeling. The RQCISD(T)/cc-PV∞QZ//B3LYP/6-311++G(d,p) method was used to compute the electronic energies. A bond additivity correction for this method has been developed to remove systematic errors in the enthalpy calculations, using the Active Thermochemical Tables as reference values. On the basis of comparison with the benchmark data, the 3σ uncertainty in the standard-state heat of formation is 0.9 kcal/mol, or within chemical accuracy. An uncertainty analysis is presented for the entropy and heat capacity. In many cases, the present values are the most accurate and comprehensive numbers available. The present work is compared to several published databases. In some cases, there are large discrepancies and errors in published databases; the present work helps to resolve these problems.

  4. Low Energy Ion-Molecule Reactions

    SciTech Connect

    James M. Farrar

    2004-05-01

    This objective of this project is to study the dynamics of the interactions of low energy ions important in combustion with small molecules in the gas phase and with liquid hydrocarbon surfaces. The first of these topics is a long-standing project in our laboratory devoted to probing the key features of potential energy surfaces that control chemical reactivity. The project provides detailed information on the utilization of specific forms of incident energy, the role of preferred reagent geometries, and the disposal of total reaction energy into product degrees of freedom. We employ crossed molecular beam methods under single collision conditions, at collision energies from below one eV to several eV, to probe potential surfaces over a broad range of distances and interaction energies. These studies allow us to test and validate dynamical models describing chemical reactivity. Measurements of energy and angular distributions of the reaction products with vibrational state resolution provide the key data for these studies. We employ the crossed beam low energy mass spectrometry methods that we have developed over the last several years.

  5. On SH Molecules in Umbral Spectra

    NASA Astrophysics Data System (ADS)

    Sinha, K.

    2015-11-01

    Following our predictions on detectability, very weak lines of the SH molecules have been reported as identified in the photospheric spectrum of the Sun. This could be the first detection of a mercapto radical in the solar spectrum, thus placing confidence in the solar abundance of sulfur. The observation additionally tested the theoretical band oscillator strength that was used. Because sunspots are cooler than the photosphere, they host a large number of molecular species. However, owing to photospheric radiation scattered into the observed umbra, no lines of SH were detected in the sunspot spectrum, where they are expected to show equivalent widths larger than those in the photosphere. Detection of weak lines in the photosphere coupled with a non-detection of the relatively strong same lines in the sunspot spectrum might raise doubts about the detection itself. We investigated the choice of photospheric and sunspot models and the microturbulence values that indicate that the predicted sunspot lines are about half as intense as reported before, and the lines remain detectable.

  6. Nonlinear optical spectroscopy of chiral molecules.

    PubMed

    Fischer, Peer; Hache, François

    2005-10-01

    We review nonlinear optical processes that are specific to chiral molecules in solution and on surfaces. In contrast to conventional natural optical activity phenomena, which depend linearly on the electric field strength of the optical field, we discuss how optical processes that are nonlinear (quadratic, cubic, and quartic) functions of the electromagnetic field strength may probe optically active centers and chiral vibrations. We show that nonlinear techniques open entirely new ways of exploring chirality in chemical and biological systems: The cubic processes give rise to nonlinear circular dichroism and nonlinear optical rotation and make it possible to observe dynamic chiral processes at ultrafast time scales. The quadratic second-harmonic and sum-frequency-generation phenomena and the quartic processes may arise entirely in the electric-dipole approximation and do not require the use of circularly polarized light to detect chirality. They provide surface selectivity and their observables can be relatively much larger than in linear optical activity. These processes also give rise to the generation of light at a new color, and in liquids this frequency conversion only occurs if the solution is optically active. We survey recent chiral nonlinear optical experiments and give examples of their application to problems of biophysical interest.

  7. Giant magnetoresistance through a single molecule.

    PubMed

    Schmaus, Stefan; Bagrets, Alexei; Nahas, Yasmine; Yamada, Toyo K; Bork, Annika; Bowen, Martin; Beaurepaire, Eric; Evers, Ferdinand; Wulfhekel, Wulf

    2011-03-01

    Magnetoresistance is a change in the resistance of a material system caused by an applied magnetic field. Giant magnetoresistance occurs in structures containing ferromagnetic contacts separated by a metallic non-magnetic spacer, and is now the basis of read heads for hard drives and for new forms of random access memory. Using an insulator (for example, a molecular thin film) rather than a metal as the spacer gives rise to tunnelling magnetoresistance, which typically produces a larger change in resistance for a given magnetic field strength, but also yields higher resistances, which are a disadvantage for real device operation. Here, we demonstrate giant magnetoresistance across a single, non-magnetic hydrogen phthalocyanine molecule contacted by the ferromagnetic tip of a scanning tunnelling microscope. We measure the magnetoresistance to be 60% and the conductance to be 0.26G(0), where G(0) is the quantum of conductance. Theoretical analysis identifies spin-dependent hybridization of molecular and electrode orbitals as the cause of the large magnetoresistance.

