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Sample records for non-polar spiropyran molecules

  1. Light- and Solvent-Controlled Self-Assembly Behavior of Spiropyran-Polyoxometalate-Alkyl Hybrid Molecules.

    Science.gov (United States)

    Chu, Yang; Saad, Ali; Yin, Panchao; Wu, Jiayingzi; Oms, Olivier; Dolbecq, Anne; Mialane, Pierre; Liu, Tianbo

    2016-08-08

    A molecular photochromic spiropyran-polyoxometalate-alkyl organic-inorganic hybrid has been synthesized and fully characterized. The reversible switching of the hydrophobic spiropyran fragment to the hydrophilic merocyanine one can be easily achieved under light irradiation at different wavelengths. This switch changes the amphiphilic feature of the hybrid, leading to a light-controlled self-assembly behavior in solution. It has been shown that the hybrid can reversibly self-assemble into vesicles in polar solvents and irreversibly into reverse vesicles in non-polar solvents. The sizes of the vesicles and the reverse vesicles are both tunable by the polarity of the solvent, with the hydrophobic interactions being the main driving force.

  2. Rotational Diffusion of a New Large Non Polar Dye Molecule in Alkanes.

    Science.gov (United States)

    Goudar, Radha; Gupta, Ritu; Kulkarni, Giridhar U; Inamdar, Sanjeev R

    2015-11-01

    Rotational reorientation times of a newly synthesized 2,5-bis(phenylethynyl)1,4-bis(dodecyloxy) benzene (DDPE) are experimentally determined in series of n-alkanes by employing steady state and time resolved fluorescence depolarization technique with a view to understand rotational dynamics of large non-polar solute molecule in non-polar solvents and few general solvents of different sizes and varying viscosity. It is observed that rotational reorientation times vary linearly as function of viscosity. The hydrodynamic stick condition describes the experimental results at low viscosities while the results tend to deviate significantly from it at higher viscosities. This is attributed to the possibility of long chains in solvents hosting a variety of chain defects (end-gauche, double-gauche, all-trans, kink, etc.) thereby reducing the effective length of the molecule, leading to a slightly reduced friction. The experimental results are compared with the predictions of Stokes-Einstein-Debye (SED) hydrodynamic theory as well as the quasi-hydrodynamic theories of Gierer-Wirtz (GW) and Dote-Kivelson-Shwartz (DKS). The predictions from these theories underestimate τr in the solvents employed in the study.

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

    CERN Document Server

    Agundez, M; de Vicente, P; Marcelino, N; Roueff, E; Fuente, A; Gerin, M; Guelin, M; Albo, C; Barcia, A; Barbas, L; Bolano, R; Colomer, F; Diez, M C; Gallego, J D; Gomez-Gonzalez, J; Lopez-Fernandez, I; Lopez-Fernandez, J A; Lopez-Perez, J A; Malo, I; Serna, J M; Tercero, F

    2015-01-01

    Cyanogen (NCCN) is the simplest member of the series of dicyanopolyynes. It has been hypothesized that this family of molecules can be important constituents of interstellar and circumstellar media, although the lack of a permanent electric dipole moment prevents its detection through radioastronomical techniques. Here we present the first solid evidence of the presence of cyanogen in interstellar clouds through the detection of its protonated form toward the cold dark clouds TMC-1 and L483. Protonated cyanogen (NCCNH+) has been identified through the J=5-4 and J=10-9 rotational transitions using the 40m radiotelescope of Yebes and the IRAM 30m telescope. We derive beam averaged column densities for NCCNH+ of (8.6+/-4.4)e10 cm-2 in TMC-1 and (3.9+/-1.8)e10 cm-2 in L483, which translate to fairly low fractional abundances relative to H2, in the range (1-10)e-12. The chemistry of protonated molecules in dark clouds is discussed, and it is found that, in general terms, the abundance ratio between the protonated ...

  4. Synthesis of New Spiropyrans With a Polyaromatic or Heteroaromatic Pendant and Their Photochromic Behaviors

    Institute of Scientific and Technical Information of China (English)

    PANG,Mei-Li(庞美丽); NIE,Yun-Tong(聂云艟); WANG,Yong-Mei(王永梅); MENG,Ji-Ben(孟继本); WANG,Ji-Tao(王积涛)

    2002-01-01

    A series of spiropyrans with a polyaromatic or heteroaromatic pendant was synthesized conveniently. Their photochromic behaviors were investigated with the aid of absorption spectral measurements. The results indicated that the compounds with the same parent spiropyran but different armmaaic pendant show significantly different photochromic properties. This may be due to the π-π orbital interaction between the polyaronatic pendant and the open photomerocyanine form of spiropyran.The results obtained are very useful in the molecule design area.

  5. Synthesis of New Spiropyrans With a Polyaromatic or Heteroaromatic Pendant and Their Photochromic Bedhaviors

    Institute of Scientific and Technical Information of China (English)

    庞美丽; 聂云艟; 王永梅; 孟继本; 王积涛

    2002-01-01

    A series of spiropyrans with a polyaromatic or heteroaromatic pendant was synthesized conveniently.Their photochromic behaviors were investigated with the aid of absorption spectral measurements.The results indicated that the compounds with the same parent spiropyran but different aromatic pendant show significantly different photochromic properties.This may be due to the π-π orbital interaction between the polyaromatic pendant and the open photomerocyanine form of spiropyran.The results obtained are very useful in the molecule design area.

  6. The influence of non polar and polar molecules in mouse motile cells membranes and pure lipid bilayers.

    Directory of Open Access Journals (Sweden)

    Francisco J Sierra-Valdez

    Full Text Available We report an experimental study of mouse sperm motility that shows chief aspects characteristic of neurons: the anesthetic (produced by tetracaine and excitatory (produced by either caffeine or calcium effects and their antagonic action. While tetracaine inhibits sperm motility and caffeine has an excitatory action, the combination of these two substances balance the effects, producing a motility quite similar to that of control cells. We also study the effects of these agents (anesthetic and excitatory on the melting points of pure lipid liposomes constituted by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC and dipalmitoyl phosphatidic acid (DPPA. Tetracaine induces a large fluidization of the membrane, shifting the liposomes melting transition temperature to much lower values. The effect of caffeine is null, but its addition to tetracaine-doped liposomes greatly screen the fluidization effect. A high calcium concentration stiffens pure lipid membranes and strongly reduces the effect of tetracaine. Molecular Dynamics Simulations are performed to further understand our experimental findings at the molecular level. We find a strong correlation between the effect of antagonic molecules that could explain how the mechanical properties suitable for normal cell functioning are affected and recovered.

  7. Synthesis of novel chalcone derivatives and their stabilization effect of spiropyran in PMMA films

    Institute of Scientific and Technical Information of China (English)

    Zheng Kai Si; Qing Zhang; Min Zhao Xue; Yuan Yuan Zhu; Liang Ming; Qiao Rong Sheng; Yan Gang Liu

    2011-01-01

    Three novel bis-chalcone derivatives with different alkyldioxy spacers were synthesized and dispersed into polymethyl methacrylate (PMMA) chloroform solution with 6-nitro-1'-ethyl-3',3'-dimethylspiro-2H-1-benzopyran-2,2'-indoline (ESP) to prepare photochromic PMMA films in a facile way. After irradiation with 365 nm UV light, the photocrosslinking reaction between chalcone units was proved to retard the decolorization of merocyanine form of the photochromic spiropyran effectively, as results of the steric hindrance produced by photocycloaddition of chalcone groups. It has been found that the bis-chalcone molecule with the shortest spacer has the most effective stabilizing effect on retardation of decoloration of spiropyran.

  8. Spiropyrans Containing the Reactive Substituents in the 2H-Chromene Moiety

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    B. S. Lukyanov

    2007-01-01

    Full Text Available Some spiropyrans containing functional substituents in the [2H]-chromene part of the molecule were synthesized and their photochromic properties in solution and solid state were investigated. The presence of the formyl group in the [2H]-chromene fragment enhances the possibility to show photochromic properties in solution.

  9. Two-Photon-Induced Isomerization of Spiropyran/Merocyanine at the Air/Water Interface Probed by Second Harmonic Generation.

    Science.gov (United States)

    Lin, Lu; Zhang, Zhen; Lu, Zhou; Guo, Yuan; Liu, Minghua

    2016-10-13

    Photochromic molecules often exhibit switchable hyperpolarizabilities upon photoisomerization between two molecular states and can be widely applied in nonlinear optical materials. Photoisomerization can occur through either one-photon or two-photon processes. Two-photon-induced isomerization has several advantages over one-photon process but has not been fully explored. In the present study, we have used second harmonic generation to investigate the two-photon-induced isomerization between spiropyran and merocyanine at the air/water interface. We show that spiropyran and merocyanine can be converted into each other reversibly with 780-nm laser-beam irradiation through two-photon processes. We also investigated the isomerization rates under various incident laser powers. Quantitative analysis revealed that the isomerization rates of spiropyran and merocyanine depend differently on the laser power. We attribute the difference to the distinct molecular structures of spiropyran and merocyanine. At the interface, nonplanar spiropyran molecules exist mainly as monomers, whereas planar merocyanine molecules form aggregates. Upon aggregation, steric hindrance effects and excitonic coupling efficiently arrest the photoisomerization of merocyanine. This work provides an in-depth understanding of two-photon-induced isomerization at the interface, which is beneficial for designing and controlling optical thin-film materials.

  10. Reversible negative photochromic sulfo-substituted spiropyrans

    Science.gov (United States)

    Gao, Hongqi; Guo, Tianqi; Chen, Yun; Kong, Yangyang; Peng, Zhihong

    2016-11-01

    A series of sulfonyl-containing spiropyrans exhibiting negative photochromism were designed and synthesized. The prepared compounds show more stability for the brightly colored state in the dark-adapted than the colorless state under visible irradiation. Negative photochromic properties and fatigue resistance of these compounds in solution were confirmed by UV spectroscopy with time variation. Single-crystal X-ray diffraction analysis, NMR and variable-time absorption spectra studies suggest that the negative photochromism of the compounds involved a ring-opening spiro Csbnd O bond cleavage of the spiropyran followed by an intramolecular proton transfer.

  11. Structure and photochromism of spiropyran assemblies

    Institute of Scientific and Technical Information of China (English)

    杜祖亮; 赵伟利; 马晓东; 朱自强; 明阳福; 樊美公; 吕安德

    1995-01-01

    Nanocluster assemblies of spiropyran compounds have been prepared by means of LB technique, and the relations between the subphase, pH value, condition of preparation and the structure of the fabricated LB film are systematically investigated. The stability, photochromic fatigue properties of the spiropyran LB film, which are of primary importance in optic signal storage applications, are also studied in detail. A kind of supermolecular film with homogeneously distributed J aggregates of similar granular size has been obtained with the optical resolution in the order of micrometer. Finally, a nondestructive readout method for such an LB film to be used as the optic signal storage film is proposed.

  12. Photo-response behavior of electrospun nanofibers based on spiropyran-cyclodextrin modified polymer†

    Science.gov (United States)

    De Sousa, Frederico B.; Guerreiro, João D. T.; Ma, Minglin; Anderson, Daniel G.; Drum, Chester L.; Sinisterra, Rubén D.; Langer, Robert

    2017-01-01

    Tunable and durable photochromic materials are a rapidly expanding area of interest, with applications ranging from biomedical devices to industrial-fields. Here we examine electrospun poly (methacrylic acid) PMAA nanofibers covalently modified with the highly photochromic molecule, spiropyran (SP) or a derivate SP which is firstly coupled to a cyclodextrin molecule (βCDSP). The photochromic properties of the starting materials and of the nanofibers were investigated. βCDSP, PMAASP and PMAA-βCDSP polymers exhibited a reverse photochromism. The kinetic results revealed a faster isomerization process for the βCDSP molecule, than that for the PMAA-βCDSP and for the PMAASP, the slowest one. The fastest isomerization is attributed to the presence of a large number of hydroxyl groups of the βCD which stabilizes the merocyanine form via hydrogen bonding, and the slowest isomerization is related to the PMAA chain structure that stabilizes the spiropyran form. Thus, combining the PMAA and βCD properties the photo-isomerization can be modulated. The photoreversibility of this material was verified by UV-visible measurements cycling visible and UV light. Infrared spectroscopy and water contact angle were used for the nanofiber surface characterization, demonstrating the presence of the spiropyran on the mats surface and also showing a minimal effect on nanofiber size and shape when compared to PMAA fiber.

  13. A Structural Analysis of Spiropyran and Spirooxazine Compounds and Their Polymorphs

    Directory of Open Access Journals (Sweden)

    Vanessa Kristina Seiler

    2017-03-01

    Full Text Available In this work, crystal structures of commercially available photochromic compounds, i.e., spiropyrans and spirooxazines, were investigated by single-crystal X-ray diffraction. A total of five new structures were obtained via isothermal evaporation experiments under different conditions, namely 1,3,3-Trimethylindolino-benzopyrylospiran (I, 1,3,3-Trimethylindolinonaphtospirooxaxine (II, 1-(2-Hydroxyethyl-3,3-dimethylindolino-6′-nitrobenzopyrylospiran (III, and 1,3,3-Trimethylindolino-8′-methoxybenzopyrylospiran (IVa and IVb. Since the basic structure of a spiropyran/-oxazine does not present typical hydrogen bond accepting and donating groups, this study illustrates the importance of additional functional groups connected to this kind of molecules to induce specific intermolecular interactions. Our results show that possible hydrogen bonding interactions are rather weak due to the high steric demand of these compounds. These results are supported by a search of the Cambridge structural database focused on related structures.

  14. Photoinduced variable stiffness of spiropyran-based composites

    Energy Technology Data Exchange (ETDEWEB)

    Samoylova, E.; Ceseracciu, L.; Allione, M.; Diaspro, A.; Barone, A. C. [Istituto Italiano di Tecnologia, via Morego 30, Genova I-16163 (Italy); Athanassiou, A. [Istituto Italiano di Tecnologia, via Morego 30, Genova I-16163 (Italy); Center for Biomolecular Nanotechnologies-Unile, Istituto Italiano di Tecnologia, via Barsanti, Arnesano (Lecce) I-73010 (Italy)

    2011-11-14

    A quantitative demonstration of reversible stiffness upon appropriate light stimulus in a spiropyran-polymeric composite is presented. The polymeric films containing 3% wt. of the photochromic spiropyran were irradiated with alternating ultraviolet and visible light and the storage modulus was measured. A reversible change in modulus of about 7% was observed. The modulus change was attributed to an interaction of the polar merocyanine with the polymeric chains and/or to a variation of effective free volume induced by merocyanine aggregates formed in the polymer upon ultraviolet irradiation. The effect is fully reversed when the merocyanine isomers turn back to the spiropyran state after visible irradiation.

  15. Dynamics of a photochromic spiropyran under aqueous conditions

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    Heckel A.

    2013-03-01

    Full Text Available The dynamics of a water soluble spiropyran is investigated by means of femtosecond transient absorption spectroscopy in the visible and infrared spectral range revealing an ultrafast reversible switching behavior under aqueous conditions with a high fatigue resistance.

  16. Interactions of a Photochromic Spiropyran with Liposome Model Membranes

    KAUST Repository

    Jonsson, Fabian

    2013-02-19

    The interactions between anionic or zwitterionic liposomes and a water-soluble, DNA-binding photochromic spiropyran are studied using UV/vis absorption and linear dichroism (LD) spectroscopy. The spectral characteristics as well as the kinetics of the thermal isomerization process in the absence and presence of the two different liposome types provide information about the environment and whether or not the spiropyran resides in the liposome membrane. By measuring LD on liposomes deformed and aligned by shear flow, further insight is obtained about interaction and binding geometry of the spiropyran at the lipid membranes. We show that the membrane interactions differ between the two types of liposomes used as well as the isomeric forms of the spiropyran photoswitch. © 2013 American Chemical Society.

  17. Spiropyran main-chain conjugated polymers.

    Science.gov (United States)

    Sommer, Michael; Komber, Hartmut

    2013-01-11

    The first main-chain conjugated copolymers based on alternating spiropyran (SP) and 9,9-dioctylfluorene (F8) units synthesized via Suzuki polycondensation (SPC) are presented. The reaction conditions of SPC are optimized to obtain materials of type P(para-SP-F8) with appreciably high molecular weights up to M(w) ≈ 100 kg mol(-1). (13)C NMR is used to identify the random orientation of the non-symmetric SP unit in P(p-SP-F8). Ultrasound-induced isomerization of P(p-SP-F8) to the corresponding merocyanine form P(p-MC-F8) yields a deep-red solution. This isomerization reaction is followed by (1)H NMR in solution using sonication, whereby the color increasingly changes to deep red. The possibility to incorporate multiple SP units into main-chain polymers significantly broadens existing SP-based polymeric architectures.

  18. Birefringent non-polarizing thin film design

    Institute of Scientific and Technical Information of China (English)

    QI Hongji; HONG Ruijin; HE Hongbo; SHAO Jianda; FAN Zhengxiu

    2005-01-01

    In this paper, 2×2 characteristic matrices of uniaxially anisotropic thin film for extraordinary and ordinary wave are deduced at oblique incidence. Furthermore, the reflectance and transmittance of thin films are calculated separately for two polarizations, which provide a new concept for designing non-polarizing thin films at oblique incidence. Besides, using the multilayer birefringent thin films, non-polarizing designs, such as beam splitter thin film at single wavelength, edge filter and antireflection thin film over visible spectral region are obtained at oblique incidence.