  8. Compactness Aromaticity of Atoms in Molecules

    PubMed Central

    Putz, Mihai V.

    2010-01-01

    A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively. PMID:20480020

  9. KK molecules with momentum-dependent interactions

    SciTech Connect

    Lemmer, R. H.

    2009-10-15

    It is shown that the momentum-dependent kaon-antikaon interactions generated via vector-meson exchange from the standard SU{sub V}(3)xSU{sub A}(3) interaction Lagrangian lead to a nonlocal potential in coordinate space that can be incorporated without approximation into a nonrelativistic version of the Bethe-Salpeter wave equation containing a radial-dependent effective kaon mass appearing in a fully symmetrized kinetic energy operator, in addition to a local potential. Estimates of the mass and decay widths of f{sub 0}(980) and a{sub 0}(980), considered as KK molecules of isospin 0 and 1, as well as for K{sup +}K{sup -} atomic bound states (kaonium) are presented and compared with previous studies of a similar nature. It is argued that without a better knowledge of hadronic form factors it is not possible to distinguish between the molecular versus elementary particle models for the structure of the light scalar mesons.

  10. Single-molecule mechanics of mussel adhesion

    NASA Astrophysics Data System (ADS)

    Lee, Haeshin; Scherer, Norbert F.; Messersmith, Phillip B.

    2006-08-01

    The glue proteins secreted by marine mussels bind strongly to virtually all inorganic and organic surfaces in aqueous environments in which most adhesives function poorly. Studies of these functionally unique proteins have revealed the presence of the unusual amino acid 3,4-dihydroxy-L-phenylalanine (dopa), which is formed by posttranslational modification of tyrosine. However, the detailed binding mechanisms of dopa remain unknown, and the chemical basis for mussels' ability to adhere to both inorganic and organic surfaces has never been fully explained. Herein, we report a single-molecule study of the substrate and oxidation-dependent adhesive properties of dopa. Atomic force microscopy (AFM) measurements of a single dopa residue contacting a wet metal oxide surface reveal a surprisingly high strength yet fully reversible, noncovalent interaction. The magnitude of the bond dissociation energy as well as the inability to observe this interaction with tyrosine suggests that dopa is critical to adhesion and that the binding mechanism is not hydrogen bond formation. Oxidation of dopa, as occurs during curing of the secreted mussel glue, dramatically reduces the strength of the interaction to metal oxide but results in high strength irreversible covalent bond formation to an organic surface. A new picture of the interfacial adhesive role of dopa emerges from these studies, in which dopa exploits a remarkable combination of high strength and chemical multifunctionality to accomplish adhesion to substrates of widely varying composition from organic to metallic. 3,4-dihydroxylphenylalanine | atomic force microscopy | mussel adhesive protein

  11. NMR quantum computation with optically polarized molecules

    NASA Astrophysics Data System (ADS)

    Verhulst, Anne; Yannoni, Constantino; Sherwood, Mark; Pomerantz, Drew; Vandersypen, Lieven; Chuang, Isaac

    2000-03-01

    Current methods for bulk NMR quantum computation rely on nuclear spin polarization present at high temperature equilibrium. This presents a challenging obstacle as the probability to find a spin in a specific state decreases exponentially in the number of spins used as qubits, causing a corresponding decrease in the signal to noise ratio of the desired NMR signal. One way to address this problem is to provide an artificial source of high polarization, such as optically pumped ^129Xe. For comparison, thermal equilibrium polarizations are only about 10-3% for ^1H in a typical NMR experiment at room temperature and in a 10 Tesla magnetic field, but with ^129Xe polarizations as high as 18% have been achieved [Happer et. al., Chem.Phys.Lett., 284, p.87-92, Feb 1998]. Using this technique, we prepare hyperpolarized liquid Xe and use it as a solvent for chloroform molecules (CHCl_3). Cross polarization (SPINOE) between ^129Xe and ^1H results in measured enhancements of the proton signal of over 300%, and evidence of transfer to ^13C. These results provide hope for the scalability of quantum computation.

  12. Selection of Prebiotic Molecules in Amphiphilic Environments

    PubMed Central

    Mayer, Christian; Schreiber, Ulrich; Dávila, María J.