  19. Fluorescence Resonance Energy Transfer Using Spiropyran and Diarylethene Photochromic Acceptors

    Directory of Open Access Journals (Sweden)

    E. A. Jares-Erijman

    2000-03-01

    Full Text Available We describe the preparation and photophysical characterization of two model compounds designed to test a new approach for the quantitative determination of Fluorescence Resonance Energy Transfer (FRET in biological systems. The method enables modulation of FRET by exploiting the unique reversible spectral properties of photochromic diarylethenes and spiropyrans to create switchable energy acceptors.

  20. Oxidative electrochemical aryl C-C coupling of spiropyrans

    NARCIS (Netherlands)

    Ivashenko, Oleksii; van Herpt, Jochem T.; Rudolf, Petra; Feringa, Ben L.; Browne, Wesley R.

    2013-01-01

    The isolation and definitive assignment of the species formed upon electrochemical oxidation of nitro-spiropyran (SP) is reported. The oxidative aryl C-C coupling at the indoline moiety of the SP radical cation to form covalent dimers of the ring-closed SP form is demonstrated. The coupling is block

  1. Applications of Spiropyran Derivatives in Analytical Chemistry%螺吡喃化合物在分析化学中的应用

    Institute of Scientific and Technical Information of China (English)

    邵娜; 张向媛; 杨荣华

    2011-01-01

    Spiropyrans, an important class of photochromic compounds that undergo reversible structural isomerization between a colorless spiropyran form and a colored merocyanine, are an attractive starting point in constructions of molecular-level devices with molecular recognition function and signal transduction ability due to their unique molecule binding ability and signal transduction function. The merocyanine may interact with their environment (solvent or matrix) leading to different photochromic responses. By exploiting such characteristics,spiropyrans have been employed not only in materials chemistry for molecular switches, but also in analytical chemistry as molecular sensors. During the past decades, a number of receptors possessing diverse spiropyran skeletons have been designed and utilized for optical sensing of metal ions, some for neutral molecules, such as nucleobases, amino acids, peptide and DNA, and a few for anions. Some work has also been done in eletrochemical sensing using spiropyran-modified electrode. This review summarizes the progress in the study of spiropyran derivatives in analytical chemistry, including their application as spectroscopic sensors for metal ions,anions and organic molecules, and also the application of spiropyran in electrochemical immuno-sensor. Traditional spiropyran derivatives containing crown ether moieties or -NO2 group, and special kinds of spiropyrans like bisspiropyran which is more super in binding selectivity, are discussed in detail.%螺吡喃作为一种有机光致变色化合物,能够发生无色闭环体螺吡喃与有色开环体部花菁之间可逆的结构异构化,由于具有特殊的分子识别能力和信号传导功能,已经成为分子探针领域极具吸引力的主体分子之一.螺吡喃不仅被广泛应用于光电材料领域作为分子器件,而且作为传感器广泛应用于分析化学领域.研究者们设计了多种具有不同结构的螺吡喃分子,将其应用

  2. Synthesis and Spectroscopic Investigation of Diketopyrrolopyrrole - Spiropyran Dyad for Fluorescent Switch Application.

    Science.gov (United States)

    Doddi, Siva; Narayanaswamy, K; Ramakrishna, Bheerappagari; Singh, Surya Prakash; Bangal, Prakriti Ranjan

    2016-11-01

    We report the synthesis and characterization of a new fluorescent dyad SP-DPP-SP(9) via efficient palladium-catalyzed Sonogashira coupling of prop-2-yn-1-yl 3-(3',3'dimethyl-6-nitrospiro[chromene-2,2'-indolin]-1'-yl)propanoatespiropyran, SP(8), a well known photochromic accepter, with 3,6-bis(5-bromothiophen-2-yl)-2,5-bis((R)-2-ethylhexyl)-2,5-dihydropyrrolo[3,4-c]pyrrole-1,4-dione, DPP(4), a highly fluorescent donor. Under visible light exposure the SP unit is in a closed hydrophobic form, whereas under UV irradiation it converts to a polar, hydrophilic open form named Merocyanine (MC), which is responsible for functioning of photo-switch application. The photochemistry pertaining to fluorescence switch, 'on/off' behaviour, of model dyad SP-DPP-SP(9) is experimentally analyzed in solution as well as in solid state in polymer matrices by photoluminescence(PL) and absorption spectroscopy. After absorption of UV light the spiropyran unit of the dyad under goes the rupture of the spiro C-O bond leading to the formation of MC. The absorption band of MC fairly overlaps to the fluorescence of DPP unit resulting quenching of fluorescence via fluorescence resonance energy transfer from exited DPP unit to ground state MC. In contrary, the fluorescence of DPP is fully regained upon transformation of MC to SP by exposure to visible light or thermal stimuli. Hence, the fluorescence intensity of dyad 9 is regulated by reversible conversion among the two states of the photochromic spiropyran units and the fluorescence resonance energy transfer (FRET) between the MC form of SP and the DPP unit. Conversely, these scrutiny of the experiment express that the design of dyad 9 is viable as efficient fluorescent switch molecule in many probable commercial applications, such as, logic gates and photonic and optical communications.

  3. EDITORIAL: Non-polar and semipolar nitride semiconductors Non-polar and semipolar nitride semiconductors

    Science.gov (United States)

    Han, Jung; Kneissl, Michael

    2012-02-01

    Throughout the history of group-III-nitride materials and devices, scientific breakthroughs and technological advances have gone hand-in-hand. In the late 1980s and early 1990s, the discovery of the nucleation of smooth (0001) GaN films on c-plane sapphire and the activation of p-dopants in GaN led very quickly to the realization of high-brightness blue and green LEDs, followed by the first demonstration of GaN-based violet laser diodes in the mid 1990s. Today, blue InGaN LEDs boast record external quantum efficiencies exceeding 80% and the emission wavelength of the InGaN-based laser diode has been pushed into the green spectral range. Although these tremenduous advances have already spurred multi-billion dollar industries, there are still a number of scientific questions and technological issues that are unanswered. One key challenge is related to the polar nature of the III-nitride wurtzite crystal. Until a decade ago all research activities had almost exclusively concentrated on (0001)-oriented polar GaN layers and heterostructures. Although the device characteristics seem excellent, the strong polarization fields at GaN heterointerfaces can lead to a significant deterioration of the device performance. Triggered by the first demonstration non-polar GaN quantum wells grown on LiAlO2 by Waltereit and colleagues in 2000, impressive advances in the area of non-polar and semipolar nitride semiconductors and devices have been achieved. Today, a large variety of heterostructures free of polarization fields and exhibiting exceptional electronic and optical properties have been demonstrated, and the fundamental understanding of polar, semipolar and non-polar nitrides has made significant leaps forward. The contributions in this Semiconductor Science and Technology special issue on non-polar and semipolar nitride semiconductors provide an impressive and up-to-date cross-section of all areas of research and device physics in this field. The articles cover a wide range of

  4. Theoretical and Experimental Study of New Photochromic Bis-Spiropyrans with Hydroxyethyl and Carboxyethyl Substituents

    Directory of Open Access Journals (Sweden)

    E. L. Mukhanov

    2013-01-01

    Full Text Available Two new asymmetrical bis-spiropyrans with nonequivalent spiropyran units have been investigated. Hydroxyethyl and carboxyethyl substituents have been used to improve thermal stability of the photoinduced merocyanine forms of the bis-spiropyrans. 2-Hydroxyethyl substituted compound is characterized by 4 times more stable merocyanine isomer. 2-Carboxyethyl substituent in the hetarene part enables chelation by metal ions and controllably stabilizes the merocyanine from thermal decay. As a result of theoretical modeling and photochemical experiments, it was shown that obtained compounds are perspective prototypes for multistate light-driven switches with improved stability of photoinduced forms.

  5. Pengaruh Prosentase Solvent Non Polar dalam Campuran Pelarut terhadap Pemisahan Senyawa Non Polar dari Minyak Nyamplung

    Directory of Open Access Journals (Sweden)

    Desy Anggraini

    2014-03-01

    Full Text Available Minyak nyamplung (Calophyllum inophyllum oil dikenal sebagai minyak yang tidak dapat dikonsumsi. Oleh sebab itu, penelitian tentang minyak ini kebanyakan hanya terfokus pada konversi minyak menjadi biodiesel. Pada penelitian ini, diharapkan agar trigliserida (senyawa non polar terpisah dengan resin beracun yang ada di dalam minyak nyamplung itu sendiri, dengan tujuan agar minyak nyamplung bisa dikonsumsi oleh manusia. Minyak nyamplung sendiri disinyalir mengandung senyawa anti HIV dan anti tumor yang sangat berfungsi bagi manusia. Resin beracun yang terdapat dalam minyak ini diidentifikasi sebagai phthalic acid ester (PAE. Trigliserida dalam minyak nyamplung sendiri berkisar antara 70-80%, sehingga jika trigliserida ini dapat terpisah dengan baik dari PAE atau komponen lain yang berbahaya dalam minyak nyamplung, bukan tidak mungkin minyak nyamplung nantinya akan dapat dikonsumsi oleh manusia. Proses isolasi trigliserida dimulai dengan memisahkan senyawa yang diinginkan dari lipid menggunakan ekstraksi pelarut-pelarut dengan dua macam variable solvent yaitu : n-hexane-methanol serta petroleum eter-methanol. Pemilihan pelarut berdasarkan atas nilai kepolaran yang dimilikinya karena solvent yang saling larut tidak dapat digunakan dalam ekstraksi ini. Rasio jumlah solvent non polar dan polar ini juga divariasikan, yaitu : 100:0, 75:25, 50:50 dan 0:100.

  6. Synthesis and redox and photophysical properties of benzodifuran-spiropyran ensembles.

    Science.gov (United States)

    Li, Hui; Ding, Jie; Chen, Songjie; Beyer, Christoph; Liu, Shi-Xia; Wagenknecht, Hans-Achim; Hauser, Andreas; Decurtins, Silvio

    2013-05-10

    Two benzodifuran (BDF)-coupled spiropyran (SP) systems and their BDF reference compounds were obtained in good yields through Huisgen-Meldal-Sharpless "click" chemistry and then subjected to investigation of their electrochemical and photophysical properties. In both SP and merocyanine (MC) forms of the coupled molecules, the BDF-based emission is quenched to around 1 % of the quantum yield of emission from the BDF reference compounds. Based on electrochemical data, this quenching is attributed to oxidative electron-transfer quenching. Irradiation at 366 nm results in ring opening to the MC forms of the BDF-coupled SP compounds and the SP reference compound with a quantum efficiency of about 50 %. The rate constants for the thermal ring closing are approximately 3.4×10(-3)  s(-1). However, in the photostationary states the MC fractions of the coupled molecules are substantially lower than that of the reference SP compound, attributed to the observed acceleration of the ring-closing reaction upon irradiation. As irradiation at 366 nm invariably also excites higher-energy transitions of the BDF units in the coupled compounds, the ring-opening reaction is accelerated relative to the SP reference, which results in lower MC fractions in the photostationary state. Reversible photochromism of these BDF-coupled SP compounds renders them promising in the field of molecular switches. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Spectroscopy analysis of spiropyran-merocyanine molecular transformation

    Energy Technology Data Exchange (ETDEWEB)

    Delgado Macuil, R; Rojas Lopez, M; Orduna Diaz, A [Centro de Investigacion en BiotecnologIa Aplicada Del IPN, Tepetitla Tlaxcala Mexico C.P. 90700 (Mexico); Camacho Pernas, V, E-mail: rdmacuil@yahoo.com.m [Universidad Politecnica de Puebla, Puebla Mexico (Mexico)

    2009-05-01

    Spiropyrans materials are very studied for their application in transduction systems for biosensors. In this work the protocol of generation of multi and mono layers films and the efficiency of the transduction system are analyzed. The analyses were based on UV/Vis and Infrared vibracional spectroscopy in Attenuated Total Reflexion mode (ATR). The films were deposited in glass substrates, using (3-Aminopropyl) trimethoxysilano like linker. The UV/Vis spectra show that the deposition protocol allows the generation of a homogenous film from the first layer. Similar results were observed in ATR. The efficiency of the films, when analyzing them after light UV irradiation, is greater in the samples with two and three layers of deposit, since its absorption peaks are most intense in UV as in ATR. The efficiency falls from the fourth deposit layer. In ATR the efficiency is assumed by the vibration of the NO bond at 1338 cm{sup -1}.

  8. Detailed Molecular Dynamics of the Photochromic Reaction of Spiropyran: A Semiclassical Dynamics Study

    Directory of Open Access Journals (Sweden)

    Gaohong Zhai

    2014-01-01

    Full Text Available A realistic semiclassical dynamics simulation study is reported for the photoinduced ring-opening reaction of spiropyran. The main simulation results show that one pathway involves hydrogen out-of-plane (HOOP torsion of phenyl ring nearby N atom in 254 fs on the excited state and the isomerization from cis- to trans-SP that is complete in about 10 ps on the ground state after the electron transition πσ*; the other dominate pathway corresponds to the ring-opening reaction of trans-SP to form the most stable merocyanine (MC product. Unlike the previous theoretical finding, one C−C bond cleavage on the real molecule rather than the C−N dissociation of the model one is more probable than the ring-opening reaction after the photoexcitation of SP. The simulation findings provide more important complementarity for interpreting experimental observations, confirming the previously theoretical studies of photochromic ring-opening process and even supplying other possible reaction mechanisms.

  9. Electrochemical Write and Read Functionality through Oxidative Dimerization of Spiropyran Self-Assembled Mono layers on Gold

    NARCIS (Netherlands)

    Ivashenko, Oleksii; Herpt, Jochem T. van; Feringa, Bernard; Rudolf, Petra; Browne, Wesley R.

    2013-01-01

    In contrast to their photochromism, the electrochemistry of spiropyrans in self-assembled monolayers has attracted only modest attention in recent years. In this contribution the electrochemical oxidation of self-assembled monolayers (SAMs) of 6-nitro-BIPS spiropyran (SP) prepared on polycrystalline

  10. Structures and photo- and thermochromic properties of spiropyrans of the 2-oxaindan series with polycondensed chromene fragments

    Energy Technology Data Exchange (ETDEWEB)

    Aldoshin, S.M.; Lokshin, V.A.; Rezonov, A.N.; Volbushko, N.V.; Shelepin, N.E.; Knyazhanskii, M.I.; Atovmyan, L.O.; Minkin, V.I.

    1987-12-01

    Spiropyrans of the 2-oxaindan series with 2H-chromene fragments benzo- and 2,3-naphthoannelated at the 7-8 bond were synthesized. The molecular structures of four of the spiropyrans obtained were determined by x-ray diffraction studies, and their photo- and thermochromic properties were studied. Annelation of arene rings significantly increases the relative stabilities of the photocolored forms of the spiropyrans. A correlation between the length of the C/sub spiro/-O bond and the capacity of spiropyrans for photocoloration was discovered. In addition, the free energies of activation of the thermochromic transformation of spiropyrans determined by dynamic NMR spectroscopy are insensitive to variations in the length of the indicated bond.

  11. Isolating the non-polar contributions to the intermolecular potential for water-alkane interactions.

    Science.gov (United States)

    Ballal, Deepti; Venkataraman, Pradeep; Fouad, Wael A; Cox, Kenneth R; Chapman, Walter G

    2014-08-14

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ε(W)/k = 220 K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-ε(W)/k = 78.2 K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally.

  12. Fluctuation capture in non-polar gases and liquids

    CERN Document Server

    Cocks, D G

    2016-01-01

    We present a new model to identify natural fluctuations in fluids, allowing us to describe localization phenomena in the transport of electrons, positrons and positronium through non-polar fluids. The theory contains no free parameters and allows for the calculation of capture cross sections $\\sigma_{cap}(\\epsilon)$ of light-particles in any non-polar fluid, required for non-equilibrium transport simulations. We postulate that localization occurs through large shallow traps before stable bound states are formed. Our results allow us to explain most of the experimental observations of changes in mobility and annihilation rates in the noble gases and liquids as well as make predictions for future experiments. Quantities which are currently inaccessible to experiment, such as positron mobilities, can be obtained from our theory. Unlike other theoretical approaches to localization, the outputs of our theory can be applied in non-equilibrium transport simulations and an extension to the determination of waiting ti...

  13. UV/Vis and NIR Light-Responsive Spiropyran Self-Assembled Monolayers

    NARCIS (Netherlands)

    Ivashenko, Oleksii; Herpt, Jochem T. van; Feringa, Ben L.; Rudolf, Petra; Browne, Wesley R.

    2013-01-01

    Self-assembled monolayers of a 6-nitro BIPS spiropyran (SP) modified with a disulfide-terminated aliphatic chain were prepared on polycrystalline gold surfaces and characterized by UV/vis absorption, surface-enhanced Raman scattering (SEAS), and X-ray photoelectron spectroscopies (XPS). The SAMs

  14. UV/Vis and NIR Light-Responsive Spiropyran Self-Assembled Monolayers

    NARCIS (Netherlands)

    Ivashenko, Oleksii; Herpt, Jochem T. van; Feringa, Ben L.; Rudolf, Petra; Browne, Wesley R.

    2013-01-01

    Self-assembled monolayers of a 6-nitro BIPS spiropyran (SP) modified with a disulfide-terminated aliphatic chain were prepared on polycrystalline gold surfaces and characterized by UV/vis absorption, surface-enhanced Raman scattering (SEAS), and X-ray photoelectron spectroscopies (XPS). The SAMs obt

  15. Automatic parametrization of non-polar implicit solvent models for the blind prediction of solvation free energies

    Science.gov (United States)

    Wang, Bao; Zhao, Zhixiong; Wei, Guo-Wei

    2016-09-01

    In this work, a systematic protocol is proposed to automatically parametrize the non-polar part of implicit solvent models with polar and non-polar components. The proposed protocol utilizes either the classical Poisson model or the Kohn-Sham density functional theory based polarizable Poisson model for modeling polar solvation free energies. Four sets of radius parameters are combined with four sets of charge force fields to arrive at a total of 16 different parametrizations for the polar component. For the non-polar component, either the standard model of surface area, molecular volume, and van der Waals interactions or a model with atomic surface areas and molecular volume is employed. To automatically parametrize a non-polar model, we develop scoring and ranking algorithms to classify solute molecules. The their non-polar parametrization is obtained based on the assumption that similar molecules have similar parametrizations. A large database with 668 experimental data is collected and employed to validate the proposed protocol. The lowest leave-one-out root mean square (RMS) error for the database is 1.33 kcal/mol. Additionally, five subsets of the database, i.e., SAMPL0-SAMPL4, are employed to further demonstrate that the proposed protocol. The optimal RMS errors are 0.93, 2.82, 1.90, 0.78, and 1.03 kcal/mol, respectively, for SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 test sets. The corresponding RMS errors for the polarizable Poisson model with the Amber Bondi radii are 0.93, 2.89, 1.90, 1.16, and 1.07 kcal/mol, respectively.

  16. Femtosecond dynamics of fundamental reaction processes in liquids: Proton transfer, geminate recombination, isomerization and vibrational relaxation. [Spiropyrans

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, B.J.

    1992-11-01

    The fast excited state intramolecular proton transfer of 3-hydroxyflavone is measured and effects of external hydrogen-bonding interactions on the proton transfer are studied. The proton transfer takes place in [approximately]240 fsec in nonpolar environments, but becomes faster than instrumental resolution of 110 fsec in methanol solution. The dynamics following photodissociation of CH[sub 2]I[sub 2] and other small molecules provide the first direct observations of geminate recombination. The recombination of many different photodissociating species occurs on a [approximately]350 fsec time scale. Results show that recombination yields but not rates depend on the solvent environment and suggest that recombination kinetics are dominated by a single collision with surrounding solvent cage. Studies of sterically locked phenyl-substituted butadienes offer new insights into the electronic structure and isomerization behavior of conjugated polyenes. Data show no simple correlation between hinderance of specific large amplitude motions and signatures of isomerizative behavior such as viscosity dependent excited state lifetimes, implying that the isomerization does not provide a suitable for simple condensed phase reaction rate theories. The spectral dynamics of a photochromic spiropyran indicate that recombination, isomerization and vibrational relaxation all play important roles in photoreactivity of complex molecules. The interplay of these microscopic phenomena and their effect on macroscopic properties such as photochromism are discussed. All the results indicate that the initial steps of the photochromic reaction process occur extremely rapidly. Laser system and computer codes for data analysis are discussed.

  17. Solvent density mode instability in non-polar solutions

    Indian Academy of Sciences (India)

    Susmita Kar; Ranjit Biswas; J Chakrabarti

    2008-08-01

    We analyse the origin of the multiple long time scales associated with the long time decay observed in non-polar solvation dynamics by linear stability analysis of solvent density modes where the effects of compressibility and solvent structure are systematically incorporated. The coupling of the solute–solvent interactions at both ground and excited states of the solute with the compressibility and solvent structure is found to have important effects on the time scales. The present theory suggests that the relatively longer time constant is controlled by the solvent compressibility, while the solvent structure at the nearest-neighbour length scale dominates the shorter time constant.

  18. Photonic Crystal Polarizing and Non-Polarizing Beam Splitters

    Institute of Scientific and Technical Information of China (English)

    GUAN Chun-Ying; SHI Jin-Hui; YUAN Li-Bo

    2008-01-01

    A polarizing beam splitter(PBS)and a non-polarizing beam splitter(NPBS)based on a photonic crystal(PC)directional coupler are demonstrated.The photonic crystal directional coupler consists of a hexagonal lattice of dielectric pillars in air and has a complete photonic band gap.The photonic band structure and the band gap map are calculated using the plane wave expansion(PWE)method.The splitting properties of the splitter are investigated numerically using the finite difference time domain(FDTD)method.

  19. An analytical method of predicting Lee-Kesler-Ploecker binary interaction coefficients: Part 1, For non-polar hydrocarbon mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Sand, J.R.

    1994-12-31

    An analytical method is proposed for finding numerical values of binary interaction coefficients for non-polar hydrocarbon mixtures when the Lee-Kesler (LK) equation of state is applied. The method is based on solving simultaneous equations, which are Ploecker`s mixing rules for pseudocritical parameters of a mixture, and the Lee-Kesler equation for the saturation line. For a hydrocarbon mixture, the method allows prediction of {kappa}{sub ij} interaction coefficients (ICs) which are close to values obtained by processing experimental p-v-t data on the saturation line and subsequent averaging. For mixtures of hydrocarbon molecules containing from 2 to 9 carbon atoms, the divergence between calculated and experimentally based ICs is no more than {plus_minus}0.4%. The possibility of extending application of this method to other non-polar substances is discussed.

  20. Comparative Evaluation of Substituent Effect on the Photochromic Properties of Spiropyrans and Spirooxazines.

    Science.gov (United States)

    Balmond, Edward I; Tautges, Brandon K; Faulkner, Andrea L; Or, Victor W; Hodur, Blanka M; Shaw, Jared T; Louie, Angelique Y

    2016-10-07

    Spiropyrans and spirooxazines represent an important class of photochromic compounds with a wide variety of applications. In order to effectively utilize and design these photoswitches it is desirable to understand how the substituents affect photochromic properties, and how the different structural motifs compare under identical conditions. In this work a small library of photoswitches was synthesized in order to comparatively evaluate the effect of substituent modifications and structure on photochromism. The library was designed to modify positions that were believed to have the greatest effect on C-O bond lability and therefore the photochromic properties. Herein we report a comparative analysis of the UV and visible light responses of 30 spiropyrans, spiroindolinonaphthopyrans, and spirooxazines. The influence of gadolinium(III) binding was also investigated on the library of compounds to determine its effect on photoswitching. Both assays demonstrated different trends in substituent and structural requirements for optimal photochromism.

  1. Photochromic Spatiotemporal Control of Bubble-Propelled Micromotors by a Spiropyran Molecular Switch.

    Science.gov (United States)

    Moo, James Guo Sheng; Presolski, Stanislav; Pumera, Martin

    2016-03-22

    Controlling the environment in which bubble-propelled micromotors operate represents an attractive strategy to influence their motion, especially when the trigger is as simple as light. We demonstrate that spiropyrans, which isomerize to amphiphilic merocyanines under UV irradiation, can act as molecular switches that drastically affect the locomotion of the micrometer-sized engines. The phototrigger could be either a point or a field source, thus allowing different modes of control to be executed. A whole ensemble of micromotors was repeatedly activated and deactivated by just altering the spiropyran-merocyanine ratio with light. Moreover, the velocity of individual micromotors was altered using a point irradiation source that caused only localized changes in the environment. Such selective manipulation, achieved here with an optical microscope and a photochromic additive in the medium, reveals the ease of the methodology, which can allow micro- and nanomotors to reach their full potential of not just stochastic, but directional controlled motion.

  2. On the rotational energy distributions of reactive, non-polar species in the interstellar medium

    CERN Document Server

    Glinski, Robert J; Downum, Clark R

    2013-01-01

    A basic model for the formation of non-equilibrium rotational energy distributions is described for reactive, homo-polar diatomic molecules and ions in the interstellar medium. Kinetic models were constructed to calculate the rotational populations of C2+ under the conditions it would experience in the diffuse interstellar medium. As the non-polar ion reacts with molecular hydrogen, but not atomic hydrogen, the thermalization of a hot nascent rotational population will be arrested by chemical reaction when the H2 density begins to be significant. Populations that deviate strongly from the local thermodynamic equilibrium are predicted for C2+ in environments where it may be detectable. Consequences of this are discussed and a new optical spectrum is calculated.

  3. Utilization of a spiropyran derivative in a polymeric film optode for selective fluorescent sensing of zinc ion

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Ying; SHAO; Na; YANG; Ronghua; LI; Ke'an; LIU; Feng; CHAN; Winghong; MO; Tian

    2006-01-01

    A new spiropyran derivative was synthesized and first utilized in a polymeric film-based optical sensor for zinc ion. Spiropyrans, combining the characteristics of metal binding and signal transduction, show potential function in the design of optical chemical sensors (optodes) toward metal ions. When embedded in a plasticized poly (vinyl chloride) (PVC) membrane, the newly synthesized spiropyran derivative 1 exhibits obvious fluorescence enhancement at 630 nm in the presence of zinc ion in aqueous solution. With the optimum condition described, the optode membrane responds to also exhibits high selectivity toward zinc ion over transition metal ions including Hg2+, Cd2+, Pb2+, Cu2+,Fe3+and common cationic ions presented in the physiological fluids.

  4. Design of non-polarizing thin film edge filters

    Institute of Scientific and Technical Information of China (English)

    GU Pei-fu; ZHENG Zhen-rong

    2006-01-01

    The separation between s- and p-polarization components invariably affects thin film edge filters used for tilted incidence and is a difficult problem for many applications, especially for optical communication. This paper presents a novel design method to obtain edge filters with non-polarization at incidence angle of 45°. The polarization separation at 50% transmittance for a long-wave-pass filter and a short-wave-pass filter is 0.3 nm and 0.1 nm respectively. The design method is based on a broadband Fabry-Perot thin-film interference filter in which the higher or lower interference band at both sides of the main transmittance peak can be used for initial design of long-wave-pass filter or short-wave-pass filter and then can be refined to reduce the transmittance ripples. The spacer 2H2L2H or 2L2H2L of the filter is usually taken. Moreover, the method for expanding the bandwidth of rejection and transmission is explained. The bandwidth of 200 nm for both rejection region and transmission band is obtained at wavelength 1550 nm. In this way, the long-wave-pass and short-wave-pass edge filters with zero separation between two polarization components can easily be fabricated.

  5. Roles of urea and TMAO on the interaction between extended non-polar peptides

    Science.gov (United States)

    Su, Zhaoqian; Dias, Cristiano

    Urea and trimethylamine n-oxide (TMAO) are small molecules known to destabilize and stabilize, respectively, the structure of proteins when added to aqueous solution. To unravel the molecular mechanisms of these cosolvents on protein structure we perform explicit all-atom molecular dynamics simulations of extended poly-alanine and polyleucine dimers. We use an umbrella sampling protocol to compute the potential of mean force (PMF) of dimers at different concentrations of urea and TMAO. We find that the large non-polar side chain of leucine is affected by urea whereas backbone atoms and alanine's side chain are not. Urea is found to occupy positions between leucine's side chains that are not accessible to water. This accounts for extra Lennard-Jones bonds between urea and side chains that favors the unfolded state. These bonds compete with urea-solvent interactions that favor the folded state. The sum of these two energetic terms provide the enthalpic driving force for unfolding. We show here that this enthalpy correlate with the potential of mean force of poly-leucine dimers. Moreover, the framework developed here is general and may be used to provide insights into effects of other small molecules on protein interactions. The effect of the TMAO will be in the presentation. Department of Physics, University Heights, Newark, New Jersey, 07102-1982.

  6. Molecular Dynamics Simulation of Behaviours of Non-Polar Droplets Merging and Interactions with Hydrophobic Surfaces

    Institute of Scientific and Technical Information of China (English)

    Y.Y.Yan; C.Y.Ji

    2008-01-01

    This paper presents a molecular dynamics simulation of the behaviours of non-polar droplets merging and also the fluid molecules interacting with a hydrophobic surface. Such behaviours and transport phenomena are popular in general micro-channel flow boiling and two-phase flow. The droplets are assumed to be composed of Lennards-Jones type molecules. Periodic boundary conditions are applied in three coordinate directions ofa 3-D system, where there exist two liquid droplets and their vapour. The two droplets merge when they come within the prescribed small distance. The merging of two droplets apart from each other at different initial distances is tested and the possible larger (or critical) non-dimensional distance, in which droplets merging can occur, is discussed. The evolution of the merging process is simulated numerically by employing the Molecular Dynamics (MD) method. For interactions with hydrophobic solid wail, a system with fluid confined between two walls is used to study the wetting phenomena of fluid and solid wail. The results are compared with those of hydrophilic wall to show the unique characteristics of hydrophobic interactions by microscopic methods.

  7. Accidental degeneracy in the spiropyran radical cation : charge transfer between two orthogonal rings inducing ultra-efficient reactivity

    NARCIS (Netherlands)

    Mendive-Tapia, David; Kortekaas, Luuk; Steen, Jorn D.; Perrier, Aurelie; Lasorne, Benjamin; Browne, Wesley R.; Jacquemin, Denis

    2016-01-01

    Photochromism of the spiropyran radical cation to the corresponding merocyanine form is investigated by a combination of electrochemical oxidation, UV/vis absorption spectroscopy, spectroelectrochemistry and first-principles calculations (TD-DFT, CAS-SCF and CAS-PT2). First, we demonstrate that the

  8. Heme and non-heme iron transporters in non-polarized and polarized cells

    Directory of Open Access Journals (Sweden)

    Yasui Yumiko

    2010-06-01

    Full Text Available Abstract Background Heme and non-heme iron from diet, and recycled iron from hemoglobin are important products of the synthesis of iron-containing molecules. In excess, iron is potentially toxic because it can produce reactive oxygen species through the Fenton reaction. Humans can absorb, transport, store, and recycle iron without an excretory system to remove excess iron. Two candidate heme transporters and two iron transporters have been reported thus far. Heme incorporated into cells is degraded by heme oxygenases (HOs, and the iron product is reutilized by the body. To specify the processes of heme uptake and degradation, and the reutilization of iron, we determined the subcellular localizations of these transporters and HOs. Results In this study, we analyzed the subcellular localizations of 2 isoenzymes of HOs, 4 isoforms of divalent metal transporter 1 (DMT1, and 2 candidate heme transporters--heme carrier protein 1 (HCP1 and heme responsive gene-1 (HRG-1--in non-polarized and polarized cells. In non-polarized cells, HCP1, HRG-1, and DMT1A-I are located in the plasma membrane. In polarized cells, they show distinct localizations: HCP1 and DMT1A-I are located in the apical membrane, whereas HRG-1 is located in the basolateral membrane and lysosome. 16Leu at DMT1A-I N-terminal cytosolic domain was found to be crucial for plasma membrane localization. HOs are located in smooth endoplasmic reticulum and colocalize with NADPH-cytochrome P450 reductase. Conclusions HCP1 and DMT1A-I are localized to the apical membrane, and HRG-1 to the basolateral membrane and lysosome. These findings suggest that HCP1 and DMT1A-I have functions in the uptake of dietary heme and non-heme iron. HRG-1 can transport endocytosed heme from the lysosome into the cytosol. These localization studies support a model in which cytosolic heme can be degraded by HOs, and the resulting iron is exported into tissue fluids via the iron transporter ferroportin 1, which is

  9. Enhanced radiation tolerance of non-polar-terminated ZnO

    Science.gov (United States)

    Charnvanichborikarn, S.; Myers, M. T.; Shao, L.; Kucheyev, S. O.

    2013-12-01

    Room-temperature heavy-ion bombardment of polar (0001) ZnO leads to the formation of intermediate peak and step features in damage-depth profiles measured by ion channeling. Here, we show that these anomalous disorder effects are strongly suppressed for crystals with (112¯0) and (101¯0) non-polar surface terminations. Possible defect interaction scenarios responsible for the enhanced radiation tolerance of non-polar-terminated ZnO are discussed.

  10. Modeling diffusion coefficients in binary mixtures of polar and non-polar compounds

    DEFF Research Database (Denmark)

    Medvedev, Oleg; Shapiro, Alexander

    2005-01-01

    The theory of transport coefficients in liquids, developed previously, is tested on a description of the diffusion coefficients in binary polar/non-polar mixtures, by applying advanced thermodynamic models. Comparison to a large set of experimental data shows good performance of the model. Only...... components and to only one parameter for mixtures consisting of non-polar components. A possibility of complete prediction of the parameters is discussed....

  11. Mechanism and energetics of O and O2 adsorption on polar and non-polar ZnO surfaces

    Science.gov (United States)

    Gorai, Prashun; Seebauer, Edmund G.; Ertekin, Elif

    2016-05-01

    Polar surfaces of semiconducting metal oxides can exhibit structures and chemical reactivities that are distinct from their non-polar surfaces. Using first-principles calculations, we examine O adatom and O2 molecule adsorption on 8 different known ZnO reconstructions including Zn-terminated (Zn-ZnO) and O-terminated (O-ZnO) polar surfaces, and non-polar surfaces. We find that adsorption tendencies are largely governed by the thermodynamic environment, but exhibit variations due to the different surface chemistries of various reconstructions. The Zn-ZnO surface reconstructions which appear under O-rich and H-poor environments are found to be most amenable to O and O2 adsorption. We attribute this to the fact that on Zn-ZnO, the O-rich environments that promote O adsorption also simultaneously favor reconstructions that involve adsorbed O species. On these Zn-ZnO surfaces, O2 dissociatively adsorbs to form O adatoms. By contrast, on O-ZnO surfaces, the O-rich conditions required for O or O2 adsorption tend to promote reconstructions involving adsorbed H species, making further O species adsorption more difficult. These insights about O2 adsorption on ZnO surfaces suggest possible design rules to understand the adsorption properties of semiconductor polar surfaces.