    2017-01-01

    A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments. PMID:28067845

  13. Water: one molecule, two surfaces, one mistake

    NASA Astrophysics Data System (ADS)

    Vega, Carlos

    2015-05-01

    In order to rigorously evaluate the energy and dipole moment of a certain configuration of molecules, one needs to solve the Schrödinger equation. Repeating this for many different configurations allows one to determine the potential energy surface (PES) and the dipole moment surface (DMS). Since the early days of computer simulation, it has been implicitly accepted that for empirical potentials the charges used to fit the PES should also be used to describe the DMS. This is a mistake. Partial charges are not observable magnitudes. They should be regarded as adjustable fitting parameters. Optimal values used to describe the PES are not necessarily the best to describe the DMS. One could use two fits: one for the PES and the other for the DMS. This is a common practice in the quantum chemistry community, but not used so often by the community performing computer simulations. This idea affects all types of modelling of water (with the exception of ab initio calculations) from coarse-grained to non-polarisable and polarisable models. We anticipate that an area that will benefit dramatically from having both, a good PES and a good DMS, is the modelling of water in the presence of electric fields.

  14. Organization of 'nanocrystal molecules' using DNA

    NASA Astrophysics Data System (ADS)

    Alivisatos, A. Paul; Johnsson, Kai P.; Peng, Xiaogang; Wilson, Troy E.; Loweth, Colin J.; Bruchez, Marcel P.; Schultz, Peter G.

    1996-08-01

    PATTERNING matter on the nanometre scale is an important objective of current materials chemistry and physics. It is driven by both the need to further miniaturize electronic components and the fact that at the nanometre scale, materials properties are strongly size-dependent and thus can be tuned sensitively1. In nanoscale crystals, quantum size effects and the large number of surface atoms influence the, chemical, electronic, magnetic and optical behaviour2-4. 'Top-down' (for example, lithographic) methods for nanoscale manipulation reach only to the upper end of the nanometre regime5; but whereas 'bottom-up' wet chemical techniques allow for the preparation of mono-disperse, defect-free crystallites just 1-10 nm in size6-10, ways to control the structure of nanocrystal assemblies are scarce. Here we describe a strategy for the synthesis of'nanocrystal molecules', in which discrete numbers of gold nanocrystals are organized into spatially defined structures based on Watson-Crick base-pairing interactions. We attach single-stranded DNA oligonucleotides of defined length and sequence to individual nanocrystals, and these assemble into dimers and trimers on addition of a complementary single-stranded DNA template. We anticipate that this approach should allow the construction of more complex two-and three-dimensional assemblies.

  15. Geometric Phases in Single Molecule Magnets

    NASA Astrophysics Data System (ADS)

    Fenochio, Brian Canchola

    The characterization of the material properties of Single Molecule Magnets (SMMs) has grown in importance over the last few decades with the rise of novel applications such as high-density magnetic storage and quantum computation. Many of the applications require the probing of SMMs with spectroscopic methods that make use of electromagnetic radiation. The interaction with these time-dependent fields leads to energy shifts, which can be attributed to the geometric phase acquired by the system or the Bloch-Siegert shift. We model an SMM by a giant spin Hamiltonian, and use Floquet perturbation theory to find the geometric phase shifts. The locations where the phase shift between two levels is zero is useful for performing accurate spectroscopies, whereas the regions where relative phase differences exist are useful in applications like quantum computing. Using the same giant spin Hamiltonian, we can use Floquet theory and Salwen perturbation theory to determine the Bloch-Siegert shift and derive a modified version of the Rabi formula for transition probabilities between the energy states Ealpha → Ealpha+/-1, Ealpha → Ealpha+/-3, and Ealpha → Ealpha+/-5 , where alpha is the index of an arbitrary initial state. The shifted eigenvalues and modified transition probabilities can be useful in spectroscopies where accurate values for the energy-splitting between magnetic states needs to be determined.

  16. Controlled Tethering Molecules via Crystal Surface Engineering

    NASA Astrophysics Data System (ADS)

    Cheng, Stephen Z. D.; Zheng, Joseph X.; Chen, William Y.

    2004-03-01

    So far, almost all experiments in tethering chain molecules onto substrates are via "grafting to" or "grafting from" polymerizations in addition to physical absorption. Issues concerning the uniformity of the tethered chain density and the molecular weight distribution of the chains tethered by polymerization always undermine the properties experimentally observed. We proposed a novel design to precisely control the tethering density of polystyrene (PS) brushes on a poly(ethylene oxide) (PEO) or a poly(L-lactic acid) (PLLA) lamellar crystal basal surface using PEO-b-PS or PLLA-b-PS diblock copolymers. As the crystallization temperature (Tc) increased in either a PEO-b-PS/mixed solution (chrolobenzene/octane) or a PLLA-b-PS/amyl acetate solution, the PEO or PLLA lamellar thickness (d) increased, and correspondingly, the number of folds per PEO or PLLA block was reduced. The reduced tethered density (Σ*) of the PS brushes thus increased. At an onset where the PS brushes are overcrowded within the solution, a drastic slope change in the relationship between (d)-1 and Tc occurs in both cases at a Σ* between 3 - 4. This illustrates that the weak to intermediate interaction changes of the PS brushes with their neighbors may be universally represented.