  12. The influence of non-polar lipids on tear film dynamics

    KAUST Repository

    Bruna, M.

    2014-04-04

    © 2014 Cambridge University Press. In this paper we examine the effect that physiological non-polar lipids, residing on the surface of an aqueous tear film, have on the film evolution. In our model we track the evolution of the thickness of the non-polar lipid layer, the thickness of the aqueous layer and the concentration of polar lipids which reside at the interface between the two. We also utilise a force balance in the non-polar lipid layer in order to determine its velocity. We show how to obtain previous models in the literature from our model by making particular choices of the parameters. We see the formation of boundary layers in some of these submodels, across which the concentration of polar lipid and the non-polar lipid velocity and film thickness vary. We solve our model numerically for physically realistic parameter values, and we find that the evolution of the aqueous layer and the polar lipid layer are similar to that described by previous authors. However, there are interesting dynamics for the non-polar lipid layer. The effects of altering the key parameters are highlighted and discussed. In particular, we see that the Marangoni number plays a key role in determining how far over the eye the non-polar lipid spreads.

  13. A divergent asymmetric approach to aza-spiropyran derivative and (1S,8aR-1-hydroxyindolizidine

    Directory of Open Access Journals (Sweden)

    Huang Pei-Qiang

    2007-11-01

    Full Text Available Abstract Background Spiroketals and the corresponding aza-spiroketals are the structural features found in a number of bioactive natural products, and in compounds possessing photochromic properties for use in the area of photochemical erasable memory, self-development photography, actinometry, displays, filters, lenses of variable optical density, and photomechanical biomaterials etc. And (1R,8aS-1-hydroxyindolizidine (3 has been postulated to be a biosynthetic precursor of hydroxylated indolizidines such as (+-lentiginosine 1, (--2-epilentiginosine 2 and (--swainsonine, which are potentially useful antimetastasis drugs for the treatment of cancer. In continuation of a project aimed at the development of enantiomeric malimide-based synthetic methodology, we now report a divergent, concise and highly diastereoselective approach for the asymmetric syntheses of an aza-spiropyran derivative 7 and (1S,8aR-1-hydroxyindolizidine (ent-3. Results The synthesis of aza-spiropyran 7 started from the Grignard addition of malimide 4. Treatment of the THP-protected 4-hydroxybutyl magnesium bromide with malimide 4 at -20°C afforded N,O-acetal 5a as an epimeric mixture in a combined yield of 89%. Subjection of the diastereomeric mixture of N,O-acetal 5a to acidic conditions for 0.5 h resulted in the formation of the desired functionalized aza-spiropyran 7 as a single diastereomer in quantitative yield. The stereochemistry of the aza-spiropyran 7 was determined by NOESY experiment. For the synthesis of ent-3, aza-spiropyran 7, or more conveniently, N,O-acetal 5a, was converted to lactam 6a under standard reductive dehydroxylation conditions in 78% or 77% yield. Reduction of lactam 6a with borane-dimethylsulfide provided pyrrolidine 8 in 95% yield. Compound 8 was then converted to 1-hydroxyindolizidine ent-3 via a four-step procedure, namely, N-debenzylation/O-mesylation/Boc-cleavage/cyclization, and O-debenzylation. Alternatively, amino alcohol 8 was mesylated

  14. Smart photovoltaics based on dye-sensitized solar cells using photochromic spiropyran derivatives as photosensitizers

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Shengbo; Ting, Hungkit; Ma, Yingzhuang; Zheng, Lingling; Zhang, Miwei [State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871 (China); Xiao, Lixin, E-mail: zjchen@pku.edu.cn, E-mail: lxxiao@pku.edu.cn; Chen, Zhijian, E-mail: zjchen@pku.edu.cn, E-mail: lxxiao@pku.edu.cn [State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871 (China); Haixi Collaborative Innovation Center for New Display Devices and Systems Integration, Fuzhou University, Fuzhou 350002 (China)

    2015-05-15

    In this paper, smart photovoltaic (SPV) devices, integrating both functions of solar cells and smart windows, was fabricated based on dye-sensitized solar cells using photochromic spiropyran derivatives SIBT as photosensitizers. SPV devices have self-regulated power conversion efficiency (PCE) and light transmission responding to the incident spectra due to the photoisomerization of SIBT. SIBT isomerize from closed-ring form to open-ring form under UV illumination, accompanied with enhanced visible light absorption and electron delocalization. Therefore, increased PCE and absorption in SPV devices were observed under UV treatment and the devices can be restored gradually to the initial status when kept in dark. The SPV devices have self-regulation of PCE and sunlight transmission responding to the changing sun spectra in different times of a day, providing a proper energy usage and a better sun-shading.

  15. Optically Defined Modal Sensors Incorporating Spiropyran-Doped Liquid Crystals with Piezoelectric Sensors

    Directory of Open Access Journals (Sweden)

    Hui-Lung Kuo

    2011-01-01

    Full Text Available We integrated a piezoelectric sensing layer lamina containing liquid crystals (LC and spiropyran (SP in a LC/SP mixture to create an optically reconfigurable modal sensor for a cantilever beam. The impedance of this LC/SP lamina was decreased by UV irradiation which constituted the underlying mechanism to modulate the voltage externally applied to the piezoelectric actuating layer. Illuminating a specific pattern onto the LC/SP lamina provided us with a way to spatially modulate the piezoelectric vibration signal. We showed that if an UV illuminated pattern matches the strain distribution of a specific mode, a piezoelectric modal sensor can be created. Since UV illumination can be changed in situ in real-time, our results confirm for the first time since the inception of smart sensors, that an optically tailored modal sensor can be created. Some potential applications of this type of sensor include energy harvesting devices, bio-chips, vibration sensing and actuating devices.

  16. Relaxation phenomena of polar non-polar liquid mixtures under low and high frequency electric field

    Indian Academy of Sciences (India)

    K Dutta; S K Sit; S Acharyya

    2003-10-01

    Simultaneous calculation of the dipole moment and the relaxation time of a certain number of non-spherical rigid aliphatic polar liquid molecules () in non-polar solvents () under 9.8 GHz electric field is possible from real $'$ and imaginary $''$ parts of the complex relative permittivity $^{*}_{}$. The low frequency and infinite frequency permittivities 0 and ∞ measured by Purohit et al [1,2] and Srivastava and Srivastava [3] at 25, 35 and 30°C respectively are used to obtain static . The ratio of the individual slopes of imaginary and real $'$ parts of high frequency (hf) complex conductivity $^{*}_{}$ with weight fractions at → 0 and the slopes of $''_{}-'_{}$ curves for different s [4] are employed to obtain s. The former method is better in comparison to the existing one as it eliminates polar–polar interaction. The hf s in Coulomb metre (C m) when compared with static and reported s indicate that ss favour the monomer formations which combine to form dimers in the hf electric field. The comparison among s shows that a part of the molecule is rotating under X-band electric field [5]. The theoretical theos from available bond angles and bond moments of the substituent polar groups attached to the parent molecules differ from the measured s and s to establish the possible existence of mesomeric, inductive and electromeric effects in polar liquid molecules.

  17. Investigation of the Phase Equilibria and Interfacial Properties for Non-polar Fluids

    Institute of Scientific and Technical Information of China (English)

    付东; 赵毅

    2005-01-01

    A self-consistent density-functional theory (DFT) was applied to investigate the phase behavior and interfacial properties of non-polar fluids. For the bulk phases, the theory was reduced to the statistical associating fluid theory(SAFF) that provides accurate descriptions of vapor-liquid phase diagrams below the critical region. The phase diagrams in the critical region were corrected by the renormalization group theory (RGT). The density profile in the surface was obtained by minimizing the grand potential. With the same set of molecular parameters, both the phase equilibria and the interfacial properties of non-polar fluids were investigated satisfactorily.

  18. Synthesis, characterization, and photophysical properties of Bodipy-spirooxazine and -spiropyran conjugates: modulation of fluorescence resonance energy transfer behavior via acidochromic and photochromic switching.

    Science.gov (United States)

    Kong, Lingcan; Wong, Hok-Lai; Tam, Anthony Yiu-Yan; Lam, Wai Han; Wu, Lixin; Yam, Vivian Wing-Wah

    2014-02-12

    Two series of Bodipy-containing photochromic spirooxazine and spiropyran derivatives have been designed, synthesized and characterized by (1)H NMR, ESI mass spectrometry and elemental analysis. Their electrochemical and photochromic properties were investigated. The photophysical, ultrafast transient absorption, and fluorescence resonance energy transfer (FRET) properties from Bodipy (donor) to the ring-opened merocyanine (acceptor) were also studied. Upon photoexcitation, all the photochromic spirooxazine- and spiropyran-containing compounds exhibited reversible photochromism. Computational studies have been performed to provide further insights into the nature of the electronic transitions for the two classes of compounds. The rate constants and activation parameters for thermal bleaching reactions of compounds SO, SP-alkyne, 1-3, and 8-10 were determined through kinetic studies in acetonitrile. The thermal bleaching reaction rate of the spiropyran-containing compounds is found to be much slower than that of the spirooxazine-containing counterparts.

  19. Electrokinetics of Polar Liquids in Contact with Non-Polar Surfaces

    CERN Document Server

    Lin, Chih-Hsiu; Chaudhury, Manoj K

    2014-01-01

    Zeta potentials of several polar protic (water, ethylene glycol, formamide) as well as polar aprotic (dimethyl sulfoxide) liquids were measured in contact with three non-polar surfaces using closed-cell electro-osmosis. The test surfaces were chemisorbed monolayers of alkyl siloxanes, fluoroalkyl siloxanes and polydimethylsiloxanes (PDMS) grafted on glass slides. All these liquids exhibited substantial electrokinetics in contact with the non-polar surfaces with these observations: the electrokinetic effect on the fluorocarbon-coated surface is the strongest; and on a PDMS grafted surface, the effect is the weakest. Even though these hygroscopic liquids contain small amounts of water, the current models of charging based on the adsorption of hydroxide ions at the interface or the dissociation of preexisting functionalities (e.g., silanol groups) appear to be insufficient to account for the various facets of the experimental observations. The results illustrate how ubiquitous the phenomenon of electro-kinetics ...

  20. Broadband non-polarizing terahertz beam splitters with variable split ratio

    KAUST Repository

    Wei, Minggui

    2017-08-15

    Seeking effective terahertz functional devices has always aroused extensive attention. Of particular interest is the terahertz beam splitter. Here, we have proposed, designed, manufactured, and tested a broadband non-polarizing terahertz beam splitter with a variable split ratio based on an all-dielectric metasurface. The metasurface was created by patterning a dielectric surface of the N-step phase gradient and etching to a few hundred micrometers. The conversion efficiency as high as 81% under the normal incidence at 0.7 THz was achieved. Meanwhile, such a splitter works well over a broad frequency range. The split ratio of the proposed design can be continuously tuned by simply shifting the metasurface, and the angle of emergences can also be easily adjusted by choosing the step of phase gradients. The proposed design is non-polarizing, and its performance is kept under different polarizations.

  1. Non-polar Solvent Microwave-Assisted Extraction of Volatile Constituents from Dried Zingiber Officinale Rosc.

    Institute of Scientific and Technical Information of China (English)

    YU Yong; WANG Zi-Ming; WANG Yu-Tang; LI Tie-Chun; CHENG Jian-Hua; LIU Zhong-Ying; ZHANG Han-Qi

    2007-01-01

    A new method, non-polar solvent microwave-assisted extraction (NPSMAE), was applied to the extraction of essential oil from Zingiber officinale Rosc. in closed-vessel system. By adding microwave absorption mediumcarbonyl iron powders (CIP) into extraction system, the essential oil was extracted by the non-polar solvent (ether)which can be heated by CIP. The constituents of essential oil obtained by NPSMAE were comparable with those obtained by hydrodistillation (HD) by GC-MS analysis, which indicates that NPSMAE is a feasible way to extract essential oil from dried plant materials. The NPSMAE took much less extraction time (5 min) than HD (180 min),and its extraction efficiency was much higher than that of conventional polar solvent microwave-assisted extraction (PSMAE) and mixed solvent microwave-assisted extraction (MSMAE). It can be a good alternative for the extraction of volatile constituents from dried plant samples.

  2. Contact angles and wettability of ionic liquids on polar and non-polar surfaces.

    Science.gov (United States)

    Pereira, Matheus M; Kurnia, Kiki A; Sousa, Filipa L; Silva, Nuno J O; Lopes-da-Silva, José A; Coutinho, João A P; Freire, Mara G

    2015-12-21

    Many applications involving ionic liquids (ILs) require the knowledge of their interfacial behaviour, such as wettability and adhesion. In this context, herein, two approaches were combined aiming at understanding the impact of the IL chemical structures on their wettability on both polar and non-polar surfaces, namely: (i) the experimental determination of the contact angles of a broad range of ILs (covering a wide number of anions of variable polarity, cations, and cation alkyl side chain lengths) on polar and non-polar solid substrates (glass, Al-plate, and poly-(tetrafluoroethylene) (PTFE)); and (ii) the correlation of the experimental contact angles with the cation-anion pair interaction energies generated by the Conductor-like Screening Model for Real Solvents (COSMO-RS). The combined results reveal that the hydrogen-bond basicity of ILs, and thus the IL anion, plays a major role through their wettability on both polar and non-polar surfaces. The increase of the IL hydrogen-bond accepting ability leads to an improved wettability of more polar surfaces (lower contact angles) while the opposite trend is observed on non-polar surfaces. The cation nature and alkyl side chain lengths have however a smaller impact on the wetting ability of ILs. Linear correlations were found between the experimental contact angles and the cation-anion hydrogen-bonding and cation ring energies, estimated using COSMO-RS, suggesting that these features primarily control the wetting ability of ILs. Furthermore, two-descriptor correlations are proposed here to predict the contact angles of a wide variety of ILs on glass, Al-plate, and PTFE surfaces. A new extended list is provided for the contact angles of ILs on three surfaces, which can be used as a priori information to choose appropriate ILs before a given application.

  3. Contact angles and wettability of ionic liquids on polar and non-polar surfaces†

    Science.gov (United States)

    Sousa, Filipa L.; Silva, Nuno J. O.; Lopes-da-Silva, José A.; Coutinho, João A. P.; Freire, Mara G.

    2016-01-01

    Many applications involving ionic liquids (ILs) require the knowledge of their interfacial behaviour, such as wettability and adhesion. In this context, herein, two approaches were combined aiming at understanding the impact of the IL chemical structures on their wettability on both polar and non-polar surfaces, namely: (i) the experimental determination of the contact angles of a broad range of ILs (covering a wide number of anions of variable polarity, cations, and cation alkyl side chain lengths) on polar and non-polar solid substrates (glass, Al-plate, and poly-(tetrafluoroethylene) (PTFE)); and (ii) the correlation of the experimental contact angles with the cation–anion pair interaction energies generated by the Conductor-like Screening Model for Real Solvents (COSMO-RS). The combined results reveal that the hydrogen-bond basicity of ILs, and thus the IL anion, plays a major role through their wettability on both polar and non-polar surfaces. The increase of the IL hydrogen-bond accepting ability leads to an improved wettability of more polar surfaces (lower contact angles) while the opposite trend is observed on non-polar surfaces. The cation nature and alkyl side chain lengths have however a smaller impact on the wetting ability of ILs. Linear correlations were found between the experimental contact angles and the cation–anion hydrogen-bonding and cation ring energies, estimated using COSMO-RS, suggesting that these features primarily control the wetting ability of ILs. Furthermore, two-descriptor correlations are proposed here to predict the contact angles of a wide variety of ILs on glass, Al-plate, and PTFE surfaces. A new extended list is provided for the contact angles of ILs on three surfaces, which can be used as a priori information to choose appropriate ILs before a given application. PMID:26554705

  4. Electric Charge Accumulation in Polar and Non-Polar Polymers under Electron Beam Irradiation

    Science.gov (United States)

    Nagasawa, Kenichiro; Honjoh, Masato; Takada, Tatsuo; Miyake, Hiroaki; Tanaka, Yasuhiro

    The electric charge accumulation under an electron beam irradiation (40 keV and 60 keV) was measured by using the pressure wave propagation (PWP) method in the dielectric insulation materials, such as polar polymeric films (polycarbonate (PC), polyethylene-naphthalate (PEN), polyimide (PI), and polyethylene-terephthalate (PET)) and non-polar polymeric films (polystyrene (PS), polypropylene (PP), polyethylene (PE) and polytetrafluoroethylene (PTFE)). The PE and PTFE (non-polar polymers) showed the properties of large amount of electric charge accumulation over 50 C/m3 and long saturation time over 80 minutes. The PP and PS (non-polar polymer) showed the properties of middle amount of charge accumulation about 20 C/m3 and middle saturation time about 1 to 20 minutes. The PC, PEN, PI and PET (polar polymers) showed the properties of small amount of charge accumulation about 5 to 20 C/m3 and within short saturation time about 1.0 minutes. This paper summarizes the relationship between the properties of charge accumulation and chemical structural formula, and compares between the electro static potential distribution with negative charged polymer and its chemical structural formula.

  5. Synthesis and spectral investigations of a new dyad with spiropyran and fluorescein units: toward information processing at the single molecular level.

    Science.gov (United States)

    Guo, Xuefeng; Zhang, Deqing; Zhou, Yucheng; Zhu, Daoben

    2003-07-11

    A new dyad 1 with two spiropyran units as the photochromic acceptors and one fluorescein unit as the fluorescent donor was synthesized and characterized. External inputs (ultraviolet light, visible light, and proton) induce the reversible changes of the structure and, concomitantly, the absorption spectrum of dyad 1 due to the presence of two spiropyran units. Only the absorption spectrum of the ME form of the spiropyran units in dyad 1 has large spectral overlap with the fluorescence spectrum of the fluorescein unit. Thus, the fluorescence intensity of dyad 1 is modulated by reversible conversion among the three states of the photochromic spiropyran units and the fluorescence resonance energy transfer (FRET) between the ME form and the fluorescein unit. Based on the fact that dyad 1 could "read out" three external input signals (ultraviolet light, visible ligh,t and proton) and "write" a compatible specific output signal (fluorescence intensity), dyad 1 described here can be considered to perform an integrated circuit function with one OR and one AND interconnected logic gates. The present results demonstrate an efficient strategy for elaborating and transmitting information at the single molecular level.

  6. Spiropyran-Isoquinoline Dyad as a Dual Chemosensor for Co(II and In(III Detection

    Directory of Open Access Journals (Sweden)

    Yong-Min Kho

    2017-09-01

    Full Text Available Spiropyran derivatives have been studied as light-regulated chemosensors for a variety of metal cations and anions, but there is little research on chemosensors that simultaneously detect multiple metal cations. In this study, a spiropyran derivative with isoquinoline, SP-IQ, was prepared and it functions investigated as a light-regulated sensor for both Co2+ and In3+ cations. A colorless nonfluorescent SP-IQ converts to a pink-colored fluorescent MC-IQ by UV irradiation or standing in the dark, and MC-IQ returns to SP-IQ with visible light. Upon UV irradiation with the Co2+ cation for 7 min, the stronger absorption at 540 nm and the similar fluorescence intensity at 640 nm are observed, compared to when no metal cation is added, due to the formation of a Co2+ complex with pink color and pink fluorescence. When placed in the dark with the In3+ cation for 7 h, the colorless solution of SP-IQ changes to the In3+ complex with yellow color and pink fluorescence, which shows strong absorption at 410 nm and strong fluorescence at 640 nm. Selective detection of the Co2+ cation with UV irradiation and the In3+ cation in the dark could be possible with SP-IQ by both absorption and fluorescence spectroscopy or by the naked eye.

  7. Electronic tera-order stabilization of photoinduced metastable species: structure of the photochromic product of spiropyran determined with in situ single crystal X-ray photodiffraction.

    Science.gov (United States)

    Naumov, Pance; Yu, Pei; Sakurai, Kenji

    2008-07-03

    The extraordinary stability of the photoinduced red form of a cationic spiropyran ( k approximately 10 (-6) s (-1) in water and approximately 10 (-6) to less than 10 (-8) s (-1) in the solid state) was employed to obtain in situ X-ray diffraction evidence of its molecular structure. By UV excitation under selected experimental conditions, on average, approximately one third of the cations in a single crystal of spiropyran iodide salt was converted and retained as the red form during the experiment. According to the structure of the mixed crystal, the ring opening, which is due to increased distance between the spiro oxygen and carbon atoms, is associated with slight molecular flattening caused by concurrent out-of-plane shift (11.2(5) degrees ) of the pyranopyridinium half and in-plane shift (4.8(7) degrees ) of the indoline half. The overall geometry change of the cation fits the steric requirements imposed by the ion packing in the crystal and can be viewed as molecular flattening caused by breaking of the spiroconjugation. The structure of the cation confirms that (at least in the case of cationic spiropyrans) the product is confined in the crystal mainly as a zwitterionic resonance structure in cis configuration similar to the (early) transition state. Although the positive charge of the closed form facilitates the ring-opening reaction by moving the reactant closer to the transition state, neither the weakening of the spiropyran C-O bond nor the space provided by the iodide alone can account for the stability of the product. Instead, the density functional theory calculations indicate that the stabilization of the red form of the cationic relative to the neutral spiropyran is thermodynamically controlled, probably through compensation of the charge within the zwitterion by the methylpyridinium group.

  8. Study on Surface Properties for Non-polar Fluids with Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    吴畏; 陆九芳; 付东; 刘金晨; 李以圭

    2004-01-01

    The density functional theory, simplified by the local density approximation and mean-field approximation, is applied to study the surface properties of pure non-polar fluids. A reasonable long rang correction is adopted to avoid the truncation of the potential. The perturbation theory is applied to establish the equation for the phase equilibrium, in which the hard-core chain fluid is as the reference fluid and the Yukawa potential is used as the perturbation term. Three parameters, elk, d and ms, are regressed from the vapor-liquid equilibria, and the surface properties, including density profile, surface tension and local surface tension profile are predicted with these parameters.

  9. Toksisitas larvisida fraksi polar dan non polar herba Eclipta alba Hassk. terhadap larva nyamuk Aedes aegypti Linn.

    Directory of Open Access Journals (Sweden)

    Rosmanida Rosmanida

    1999-12-01

    Full Text Available Dengue Haemorrhagic Fever is a disease caused by virus and spread out by mosquitoes. Until now Aedes aegypti is thought as important vector in spreading procces of this disease. The general technique with synthetic chemical insecticide used to control density of mosquito population but this way causes the resistence of insect target, kill the untarget insect, and disturbs the environment quality. Due this problem, insecticide from plant is one of alternative such as Eclipta alba (Urang aring. The research aimed to distinguish toxicity larvacida degree between the polar fraction and non polar herba Eclipta alba to the growth of mosquito larva of Aedes aegypti. The experimental method applied with the complete random design used in this research. Each treatment to mosquito larvae of Aedes aegypti had replictions and the data was analyzed of Variance (ANOVA. The result showed that non polar fraction has the higher toxicity effect compared with the polar fraction. The concentration of LC non polar fraction 319.1826 ppm50, and concentration LC50 polar fraction is 1033.888 ppm and instar larva change of non polar fraction give higher elimination than polar fraction, non polar is 24% from population has change into IV instar and non polar 45%.

  10. Evaluation of various techniques for separation of non-polar modifier concentrates from petroleum waxy by-products

    Directory of Open Access Journals (Sweden)

    Fathi S. Soliman

    2014-09-01

    Full Text Available Two petroleum waxy by-products (light and middle slack wax crudes were evaluated for separation of non-polar modifiers by using different techniques. The results showed that, the light slack wax is selected as a suitable wax for separation of n-alkanes with even number of carbon atoms ranging from C20 to C26 for their high n-paraffin contents and can be used as non-polar structural modifiers. Different separation techniques; multistage fractional crystallization and liquid–solid chromatography; followed by the urea adduction technique have been used to separate non-polar modifier concentrates from the light slack wax crude. The light slack wax, its saturate components, the hard wax fractions isolated from light slack wax by the multistage fractional crystallization technique and their adducts were analyzed by GC to characterize and compare the produced components. The resulting data reveal that, the adducts of light slack wax and its saturate components; can be used as non-polar modifier concentrates of low carbon atoms (C20 + C22. From an economic point of view, the light slack wax adduct is selected as a non-polar modifier concentrate whereas, the separation step can be neglected to save energy. Meanwhile, the adduct of the hard wax isolated at 30 °C can be used as the preferable non-polar modifier concentrate of the high carbon number atoms (C24 + C26.

  11. Non-Polar Natural Products from Bromelia laciniosa, Neoglaziovia variegata and Encholirium spectabile (Bromeliaceae

    Directory of Open Access Journals (Sweden)

    Ole Johan Juvik

    2017-09-01

    Full Text Available Extensive regional droughts are already a major problem on all inhabited continents and severe regional droughts are expected to become an increasing and extended problem in the future. Consequently, extended use of available drought resistant food plants should be encouraged. Bromelia laciniosa, Neoglaziovia variegata and Encholirium spectabile are excellent candidates in that respect because they are established drought resistant edible plants from the semi-arid Caatinga region. From a food safety perspective, increased utilization of these plants would necessitate detailed knowledge about their chemical constituents. However, their chemical compositions have previously not been determined. For the first time, the non-polar constituents of B. laciniosa, N. variegata and E. spectabile have been identified. This is the first thorough report on natural products from N. variegata, E. spectabile, and B. laciniosa. Altogether, 20 non-polar natural products were characterized. The identifications were based on hyphenated gas chromatography-high resolution mass spectrometry (GC-HRMS and supported by 1D and 2D Nuclear Magnetic Resonance (NMR plant metabolomics.

  12. High indium non-polar InGaN clusters with infrared sensitivity grown by PAMBE

    Directory of Open Access Journals (Sweden)

    Shruti Mukundan

    2015-03-01

    Full Text Available Studies on the optical properties of InGaN alloy of relatively higher indium content are of potential interest to understand the effect of indium content on the optical band gap of epitaxial InGaN. We report the growth of self assembled non-polar high indium clusters of In0.55Ga0.45N over non-polar (11-20 a-plane In0.17Ga0.83N epilayer grown on a-plane (11-20GaN/(1-102 r-plane sapphire substrate using plasma assisted molecular beam epitaxy (PAMBE. Such structures are potential candidates for high brightness LEDs emitting in longer wavelengths. The high resolution X-ray diffraction studies revealed the formation of two distinct compositions of InxGa1−xN alloys, which were further confirmed by photoluminescence studies. A possible mechanism for the formation of such structure was postulated which was supported with the results obtained by energy dispersive X-ray analysis. The structure hence grown when investigated for photo-detecting properties, showed sensitivity to both infrared and ultraviolet radiations due to the different composition of InGaN region.

  13. Morphological, structural and electrical investigations on non-polar a-plane ZnO epilayers

    Science.gov (United States)

    Lautenschlaeger, Stefan; Eisermann, Sebastian; Hofmann, Michael N.; Roemer, Udo; Pinnisch, Melanie; Laufer, Andreas; Meyer, Bruno K.; von Wenckstern, Holger; Lajn, Alexander; Schmidt, Florian; Grundmann, Marius; Blaesing, Juergen; Krost, Alois

    2010-07-01

    We report on the growth of non-polar a-plane ZnO by CVD on r-plane-sapphire-wafers, a-plane GaN-templates and a-plane ZnO single-crystal substrates. Only the homoepitaxial growth approach leads to a Frank-van-der-Merwe growth mode, as shown by atomic force microscopy. The X-ray-diffraction spectra of the homoepitaxial thin films mirror the excellent crystalline quality of the ZnO substrate. The morphological and the structural quality of the homoepitaxial films is comparable to the best results for the growth on c-plane ZnO-substrates. The impurity incorporation, especially of group III elements, seems to be reduced when growing on the non-polar a-plane surface compared to the c-plane films as demonstrated by secondary ion mass spectrometry (SIMS). Optical properties have been investigated using low temperature photoluminescence measurements. We employed capacitance-voltage measurements ( C- V) to measure the background carrier density and its profile from substrate/film interface throughout the film to the surface. In thermal admittance spectroscopy (TAS) specific traps could be distinguished, and their thermal activation energies and capture cross sections could be determined.

  14. High indium non-polar InGaN clusters with infrared sensitivity grown by PAMBE

    Energy Technology Data Exchange (ETDEWEB)

    Mukundan, Shruti; Mohan, Lokesh; Chandan, Greeshma; Krupanidhi, S. B., E-mail: sbk@mrc.iisc.ernet.in; Shinde, Satish; Nanda, K. K. [Materials Research Centre, Indian Institute of Science, Bangalore 560012 (India); Roul, Basanta [Materials Research Centre, Indian Institute of Science, Bangalore 560012 (India); Central Research Laboratory, Bharat Electronics, Bangalore 560013 (India); Maiti, R.; Ray, S. K. [Department of Physics, Indian Institute of Technology, Kharagpur (India)

    2015-03-15

    Studies on the optical properties of InGaN alloy of relatively higher indium content are of potential interest to understand the effect of indium content on the optical band gap of epitaxial InGaN. We report the growth of self assembled non-polar high indium clusters of In{sub 0.55}Ga{sub 0.45}N over non-polar (11-20) a-plane In{sub 0.17}Ga{sub 0.83}N epilayer grown on a-plane (11-20)GaN/(1-102) r-plane sapphire substrate using plasma assisted molecular beam epitaxy (PAMBE). Such structures are potential candidates for high brightness LEDs emitting in longer wavelengths. The high resolution X-ray diffraction studies revealed the formation of two distinct compositions of In{sub x}Ga{sub 1−x}N alloys, which were further confirmed by photoluminescence studies. A possible mechanism for the formation of such structure was postulated which was supported with the results obtained by energy dispersive X-ray analysis. The structure hence grown when investigated for photo-detecting properties, showed sensitivity to both infrared and ultraviolet radiations due to the different composition of InGaN region.

  15. Application of response surface methodology for exploring β-cyclodextrin effects on the decoloration of spiropyran complexes

    Science.gov (United States)

    Wang, Li-Fen

    2016-10-01

    Response surface method is applied here to trace the photochromic path and explore the substituent and β-cyclodextrin effects on the decoloration of the spiropyran/β-cyclodextrin polymer (SP/CDP) complex. Calculations support the ultraviolet/visible experimental results, suggesting that introducing an electron-withdrawing group to the benzopyryl moiety of SPs favors an enhancement in their decoloration, whereas replacing the benzopyryl with a naphthopyryl moiety obstructs their decoloration. CDP complexation weakens the C1sbnd O bond of the closed SP form and enhances the polar zwitterionic structure in the open photomerocynine form. However, the electron-withdrawing group strengthens the interaction of benzopyryl SPs with CDP, thereby hindering their decoloration.

  16. Photochromic paper from wood pulp modification via layer-by-layer assembly of pulp fiber/chitosan/spiropyran.

    Science.gov (United States)

    Tian, Xiaojun; Wang, Bin; Li, Jinpeng; Zeng, Jinsong; Chen, Kefu

    2017-02-10

    Cellulosic fiber introducing with photochromic properties can be used in many fields such as security packaging, printing paper, and rewritable paper. To introduce photochromic property to individual fiber, a polyelectrolyte composite layer composed of cationic chitosan (CS) and anionic carboxyl-containing spiropyran (SPCOOH) on pulp fibers was designed using layer-by-layer assembly technique. Scanning electron microscope observation showed that the SPCOOH was successfully absorbed onto the surface of fiber. The photochromic characteristic of LbL-treated fiber could be triggered by UV-vis absorption spectrum and the LbL-treated fibers had a good compatibility with pulp fibers. This study gives a highly effective method to impart the photochromic characteristic to paper.

  17. Role of the electronegativity for the interface properties of non-polar heterostructures

    KAUST Repository

    Nazir, Safdar

    2012-04-01

    Density functional theory is used to investigate the interfaces in the non-polar ATiO 3/SrTiO 3 (A=Pb, Ca, Ba) heterostructures. All TiO 2-terminated interfaces show an insulating behavior. By reduction of the O content in the AO, SrO, and TiO 2 layers, metallic interface states develop, due to the occupation of the Ti 3d orbitals. For PbTiO 3/SrTiO 3, the Pb 6p states cross the Fermi energy. O vacancy formation energies depend strictly on the electronegativity and the effective volume of the A ion, while the main characteristics of the interface electronic states are maintained. © Europhysics Letters Association, 2012.

  18. Homoepitaxial HVPE-GaN growth on non-polar and semi-polar seeds

    Science.gov (United States)

    Amilusik, M.; Sochacki, T.; Lucznik, B.; Fijalkowski, M.; Smalc-Koziorowska, J.; Weyher, J. L.; Teisseyre, H.; Sadovyi, B.; Bockowski, M.; Grzegory, I.

    2014-10-01

    In this work homoepitaxial HVPE-GaN growth on non-polar and semi-polar GaN seeds was described. Two crystallization processes, in the same experimental conditions but using different carrier gases: N2 and H2, were performed. An influence of growth directions and growth conditions on the growth rate and properties (morphology, structural quality and oxygen and silicon contaminations) of obtained crystals were investigated and discussed. It was shown that the growth rate strongly depends on the growth direction and the carrier gas. It was demonstrated that for the semi-polar [20-21] direction it was possible to obtain high quality and highly conductive (without intentional doping) gallium nitride layers.

  19. Variability of non-polar secondary metabolites in the red alga Portieria.

    Science.gov (United States)

    Payo, Dioli Ann; Colo, Joannamel; Calumpong, Hilconida; de Clerck, Olivier

    2011-01-01

    Possible sources of variation in non-polar secondary metabolites of Portieria hornemannii, sampled from two distinct regions in the Philippines (Batanes and Visayas), resulting from different life-history stages, presence of cryptic species, and/or spatiotemporal factors, were investigated. PCA analyses demonstrated secondary metabolite variation between, as well as within, five cryptic Batanes species. Intraspecific variation was even more pronounced in the three cryptic Visayas species, which included samples from six sites. Neither species groupings, nor spatial or temporal based patterns, were observed in the PCA analysis, however, intraspecific variation in secondary metabolites was detected between life-history stages. Male gametophytes (102 metabolites detected) were strongly discriminated from the two other stages, whilst female gametophyte (202 metabolites detected) and tetrasporophyte (106 metabolites detected) samples were partially discriminated. These results suggest that life-history driven variations, and possibly other microscale factors, may influence the variation within Portieria species.