  17. Molecules to migration: pressures of life.

    PubMed

    Vosloo, André

    2010-01-01

    The highly successful Fourth International Conference in Africa for Comparative Physiology and Biochemistry (ICA-CPB) was held in the Maasai Mara National Reserve in July 2008. The theme of the meeting was "Molecules to Migration: Pressures of Life." To enhance the theme, the venue and timing of the meeting were chosen to coincide with the arrival of approximately 1.4 million wildebeest on their annual migration from the Serengeti National Park in Tanzania. Like the three previous ICA-CPB meetings, the discussion topics and the resulting collection of synthesia presented here were very diverse. The articles in this special collection reflect the authors' interest in broadening our understanding of the field of comparative physiology and biochemistry and their commitment to engaging in global research with international colleagues. These articles are brief, synthetic reviews integrating information presented at and inspired by the meeting. From seasonal migration and reproduction in birds, to cardiovascular system development in vertebrates, to strategies for hypoxia survival, papers range from specific to broad interactions. What they all have in common: they increase our understanding of how animals are affected by and respond to the pressures of life.

  18. Quantum Monte Carlo for atoms and molecules

    SciTech Connect

    Barnett, R.N.

    1989-11-01

    The diffusion quantum Monte Carlo with fixed nodes (QMC) approach has been employed in studying energy-eigenstates for 1--4 electron systems. Previous work employing the diffusion QMC technique yielded energies of high quality for H{sub 2}, LiH, Li{sub 2}, and H{sub 2}O. Here, the range of calculations with this new approach has been extended to include additional first-row atoms and molecules. In addition, improvements in the previously computed fixed-node energies of LiH, Li{sub 2}, and H{sub 2}O have been obtained using more accurate trial functions. All computations were performed within, but are not limited to, the Born-Oppenheimer approximation. In our computations, the effects of variation of Monte Carlo parameters on the QMC solution of the Schroedinger equation were studied extensively. These parameters include the time step, renormalization time and nodal structure. These studies have been very useful in determining which choices of such parameters will yield accurate QMC energies most efficiently. Generally, very accurate energies (90--100% of the correlation energy is obtained) have been computed with single-determinant trail functions multiplied by simple correlation functions. Improvements in accuracy should be readily obtained using more complex trial functions.

  19. Glucose sensing molecules having selected fluorescent properties

    DOEpatents

    Satcher, Jr., Joe H.; Lane, Stephen M.; Darrow, Christopher B.; Cary, Douglas R.; Tran, Joe Anh

    2004-01-27

    An analyte sensing fluorescent molecule that employs intramolecular electron transfer is designed to exhibit selected fluorescent properties in the presence of analytes such as saccharides. The selected fluorescent properties include excitation wavelength, emission wavelength, fluorescence lifetime, quantum yield, photostability, solubility, and temperature or pH sensitivity. The compound comprises an aryl or a substituted phenyl boronic acid that acts as a substrate recognition component, a fluorescence switch component, and a fluorophore. The fluorophore and switch component are selected such that the value of the free energy for electron transfer is less than about 3.0 kcal mol.sup.-1. Fluorescent compounds are described that are excited at wavelengths greater than 400 nm and emit at wavelengths greater than 450 nm, which is advantageous for optical transmission through skin. The fluorophore is typically selected from transition metal-ligand complexes and thiazine, oxazine, oxazone, or oxazine-one as well as anthracene compounds. The fluorescent compound can be immobilized in a glucose permeable biocompatible polymer matrix that is implantable below the skin.

  20. Spectroscopy of ultracold trapped cesium Feshbach molecules

    SciTech Connect

    Mark, M.; Knoop, S.; Danzl, J. G.; Kraemer, T.; Naegerl, H.-C.; Ferlaino, F.; Chin, C.; Grimm, R.

    2007-10-15

    We explore the rich internal structure of Cs{sub 2} Feshbach molecules. Pure ultracold molecular samples are prepared in a CO{sub 2}-laser trap, and a multitude of weakly bound states is populated by elaborate magnetic-field ramping techniques. Our methods use different Feshbach resonances as input ports and various internal level crossings for controlled state transfer. We populate higher partial-wave states of up to eight units of rotational angular momentum (l-wave states). We investigate the molecular structure by measurements of the magnetic moments for various states. Avoided level crossings between different molecular states are characterized through the changes in magnetic moment and by a Landau-Zener tunneling method. Based on microwave spectroscopy, we present a precise measurement of the magnetic-field-dependent binding energy of the weakly bound s-wave state that is responsible for the large background scattering length of Cs. This state is of particular interest because of its quantum-halo character.