  20. Variability of Non-Polar Secondary Metabolites in the Red Alga Portieria

    Directory of Open Access Journals (Sweden)

    Olivier de Clerck

    2011-11-01

    Full Text Available Possible sources of variation in non-polar secondary metabolites of Portieria hornemannii, sampled from two distinct regions in the Philippines (Batanes and Visayas, resulting from different life-history stages, presence of cryptic species, and/or spatiotemporal factors, were investigated. PCA analyses demonstrated secondary metabolite variation between, as well as within, five cryptic Batanes species. Intraspecific variation was even more pronounced in the three cryptic Visayas species, which included samples from six sites. Neither species groupings, nor spatial or temporal based patterns, were observed in the PCA analysis, however, intraspecific variation in secondary metabolites was detected between life-history stages. Male gametophytes (102 metabolites detected were strongly discriminated from the two other stages, whilst female gametophyte (202 metabolites detected and tetrasporophyte (106 metabolites detected samples were partially discriminated. These results suggest that life-history driven variations, and possibly other microscale factors, may influence the variation within Portieria species.

  1. Application of classical thermodynamics to the conductivity in non-polar media

    Science.gov (United States)

    Gourdin-Bertin, S.; Chassagne, C.

    2016-06-01

    Electrical conductivity in non-polar media is a subject which recently regained interest. If most of experiments and theoretical developments were done more than 50 years ago, new experiments and theories have been recently published. As the electrical conductivity describes, at low field, the equilibrium state of a system, it is natural to apply theories based on equilibrium thermodynamics. In this article, well-established classical thermodynamics and solvations models are applied to recently published data. This enables to get a new insight in intriguing phenomena, such as the linear dependence of the conductivity on the concentration of ionic surfactant and the evaluation of conductivity for the mixture of two miscible fluids, such as alcohol and alcane, which have very different conductivities.

  2. Molecular dynamics analysis of the friction between a water-methanol liquid mixture and a non-polar solid crystal surface

    Science.gov (United States)

    Nakaoka, Satoshi; Yamaguchi, Yasutaka; Omori, Takeshi; Joly, Laurent

    2017-05-01

    We performed molecular dynamics analysis of the momentum transfer at the solid-liquid interface for a water-methanol liquid mixture between parallel non-polar solid walls in order to understand the strong decrease of the friction coefficient (FC) induced by the methanol adsorption at the surface observed in our previous work [S. Nakaoka et al., Phys. Rev. E 92, 022402 (2015)]. In particular, we extracted the individual contributions of water and methanol molecules to the total FC and found that the molecular FC for methanol was larger than that for water. We further showed that the reduction of the total solid-liquid FC upon the increase of the methanol molar fraction in the first adsorption layer occurred as a result of a decrease in the molecular number density as well as a decrease in the molecular FCs of both molecules. Analysis of the molecular orientation revealed that the decrease of the molecular FC of methanol resulted from changes of the contact feature onto the solid surface. Specifically, methanol molecules near the solid surface had their C-O bond parallel to the surface with both CH3 and O sites contacting the solid at low methanol molar fraction, while they had their C-O bond outward from the surface with only the CH3 site contacting the solid at higher methanol molar fraction. The mechanisms discussed in this work could be used to search for alternative water additives to further reduce the solid-liquid friction.

  3. Evaluation of Extraction Protocols for Simultaneous Polar and Non-Polar Yeast Metabolite Analysis Using Multivariate Projection Methods

    Directory of Open Access Journals (Sweden)

    Nicolas P. Tambellini

    2013-07-01

    Full Text Available Metabolomic and lipidomic approaches aim to measure metabolites or lipids in the cell. Metabolite extraction is a key step in obtaining useful and reliable data for successful metabolite studies. Significant efforts have been made to identify the optimal extraction protocol for various platforms and biological systems, for both polar and non-polar metabolites. Here we report an approach utilizing chemoinformatics for systematic comparison of protocols to extract both from a single sample of the model yeast organism Saccharomyces cerevisiae. Three chloroform/methanol/water partitioning based extraction protocols found in literature were evaluated for their effectiveness at reproducibly extracting both polar and non-polar metabolites. Fatty acid methyl esters and methoxyamine/trimethylsilyl derivatized aqueous compounds were analyzed by gas chromatography mass spectrometry to evaluate non-polar or polar metabolite analysis. The comparative breadth and amount of recovered metabolites was evaluated using multivariate projection methods. This approach identified an optimal protocol consisting of 64 identified polar metabolites from 105 ion hits and 12 fatty acids recovered, and will potentially attenuate the error and variation associated with combining metabolite profiles from different samples for untargeted analysis with both polar and non-polar analytes. It also confirmed the value of using multivariate projection methods to compare established extraction protocols.

  4. Remarks on energetic conditions for positronium formation in non-polar solids. Coupled Dipole Method application

    CERN Document Server

    Pietrow, Marek

    2015-01-01

    A numerical program calculating an energy of a positron or (and) an electron near the free volume in solid n-alkanes has been build. The theory of interaction of e+ or (and) e- with this non-polar media based on polarizability has been introduced. The energy of the e+ -- e- pair in the bulk was compared to that calculated when the pair forms a positronium (Ps) inside the free volume. The calculations are based on the Coupled Dipole Method and the dipole-dipole interaction energy for induced dipoles is taken into account. Furthermore, a correction of a local permittivity for the e+ -- e- interaction is calculated taking into account the non-isotropic medium between them. The method is a step toward more accurate calculations of energetic conditions during the Ps formation in matter. The possibility of emission of the excess energy of the Ps formation as electromagnetic radiation is discussed. It is argued that if this radiation is observed, it can be used as a new spectroscopic tool providing information about...

  5. In-gap states on the non-polar (110) surface of SmB6

    Science.gov (United States)

    Denlinger, J. D.; Jang, Sooyoung; Min, C.-H.; Reinert, F.; Kang, Boyoun; Cho, B.-K.; Kim, D. J.; Fisk, Z.; Allen, J. W.

    Mixed-valent SmB6 with a temperature-dependent bulk gap is the first candidate example of a new class of strongly correlated topological insulators with f- d band inversion. The topological origin of in-gap states on cleaved (001) surfaces as measured by angle-resolved photoemission (ARPES) is not without controversy, since the X states span the full ~20 meV hybridization gap at low temperature without exhibiting any clear Dirac point. Furthermore, reports exist of band-bending due to the polarity of the (001) surface and depth-dependent deviations from bulk stoichiometry or Sm valency. In this work we explore ARPES of the non - polar (110) surface of SmB6 prepared by polishing and high-temperature annealing. We find in-gap states at X and Y points with very similar properties as the (001) X states. We discuss the relevance of these findings to the TI and other proposed models, and to the recent discrepancy between 2D and 3D interpretations of dHvA Fermi surface orbits. Supported by U.S. DOE at the Advanced Light Source (DE-AC02-05CH11231).

  6. Composition of the non-polar extracts and antimicrobial activity of Chorisia insignis HBK. leaves

    Directory of Open Access Journals (Sweden)

    Salma Ahmed Mahmoud El Sawi

    2014-12-01

    Full Text Available Objective: To investigate the chemical constituents of the petroleum ether extract and the ether fraction of the 70% ethanol extract of Chorisia insignis HBK. leaves, as well as screen its antimicrobial activity. Methods: Different chromatographic methods were applied to investigate the non-polar extracts and the diffusion assay method was applied to study the antimicrobial activity. Results: A total of 50 compounds from the unsaponifiable matter and 20 fatty acid methyl esters were identified from the petroleum ether extract by GC/MS analysis. n-Hentriacontane, n-tritriacontane, stigmastanol, 3-methoxy-5, 6-dihydrostigmasterol, 7,8-dihydroergosterol, 4-methylcholesterol, cholestanol, multiflorenol, cholest-5-en-3-one, cholest-6-one, 5,6- dihydroergosterol, stigmasterol, dihydroalbigenin and 11-methyl-Δ5,7,9,15,17,23-triacont-hex-ene were isolated from the petroleum ether extract. Methyl heptacosanoate and quinic acid ester of rhamnose were isolated from the ether fraction of the 70% ethanol extract. Antimicrobial activity of the total alcohol extract and the successive fractions showed that the ether and the ethyl acetate fractions have potent antibacterial activity against Bacillus subtilis and Bacillus cereus. Conclusions: The ether and the ethyl acetate fractions could be used in pharmaceutical formulations as antibacterial agents against Bacillus subtilis and Bacillus cereus, and further clinical trials should be performed in order to support the above investigations.

  7. Piezoelectricity and rotostriction through polar and non-polar coupled instabilities in bismuth-based piezoceramics

    Science.gov (United States)

    Acosta, Matias; Schmitt, Ljubomira A.; Cazorla, Claudio; Studer, Andrew; Zintler, Alexander; Glaum, Julia; Kleebe, Hans-Joachim; Donner, Wolfgang; Hoffman, Mark; Rödel, Jürgen; Hinterstein, Manuel

    2016-07-01

    Coupling of order parameters provides a means to tune functionality in advanced materials including multiferroics, superconductors, and ionic conductors. We demonstrate that the response of a frustrated ferroelectric state leads to coupling between order parameters under electric field depending on grain orientation. The strain of grains oriented along a specific crystallographic direction, , is caused by converse piezoelectricity originating from a ferrodistortive tetragonal phase. For hhh> oriented grains, the strain results from converse piezoelectricity and rotostriction, as indicated by an antiferrodistortive instability that promotes octahedral tilting in a rhombohedral phase. Both strain mechanisms combined lead to a colossal local strain of (2.4 ± 0.1) % and indicate coupling between oxygen octahedral tilting and polarization, here termed “rotopolarization”. These findings were confirmed with electromechanical experiments, in situ neutron diffraction, and in situ transmission electron microscopy in 0.75Bi1/2Na1/2TiO3-0.25SrTiO3. This work demonstrates that polar and non-polar instabilities can cooperate to provide colossal functional responses.

  8. UV-induced self-assembly of the inclusion complexes formed between a long-chain photochromic spiropyran and cyclodextrins

    Institute of Scientific and Technical Information of China (English)

    隋强; 周金渭; 何炜; 李仲杰; 王艳乔

    1999-01-01

    Photochromic spiropyran with a long chain alkyl substitute can form axial complexes with α-, β-, and γ-cyclodextrin, respectively. The complexes show normal photochromism. The novel property of the colored forms of the inclusion complexes is that they can assemble into dimers at relatively low concentration or J-aggregates at relatively high concentration. For α-, β-, and γ-cyclodextrin, λmax of the J-aggregates appear at 700 650, and 630 nm, respectively. The sizes of the cavities of cyclodextrins have very little effect on the spectra and decoloration kinetics of the dimers, but have great effects on the spectra of the J-aggregates. Unlike the charge transfer complex of Krongauz, the decoloration process of the dimers or J-aggregates cannot be described by an exponential or a two-exponential kinetics, but obey half-order kinetics very well. Another result that can be deduced from the kinetic analysis is that unlike the dimers formed in apolar solvents or in polymers, which consist of a color

  9. Preparation of stimuli-responsive functionalized latex nanoparticles: the effect of spiropyran concentration on size and photochromic properties.

    Science.gov (United States)

    Abdollahi, Amin; Mahdavian, Ali Reza; Salehi-Mobarakeh, Hamid

    2015-10-06

    Incorporation of photochromic compounds to polymer matrix through chemical bonding results in an enhancement of photoactivity and stabilization of optical properties. Here, spiropyran ethyl acrylate monomer (SPEA) was synthesized, and then photochromic particles bearing epoxy functional groups were prepared through semicontinuous emulsion copolymerization. Dynamic light scattering (DLS) and scanning electron microscopy (SEM) results depicted an increase in particle size and particle size distribution with the increase in SPEA monomer-surfactants ratio. Studies on photochromic properties by UV-vis analysis demonstrated a decrease in the absorption intensity despite the increase in SPEA content due to the enhancement in particle size. The prepared acrylic copolymer particles showed reasonable photostability, photoreversibility, and fast photoresponsivness according to the convenient test methods under UV/vis irradiation. DSC and DMTA analyses indicate an increase in Tg of the obtained copolymers with the increase in SPEA content. Finally, stimuli-responsive cellulosic papers were prepared by impregnation, and their photochromic behavior was investigated in dry and wet forms in various media under UV radiation. Morphology studies, due to stabilization of the photochromic copolymer on cellulose fibers, were conducted by SEM micrographs and showed good adhesion and compatibility between the two phases.

  10. Preparation of silica coatings heavily doped with spiropyran using perhydropolysilazane as the silica source and their photochromic properties.

    Science.gov (United States)

    Yamano, Akihiro; Kozuka, Hiromitsu

    2009-04-30

    Silica coatings doped with spiropyran (SP) were prepared using xylene solutions of perhydropolysilazane (PHPS) as the silica source, where the SP-doped PHPS coatings were prepared by spin-coating and the PHPS-to-silica conversion was achieved by exposing the coatings to the vapor from aqueous ammonia at room temperature. The films could be heavily doped with SP at SP/(SP + PHPS) mass ratio as high as 0.2. The as-deposited SP-doped PHPS films were transparent and light-yellow, which turned to red as the PHPS-to-silica conversion proceeded, where the absorbance at 500 nm increased. When the films were stored in air in the dark for 73 h after the exposure treatment, the absorbance at 500 nm further increased, where the film turned from red to dark red. The SP-doped silica coatings thus obtained showed reversible photochromic reaction, where the absorbance at 500 nm decreased and increased when the films were irradiated with visible and ultraviolet light, respectively. The pencil hardness of the films was higher than 9H at a load of 1 kg, while significant amount of SP was leached out when the films were soaked in xylene.

  11. Schottky contact formation on polar and non-polar AlN

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, Pramod; Bryan, Isaac; Bryan, Zachary; Tweedie, James; Kirste, Ronny; Collazo, Ramon; Sitar, Zlatko [Department of Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27695-7919 (United States)

    2014-11-21

    The interfaces of m- and c-plane AlN with metals of different work functions and electro-negativities were characterized and the Schottky barrier heights were measured. The Schottky barrier height was determined by measuring the valence band maximum (VBM) with respect to the Fermi level at the surface (interface) before (after) metallization. VBM determination included accurate modeling and curve fitting of density of states at the valence band edge with the XPS data. The experimental behavior of the barrier heights could not be explained by the Schottky-Mott model and was modeled using InterFace-Induced Gap States (IFIGS). A slope parameter (S{sub X}) was used to incorporate the density of surface states and is a measure of Fermi level pinning. The experimental barriers followed theoretical predictions with a barrier height at the surface Fermi level (Charge neutrality level (CNL)) of ∼2.1 eV (∼2.7 eV) on m-plane (c-plane) and S{sub X} ∼ 0.36 eV/Miedema unit. Slope parameter much lower than 0.86 implied a surface/interface states dominated behavior with significant Fermi level pinning and the measured barrier heights were close to the CNL. Titanium and zirconium provided the lowest barriers (1.6 eV) with gold providing the highest (2.3 eV) among the metals analyzed on m-plane. It was consistently found that barrier heights decreased from metal polar to non-polar surfaces, in general, due to an increasing CNL. The data indicated that charged IFIGS compensate spontaneous polarization charge. These barrier height and slope parameter measurements provided essential information for designing Schottky diodes and other contact-based devices on AlN.

  12. Nitrobenzene anti-parallel dimer formation in non-polar solvents

    Directory of Open Access Journals (Sweden)

    Toshiyuki Shikata

    2014-06-01

    Full Text Available We investigated the dielectric and depolarized Rayleigh scattering behaviors of nitrobenzene (NO2-Bz, which is a benzene mono-substituted with a planar molecular frame bearing the large electric dipole moment 4.0 D, in non-polar solvents solutions, such as tetrachloromethane and benzene, at up to 3 THz for the dielectric measurements and 8 THz for the scattering experiments at 20 °C. The dielectric relaxation strength of the system was substantially smaller than the proportionality to the concentration in a concentrated regime and showed a Kirkwood correlation factor markedly lower than unity; gK ∼ 0.65. This observation revealed that NO2-Bz has a tendency to form dimers, (NO2-Bz2, in anti-parallel configurations for the dipole moment with increasing concentration of the two solvents. Both the dielectric and scattering data exhibited fast and slow Debye-type relaxation modes with the characteristic time constants ∼7 and ∼50 ps in a concentrated regime (∼15 and ∼30 ps in a dilute regime, respectively. The fast mode was simply attributed to the rotational motion of the (monomeric NO2-Bz. However, the magnitude of the slow mode was proportional to the square of the concentration in the dilute regime; thus, the mode was assigned to the anti-parallel dimer, (NO2-Bz2, dissociation process, and the slow relaxation time was attributed to the anti-parallel dimer lifetime. The concentration dependencies of both the dielectric and scattering data show that the NO2-Bz molecular processes are controlled through a chemical equilibrium between monomers and anti-parallel dimers, 2NO2-Bz ↔ (NO2-Bz2, due to a strong dipole-dipole interaction between nitro groups.

  13. Synthesis of Novel Iono- and Photochromic Spiropyrans Derived from 6,7-Dihydroxy-8-Formyl-4-Methyl-2H-Chromene-2-One

    Directory of Open Access Journals (Sweden)

    Olga G. Nikolaeva

    2009-01-01

    Full Text Available Novel photochromic spiropyrans (SPPs containing 6′-hydroxy group were synthesized and their spectral properties as well as abilities for complexation with metal ions studied. In solutions they exist as equilibrium mixture of spirocyclic (A and merocyanine (B isomers. The largest content of merocyanine form was found for the derivative with an electron-donating methyl group in position 5 of hetaryl fragment. The irradiation of SPPs in acetonitrile shifts the equilibrium to the B form. Similar effect causes the addition of metal cations due to formation of colored complexes with merocyanine isomers.

  14. Non-polar lipids accumulate during storage of transfusion products and do not contribute to the onset of transfusion-related acute lung injury.

    Science.gov (United States)

    Peters, A L; Vervaart, M A T; van Bruggen, R; de Korte, D; Nieuwland, R; Kulik, W; Vlaar, A P J

    2017-01-01

    The accumulation of non-polar lipids arachidonic acid, 5-hydroxyeicosatetraenoic acid (HETE), 12-HETE and 15-HETE during storage of transfusion products may play a role in the onset of transfusion-related acute lung injury (TRALI), a syndrome of respiratory distress after transfusion. We investigated non-polar lipid accumulation in red blood cells (RBCs) stored for 42 days, plasma stored for 7 days at either 4 or 20°C and platelet (PLT) transfusion products stored for 7 days. Furthermore, we investigated whether transfusion of RBCs with increased levels of non-polar lipids induces TRALI in a 'two-hit' human volunteer model. All products were produced following Dutch Blood Bank protocols and are according to European standards. Non-polar lipids were measured with high-performance liquid chromotography followed by mass spectrometry. All non-polar lipids increased in RBCs after 21 days of storage compared to baseline. The non-polar lipid concentration in plasma increased significantly, and the increase was even more pronounced in products stored at 20°C. In platelets, baseline levels of 5-HETE and 15-HETE were higher than in RBCs or plasma. However, the non-polar lipids did not change significantly during storage of PLT products. Infusion of RBCs with increased levels of non-polar lipids did not induce TRALI in LPS-primed human volunteers. We conclude that non-polar lipids accumulate in RBC and plasma transfusion products and that accumulation is temperature dependent. Accumulation of non-polar lipids does not appear to explain the onset of TRALI (Dutch Trial Register - NTR4455). © 2016 International Society of Blood Transfusion.

  15. The atomic structure of polar and non-polar InGaN quantum wells and the green gap problem.

    Science.gov (United States)

    Humphreys, C J; Griffiths, J T; Tang, F; Oehler, F; Findlay, S D; Zheng, C; Etheridge, J; Martin, T L; Bagot, P A J; Moody, M P; Sutherland, D; Dawson, P; Schulz, S; Zhang, S; Fu, W Y; Zhu, T; Kappers, M J; Oliver, R A

    2017-02-03

    We have used high resolution transmission electron microscopy (HRTEM), aberration-corrected quantitative scanning transmission electron microscopy (Q-STEM), atom probe tomography (APT) and X-ray diffraction (XRD) to study the atomic structure of (0001) polar and (11-20) non-polar InGaN quantum wells (QWs). This paper provides an overview of the results. Polar (0001) InGaN in QWs is a random alloy, with In replacing Ga randomly. The InGaN QWs have atomic height interface steps, resulting in QW width fluctuations. The electrons are localised at the top QW interface by the built-in electric field and the well-width fluctuations, with a localisation energy of typically 20meV. The holes are localised near the bottom QW interface, by indium fluctuations in the random alloy, with a localisation energy of typically 60meV. On the other hand, the non-polar (11-20) InGaN QWs contain nanometre-scale indium-rich clusters which we suggest localise the carriers and produce longer wavelength (lower energy) emission than from random alloy non-polar InGaN QWs of the same average composition. The reason for the indium-rich clusters in non-polar (11-20) InGaN QWs is not yet clear, but may be connected to the lower QW growth temperature for the (11-20) InGaN QWs compared to the (0001) polar InGaN QWs.

  16. The flotation of Roşia Poieni copper ore in column machine, with non-polar oils addition

    Directory of Open Access Journals (Sweden)

    Ciocani V.

    2005-11-01

    Full Text Available The most important natural resource of copper in Romania is the ore deposit of Roşia Poieni. At present, the utilization of Roşia Poieni poorphyry copper ore is possible by extraction in quarry of the mass ore and mineral processing into a technological flux with modest results for the value of metal recovery in concentrate 70-72 % and an average contents of 16,5 % Cu. Our researches were directed to studies regarding test and utilisation of special procedure of flotation – addition of the non-polar oil – applied to advanced grinding ore with column type machines.

  17. Radiative recombination mechanisms in polar and non-polar InGaN/GaN quantum well LED structures

    Science.gov (United States)

    Badcock, T. J.; Ali, M.; Zhu, T.; Pristovsek, M.; Oliver, R. A.; Shields, A. J.

    2016-10-01

    We study the photoluminescence internal quantum efficiency (IQE) and recombination dynamics in a pair of polar and non-polar InGaN/GaN quantum well (QW) light-emitting diode (LED) structures as a function of excess carrier density and temperature. In the polar LED at 293 K, the variation of radiative and non-radiative lifetimes is well described by a modified ABC type model which accounts for the background carrier concentration in the QWs due to unintentional doping. As the temperature is reduced, the sensitivity of the radiative lifetime to excess carrier density becomes progressively weaker. We attribute this behaviour to the reduced mobility of the localised electrons and holes at low temperatures, resulting in a more monomolecular like radiative process. Thus we propose that in polar QWs, the degree of carrier localisation determines the sensitivity of the radiative lifetime to the excess carrier density. In the non-polar LED, the radiative lifetime is independent of excitation density at room temperature, consistent with a wholly excitonic recombination mechanism. These findings have significance for the interpretation of LED efficiency data within the context of the ABC recombination model.

  18. Effects of n-alkanes on compositions of cellular non-polar lipids in Aspergillus sp. isolated from soils

    Energy Technology Data Exchange (ETDEWEB)

    Miyazima, M.; Iida, M.; Iizuka, H.

    1985-01-01

    A strain of hydrocarbon-using filamentous fungi, Aspergillus sp. No. 250-2, was grown on n-alkanes (C/sub 11/ to C/sub 16/) and glucose as the sole carbon and energy sources, and the distribution of cellular non-polar lipids was determined. The non-polar lipids were examined by thin-layer chromatography; they were sterols, sterol esters, diglycerides, triglycerides, and free fatty acids, and the major lipids were free fatty acids and triglycerides on all substrates. Free fatty acids were mainly even-chain saturated acids on all substrates. When grown on n-C/sub 11/ to 15, the unsaturated fatty acids were mainly incorporated into triglyceride, but there were saturated fatty acids with n-C/sub 16/ and glucose. The proportion of C/sub 16/.0 acid was increased markedly in n-C/sub 16/-grown cells, but C18:0 acid was increased in glucose-grown cells. Compositions of odd-chain fatty acids were slightly increased in both free fatty acids and triglycerides from n-C/sub 15/-grown cells. It is suggested that n-alkanes as substrates influenced the incorporation of fatty acids into triglyceride.

  19. Characterisation and analytical potential of a photo-responsive polymeric material based on spiropyran.

    Science.gov (United States)

    Byrne, Robert; Ventura, Claudia; Benito Lopez, Fernando; Walther, Adelheid; Heise, Andreas; Diamond, Dermot

    2010-12-15

    In this paper we consider the critical issues inhibiting the widespread deployment of bio/chemo-sensors in wireless sensor networks. Primary among these is the problem of performing calibration at remote locations, and the consequent need for integrated fluidic systems for performing tasks like sampling, calibration and detection. Our conclusion is that low-cost, bio/chemo-sensing platforms that provide reliable information over long periods of use will only be realised through the use of microfluidic platforms that are much more biomimetic in nature than technologies employed in current devices. Central to driving down costs will be the development of fluidic platforms with integrated soft polymer actuators that will replace existing pumps and valves. A particularly attractive approach is to employ photo-controlled polymer actuators, wherein the status of the material can be effectively switched using light, as this allows physical separation of the control layer from the fluidic platform layer in a planar system. This, in principle, should greatly simplify manufacturing and therefore drive down costs. In this paper, we describe a polymeric gel and a linear polymer modified with a photochromic moiety and show that it is possible to utilize photochromic molecules for performing sensing and actuating functions.

  20. Hydration of non-polar anti-parallel β-sheets

    Energy Technology Data Exchange (ETDEWEB)

    Urbic, Tomaz [Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana (Slovenia); Dias, Cristiano L., E-mail: cld@njit.edu [Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982 (United States)

    2014-04-28

    In this work we focus on anti-parallel β-sheets to study hydration of side chains and polar groups of the backbone using all-atom molecular dynamics simulations. We show that: (i) water distribution around the backbone does not depend significantly on amino acid sequence, (ii) more water molecules are found around oxygen than nitrogen atoms of the backbone, and (iii) water molecules around nitrogen are highly localized in the planed formed by peptide backbones. To study hydration around side chains we note that anti-parallel β-sheets exhibit two types of cross-strand pairing: Hydrogen-Bond (HB) and Non-Hydrogen-Bond (NHB) pairing. We show that distributions of water around alanine, leucine, and valine side chains are very different at HB compared to NHB faces. For alanine pairs, the space between side chains has a higher concentration of water if residues are located in the NHB face of the β-sheet as opposed to the HB face. For leucine residues, the HB face is found to be dry while the space between side chains at the NHB face alternates between being occupied and non-occupied by water. Surprisingly, for valine residues the NHB face is dry, whereas the HB face is occupied by water. We postulate that these differences in water distribution are related to context dependent propensities observed for β-sheets.

  1. Electric Deflection of Rotating Molecules

    CERN Document Server

    Gershnabel, E

    2010-01-01

    We provide a theory of the deflection of polar and non-polar rotating molecules by inhomogeneous static electric field. Rainbow-like features in the angular distribution of the scattered molecules are analyzed in detail. Furthermore, we demonstrate that one may efficiently control the deflection process with the help of short and strong femtosecond laser pulses. In particular the deflection process may by turned-off by a proper excitation, and the angular dispersion of the deflected molecules can be substantially reduced. We study the problem both classically and quantum mechanically, taking into account the effects of strong deflecting field on the molecular rotations. In both treatments we arrive at the same conclusions. The suggested control scheme paves the way for many applications involving molecular focusing, guiding, and trapping by inhomogeneous fields.

  2. In situ Observation of the Photochromism in the Langmuir Monolayer of a Non—typical Amphiphilic Spiropyran Derivative at the Air/Water Interface

    Institute of Scientific and Technical Information of China (English)

    贡浩飞; 唐季安; 王聪敏; 樊美公; 刘鸣华

    2003-01-01

    In situ photochromic process in the monolayer of aphotochromic spiropyran derivative without long alkyl chain,was investigated.The photochromism at the air/water interface under differnet surface pressures was studied by surface pressure-area isotherms,surface pressure-time curves,area-time curves and Brewster angle microscopy.Both forms of the compound were found to form monolayers at the air/water interface althouhg it does not have long alkyl chain.A large area expansion in the monolayer corresponding to a zreoth order reaction was found at the initial stage of the UV light irradiation.A series of dynamic investigations revealed that at high pressure after phase transition in the monolayer,the surface pressure changes greatly umder alternative irradiation of UV and visible light.An obvious morphological change accompanying with the photochromism was observed in situ.

  3. Double relaxation phenomena of associated binary polar liquid mixture in non-polar solvent under high frequency electric field

    Energy Technology Data Exchange (ETDEWEB)

    Sahoo, S. [Department of Electronics and Instrumentation Engg (India)], E-mail: swapansit@yahoo.co.in; Sit, S.K. [Department of Physics, Dr. Meghnad Saha Institute of Technology, Debhog, Haldia, Purba Medinipore, West Bengal 721657 (India)

    2009-06-25

    Double relaxation times {tau}{sub 2} and {tau}{sub 1} due to whole molecular rotation and the flexible parts of the binary polar liquid mixture (jk) 3-bromoaniline and 1-propanol dissolved in non-polar solvent (i) benzene were estimated in terms of measured real {chi}{sup '}{sub ijk}, imaginary {chi}{sup ''}{sub ijk} parts of complex high frequency orientational susceptibility {chi}{sub ijk}{sup *} and {chi}{sub 0ijk} which is real at 20, 30, 40 and 47 deg. C experimental temperatures for 0.0, 0.25, 0.50,0.75 and 1.00 mole fractions x{sub j}'s of 1-propanol under 9.1 GHz electric field. The slopes {omega}({tau}{sub 2} + {tau}{sub 1}) and intercepts {omega}{sup 2}{tau}{sub 2}{tau}{sub 1} of the analytical straight line equations used to estimate {tau}{sub 2} and {tau}{sub 1} were derived from Bergmann's equation [U. Saha, S.K. Sit, R.C. Basak, S. Acharyya, J. Phys. D: Appl. Phys. 27 (1994) 596] based on two Debye type dispersion model of binary polar mixture. The systems 3-bromoaniline in C{sub 6}H{sub 6} and 1-propanol in C{sub 6}H{sub 6} show {tau}{sub 2} and {tau}{sub 1} only at 47 deg. C temperature like 3-bromoaniline + 1-propanol in C{sub 6}H{sub 6} at 20 and 47 deg. C temperatures for 0.25 and 0.50 mole fractions x{sub j}'s of 1-propanol. The binary polar mixture for x{sub j} = 0.75 of 1-propanol is an exception exhibiting double relaxation times at all the experimental temperatures. The relative contributions c{sub 1} and c{sub 2} due to {tau}{sub 1} and {tau}{sub 2} for eight non-rigid systems were calculated from Froehlich's equation as well as graphical plots of {chi}{sup '}{sub ijk}/{chi}{sub 0ijk}-w{sub jk} and {chi}{sup ''}{sub ijk}/{chi}{sub 0ijk}-w{sub jk} curve at w{sub jk}{yields}0. c{sub 1} and c{sub 2} are positive for Froehlich's method whereas most of the c{sub 2}'s are negative for graphical method. The dipole moments {mu}{sub 2} and {mu}{sub 1} for all the systems are calculated from

  4. Microstructure of non-polar GaN on LiGaO2 grown by plasma-assisted MBE.

    Science.gov (United States)

    Shih, Cheng-Hung; Huang, Teng-Hsing; Schuber, Ralf; Chen, Yen-Liang; Chang, Liuwen; Lo, Ikai; Chou, Mitch Mc; Schaadt, Daniel M

    2011-06-15

    We have investigated the structure of non-polar GaN, both on the M - and A-plane, grown on LiGaO2 by plasma-assisted molecular beam epitaxy. The epitaxial relationship and the microstructure of the GaN films are investigated by transmission electron microscopy (TEM). The already reported epi-taxial relationship and for M -plane GaN is confirmed. The main defects are threading dislocations and stacking faults in both samples. For the M -plane sample, the density of threading dislocations is around 1 × 1011 cm-2 and the stacking fault density amounts to approximately 2 × 105 cm-1. In the A-plane sample, a threading dislocation density in the same order was found, while the stacking fault density is much lower than in the M -plane sample.

  5. [Four new compounds from the non-polar extract of the plant Amyris brenesii (Rutaceae) from Costa Rica].

    Science.gov (United States)

    Chavarría, Max; Castro, Victor; Poveda, Luis; Renato, Murillo

    2008-09-01

    Fractionation of a non polar extract of the aerial parts of Amyris brenesii collected in Rio Cuarto, Grecia, Costa Rica has resulted in the isolation of four new compounds, 6-hidroxy-6-O-(3-hidroxymethyl-3-methylalyl)-angelicin 1, 6-(N-acetyl-2-etanamin)-2,2-dimethyl-2H-cromen 2, the lignan 2,5-dehidrohinokinin 3 and N-acetyl-O-(geranyl)-tiramine 4. In addition, we isolated six previously known compounds: the lignans hinokinin 5 and Justicidin E 6, the coumarins scopoletin 7 and marmesin 8, 24-moretenoic acid 9, and the nitrogen compound O-(3,3-dimethylalyl)-halfordinol 10. All the separations were done with chromatographic techniques and the structures were elucidated by using 1D and 2D NMR techniques.

  6. Efficient Extraction of Astaxanthin from Phaffia rhodozyma with Polar and Non-polar Solvents after Acid Washing

    Institute of Scientific and Technical Information of China (English)

    YIN Chunhua; YANG Shuzhen; LIU Xiaolu; YAN Hai

    2013-01-01

    method of extracting astaxanthin from Phaffia rhodozyma with various solvents after acid washing was investigated.The extraction efficiency was distinctly increased after acid washing of P.rhodozyma cells.When the concentration of HCl was 0.4 mol·L-,the highest extraction efficiency of astaxanthin was achieved which was about three times higher than the control.Acetone or benzene as single polar or non-polar solvent was the most effective solvent in our research.With a combination of isopropanol and n-hexane (volume ratio of 2 ∶ 1),the maximal extraction efficiency was achieved,approximately 60% higher than that obtained with a single solvent.The liquid-solid ratio and the extracting time were also optimized.Under the optimum extraction conditions,the extraction yield of astaxanthin exceeded 98%.

  7. Simultaneous analysis method for polar and non-polar ginsenosides in red ginseng by reversed-phase HPLC-PAD.

    Science.gov (United States)

    Lee, Sa-Im; Kwon, Ha-Jeong; Lee, Yong-Moon; Lee, Je-Hyun; Hong, Seon-Pyo

    2012-02-23

    The paper describes the development of a simultaneous determination method for polar and non-polar ginsenosides in red ginseng with a reversed-phase high-performance liquid chromatography-pulsed amperometric detection method. This method could be applied directly without any pretreatment steps and enabled the performance of highly sensitive analysis within 1h. The detection (S/N=3) and quantification (S/N=10) limits for the ginsenosides ranged 0.02-0.10 ng and 0.1-0.3 ng, respectively. The linear regression coefficients ranged 0.9975-0.9998. Intra- and inter-day precisions were <9.91%. The mean recoveries ranged 98.08-103.06%. The total amount of ginsenosides in the hairy root of red ginseng was higher than that in the main root.

  8. Conversion of polar and non-polar algae oil lipids to fatty acid methyl esters with solid acid catalysts--A model compound study.

    Science.gov (United States)

    Asikainen, Martta; Munter, Tony; Linnekoski, Juha

    2015-09-01

    Bio-based fuels are becoming more and more important due to the depleting fossil resources. The production of biodiesel from algae oil is challenging compared to terrestrial vegetable oils, as algae oil consists of polar fatty acids, such as phospholipids and glycolipids, as well as non-polar triglycerides and free fatty acids common in vegetable oils. It is shown that a single sulphonated solid acid catalyst can perform the esterification and transesterification reactions of both polar and non-polar lipids. In mild reaction conditions (60-70 °C) Nafion NR50 catalyst produces methyl palmitate (FAME) from the palmitic acid derivatives of di-, and tri-glyceride, free fatty acid, and phospholipid with over 80% yields, with the glycolipid derivative giving nearly 40% yields of FAME. These results demonstrate how the polar and non-polar lipid derivatives of algal oil can be utilised as feedstocks for biodiesel production with a single catalyst in one reaction step.

  9. Effects of Si-doping on structural, electrical, and optical properties of polar and non-polar AlGaN epi-layers

    Science.gov (United States)

    Yang, Hongquan; Zhang, Xiong; Wang, Shuchang; Wang, Yi; Luan, Huakai; Dai, Qian; Wu, Zili; Zhao, Jianguo; Cui, Yiping

    2016-08-01

    The polar (0001)-oriented c-plane and non-polar (11 2 bar 0) -oriented a-plane wurtzite AlGaN epi-layers were successfully grown on polar (0001)-oriented c-plane and semi-polar (1 1 bar 02) -oriented r-plane sapphire substrates, respectively with various Si-doping levels in a low pressure metal organic chemical vapor deposition (MOCVD) system. The morphological, structural, electrical, and optical properties of the polar and non-polar AlGaN epi-layers were studied with scanning electron microscopy (SEM), X-ray diffraction (XRD), Hall effect, and Raman spectroscopy. The characterization results show that Si dopants incorporated into the polar and non-polar AlGaN films induced a relaxation of compressive residual strain and a generation of biaxial tensile strain on the surface in consequence of the dislocation climbing. In particular, it was found that the Si-induced compressive strain relaxation in the non-polar AlGaN samples can be promoted by the structural anisotropy as compared with the polar counterparts. The gradually increased relaxation of compressive residual strain in both polar and non-polar AlGaN samples with increasing Si-doping level was attributed to the Si-induced enhancement in the opportunity for the dislocations to interact and annihilate. This implies that the crystal quality for both polar and non-polar AlGaN epi-layers can be remarkably improved by Si-doping.

  10. An Analytic Equation of State Based on SAFT-CP for Binary Non-Polar Alkane Mixtures Across the Critical Point

    Institute of Scientific and Technical Information of China (English)

    周文来; 密建国; 贺刚; 于燕梅; 陈健

    2003-01-01

    The description using an analytic equation of state of thermodynamic properties near the critical points of fluids and their mixtures remains a challenging problem in the area of chemical engineering. Based on the statistical associating fluid theory across the critical point (SAFT-CP), an analytic equation of state is established in this work for non-polar mixtures. With two binary parameters, this equation of state can be used to calculate not only vapor-liquid equilibria but also critical properties of binary non-polar alkane mixtures with acceptable deviations.

  11. Non-polar In x Ga1-x N/GaN quantum dots: impact of dot size and shape anisotropies on excitonic and biexcitonic properties

    Science.gov (United States)

    Kanta Patra, Saroj; Schulz, Stefan

    2017-01-01

    In this work, we present a theoretical analysis of the built-in potential, the excitonic and biexcitonic properties of non-polar InGaN/GaN quantum dots by means of self-consistent Hartree calculations using \\mathbf{k}\\centerdot \\mathbf{p} theory. Special attention is paid to the impact of dot size and shape anisotropies on the results. Our calculations reveal that even though non-polar InGaN/GaN quantum dots exhibit strongly reduced built-in fields when compared to c-plane dots, the excitonic and biexcitonic properties are significantly affected by these residual fields. Furthermore, changes in the built-in field when the geometrical dot features are modified, result in an unusual variation of the exciton binding energy. All these findings highlight that the dot geometry significantly affects electronic and optical properties of non-polar InGaN/GaN systems. This is further supported by comparing our theoretical data with experimental literature results. Here, we analyze also trends in exciton and biexciton binding energies and discuss the potential use of non-polar InGaN/GaN dots for entangled photon emission via the time reordering scheme.

  12. Non-polar Extraction Effect Analysis of Mimusops elengi (L. bark to Larvae of Aedes aegypti (L.

    Directory of Open Access Journals (Sweden)

    Mutiara Widawati

    2012-11-01

    Full Text Available Tanjung or Mimusops elengi is one of a tree that has many therapeutic effects and has been widely studied as an alternative drug like anti-inflammatory agent, diarrhea, and asthma. This study tested the larvicidal ability of Tanjung bark extract for larvae of Aedes aegypti. The solvent that will be used for Mimusops elengi stem extraction in this research is semi-polar and non-polar solvent, which is ethyl acetate and hexane. The method used in this research was reflux extraction and proceed further with fractionation that has been analyzed by thin layer chromatography. The larvicidal activity of Mimusops elengi extract was tested using a bioassay method that has been established by WHO to determine LC50 and LC9O which can be processed further in order to compare the ejjicacy ofsolvent used. The LC50 value of the extract 1,2 and 3, were each 59.36 ppm, 82.53 ppm, and 110.42 ppm. The experimental results showed that hexane has the most powerful larvicidal ability compared to other extracts.

  13. Non-polar organic compounds in marine aerosols over the northern South China Sea: Influence of continental outflow.

    Science.gov (United States)

    Zhao, Yan; Zhang, Yingyi; Fu, Pingqing; Ho, Steven Sai Hang; Ho, Kin Fai; Liu, Fobang; Zou, Shichun; Wang, Shan; Lai, Senchao

    2016-06-01

    Filter samples of total suspended particle (TSP) collected during a cruise campaign over the northern South China Sea (SCS) from September to October 2013 were analyzed for non-polar organic compounds (NPOCs) as well as organic carbon (OC), elemental carbon (EC) and water-soluble ions. A total of 115 NPOCs species in groups of n-alkanes, polycyclic aromatic hydrocarbons (PAHs), iso-/antiso-alkanes, hopanes, steranes, methylalkanes, branched alkanes, cycloalkanes, alkenes and phthalates were detected. The characteristics of NPOCs in marine TSP samples were investigated to understand the sources from the Asian continent and other regions. The concentrations of total NPOCs ranged from 19.8 to 288.2 ng/m(3) with an average of 87.9 ng/m(3), which accounted for 0.8-1.7% (average 1.0%) of organic matter (OM). n-Alkanes was the predominant group, accounting for 43.1-79.5%, followed by PAHs (5.5-44.4%) and hopanes (1.6-11.4%). We found that primary combustion (biomass burning/fossil fuel combustion) was the dominant source for the majority of NPOCs (89.1%). Biomass burning in southern/southeastern China via long-range transport was proposed to be a major contributor of NPOCs in marine aerosols over the northern SCS, suggested by the significant correlations between nss-K(+) and NPOCs groups as well as the analysis of air mass back-trajectory and fire spots. For the samples with strong continental influence, the strong enhancement in concentrations of n-alkanes, PAHs, hopanes and steranes were attributed to fossil fuel (coal/petroleum) combustion. In addition, terrestrial plants waxes were another contributor to NPOCs.

  14. Observation of mid-infrared intersubband absorption in non-polar m-plane AlGaN/GaN multiple quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Kotani, Teruhisa, E-mail: kotani.teruhisa@sharp.co.jp [Institute for Nano Quantum Information Electronics, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Life and Environment Laboratories, Sharp Corporation, 2613-1 Ichinomoto-cho, Tenri, Nara 632-8567 (Japan); Arita, Munetaka [Institute for Nano Quantum Information Electronics, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Arakawa, Yasuhiko [Institute for Nano Quantum Information Electronics, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8505 (Japan)

    2014-12-29

    Mid-infrared (4.20–4.84 μm) intersubband absorption in non-polar m-plane Al{sub 0.5}Ga{sub 0.5}N/GaN multiple-quantum wells is observed at room temperature. 10 period Al{sub 0.5}Ga{sub 0.5}N/GaN multiple-quantum wells were grown on free-standing m-plane GaN substrates by metalorganic chemical vapor deposition (MOCVD), and the high-quality structural and optical properties are revealed by x-ray diffraction and photoluminescence studies. Through this we have demonstrated that MOCVD grown non-polar m-plane AlGaN/GaN quantum wells are a promising material for mid-infrared intersubband devices.

  15. 功能分子设计合成及原理性的分子尺寸器件研究%Minireview: molecular level devices based on electroactive tetrathiafulvalene and photochromic spiropyran

    Institute of Scientific and Technical Information of China (English)

    郭雪峰; 张德清; 朱道本

    2008-01-01

    This Minireview details the design, development, and demonstration of chemical strategies that are used to create molecular level devices and implement digital processing and communication. The design principle here is to integrate two informationally rich but relatively simple nanobuilding blocks with their complements through photoinduced electron transfer, redox processes, conformational changes,photoindueed energy and proton transfer, and supramolecular events into functional molecular devices.Depending on the abundant electrochemical properties of TTF, lots of D-A-D supramolecules and[2]rotaxanes with the different linkages were synthesized for studying photoinduced transient electron transfer and nanoreeording abilities. Also detailed below are the methods to take advantage of the distinct abilities of electron, energy, and proton transfer of photochromic spiropyran to design supramolecular ensembles and control their absorption, fluorescence, and conductive properties by light and chemical reagents. Based on the spectral and electrochemical behaviors of these ensembles, a whole bunch of novel molecular switches, logic gates, and molecular circuits were constructed. At last, we present an interesting insight into designing a new type of luminescent spiropyan molecules with stable merocyanine open form in solution as well as in the solid state.%详细综述了一些用于制备分子尺寸器件的化学策略的设计、发展和演示.其设计思想是通过各式各样的光诱导的电子、能量和质子转移机理,氧化还原反应,构象变化以及超分子原理,分别将2个信息量丰富而结构又比较简单的四硫富瓦烯和光致变色的螺吡喃分子,与它们性质互补的不同组分集成在一起来构建功能分子器件,用于完成快速的数字处理和传输.首先凭借四硫富瓦烯丰富的电化学性质,大量的D-A-D超分子和环轴烃分子已经被设计并成功合成.时间分辨的吸收和荧光光谱研

  16. Controlling Plasmon-Enhanced Fluorescence via Intersystem Crossing in Photoswitchable Molecules.

    Science.gov (United States)

    Wang, Mingsong; Hartmann, Gregory; Wu, Zilong; Scarabelli, Leonardo; Rajeeva, Bharath Bangalore; Jarrett, Jeremy W; Perillo, Evan P; Dunn, Andrew K; Liz-Marzán, Luis M; Hwang, Gyeong S; Zheng, Yuebing

    2017-08-21

    By harnessing photoswitchable intersystem crossing (ISC) in spiropyran (SP) molecules, active control of plasmon-enhanced fluorescence in the hybrid systems of SP molecules and plasmonic nanostructures is achieved. Specifically, SP-derived merocyanine (MC) molecules formed by photochemical ring-opening reaction display efficient ISC due to their zwitterionic character. In contrast, ISC in quinoidal MC molecules formed by thermal ring-opening reaction is negligible. The high ISC rate can improve fluorescence quantum yield of the plasmon-modified spontaneous emission, only when the plasmonic electromagnetic field enhancement is sufficiently high. Along this line, extensive photomodulation of fluorescence is demonstrated by switching the ISC in MC molecules at Au nanoparticle aggregates, where strongly enhanced plasmonic hot spots exist. The ISC-mediated plasmon-enhanced fluorescence represents a new approach toward controlling the spontaneous emission of fluorophores near plasmonic nanostructures, which expands the applications of active molecular plasmonics in information processing, biosensing, and bioimaging. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Molecule nanoweaver

    Science.gov (United States)

    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.

  18. Growth of non-polar (11-20 InGaN quantum dots by metal organic vapour phase epitaxy using a two temperature method

    Directory of Open Access Journals (Sweden)

    J. T. Griffiths

    2014-12-01

    Full Text Available Non-polar (11-20 InGaN quantum dots (QDs were grown by metal organic vapour phase epitaxy. An InGaN epilayer was grown and subjected to a temperature ramp in a nitrogen and ammonia environment before the growth of the GaN capping layer. Uncapped structures with and without the temperature ramp were grown for reference and imaged by atomic force microscopy. Micro-photoluminescence studies reveal the presence of resolution limited peaks with a linewidth of less than ∼500 μeV at 4.2 K. This linewidth is significantly narrower than that of non-polar InGaN quantum dots grown by alternate methods and may be indicative of reduced spectral diffusion. Time resolved photoluminescence studies reveal a mono-exponential exciton decay with a lifetime of 533 ps at 2.70 eV. The excitonic lifetime is more than an order of magnitude shorter than that for previously studied polar quantum dots and suggests the suppression of the internal electric field. Cathodoluminescence studies show the spatial distribution of the quantum dots and resolution limited spectral peaks at 18 K.

  19. Fatty acid profiles of polar and non-polar lipids of Pleurotus ostreatus and P. cornucopiae var. 'citrino-pileatus' grown at different temperatures.

    Science.gov (United States)

    Pedneault, Karine; Angers, Paul; Avis, Tyler J; Gosselin, André; Tweddell, Russell J

    2007-10-01

    The application of fatty acid (FA) composition data has now extended to studies of physiology, chemotaxonomy, and intrageneric differentiation, as well as to studies of human nutrition. Environmental factors such as nutritional components, oxygen, and temperature are known to affect lipid content and composition in living organisms, including fungi. In the present study, the polar and non-polar lipid content of Pleurotus ostreatus and P. cornucopiae var. citrino-pileatus fruiting bodies produced at temperatures ranging from 12-27 degrees C and from 17-27 degrees C, respectively, were analysed to evaluate the effect of temperature on lipid composition in these mushrooms. Results showed that lowering the growth temperature below 17 degrees C generally provided an expected increase in FA unsaturation in polar and non-polar lipids of P. ostreatus. Although raising the temperature above 17 degrees C did not show any clear-cut tendency in FA unsaturation, it did reveal that growth temperature had a differential effect on the FA profiles in fruiting bodies of P. ostreatus and P. cornucopiae. This study suggests that care should be taken when using FA content and unsaturation data for physiological, chemotaxonomic, and intrageneric differentiation studies, and that it may be possible to manipulate lipid unsaturation in Pleurotus spp. through modified growth temperatures.

  20. THE INFLUENCE OF POLAR AND NON-POLAR EMOLLIENTS ON THE STRUCTURE AND SKIN MOISTURIZING POTENTIAL OF THE EMULSIONS STABILIZED BY MIXED EMULSIFIER

    Directory of Open Access Journals (Sweden)

    Dragana Stojiljković

    2016-06-01

    Full Text Available The appropriate moisture content in the stratum corneum, as a superficial layer of the epidermis, provides softness and flexibility of the skin in different environmental conditions, and maintaining of skin humidity is very important in dermatology and dermocosmetology. In this paper, we investigated the skin moisturizing potential after a single application and structure of the emulsion of o/w type, stabilized by mixed emulsifier glycerylmonostearate self-emulsifying (GMSse, which contained polar emollients (PEG-7 glicerylcocoate and myristyl myristate and non-polar emollient (liquid paraffin, in a concentration of 10% (emulsions E1-E3, respectively. The emulsion structure was investigated by polarization microscopy, and the presence of different anisotropic structure was observed. The moisturizing potential after a single application and skin pH were investigated by skin bioengineering. Emulsions with polar emollients (E1 and E2 showed a statistically significant increase in skin moisture content after 30 minutes; 300 min after applications it did not exist; emulsion with a non-polar emollient (E3 showed significant moisturizing potential after 30 min and after 300 min probably as a consequence of occlusion. Nature and polarity of emollients affected the structure and properties of emulsions stabilized by anisotropic structures, and also the moisturizing level and pH of the skin immediately after their application.

  1. Atmospheric pressure chemical ionization studies of non-polar isomeric hydrocarbons using ion mobility spectrometry and mass spectrometry with different ionization techniques

    Science.gov (United States)

    Borsdorf, H.; Nazarov, E. G.; Eiceman, G. A.

    2002-01-01

    The ionization pathways were determined for sets of isomeric non-polar hydrocarbons (structural isomers, cis/trans isomers) using ion mobility spectrometry and mass spectrometry with different techniques of atmospheric pressure chemical ionization to assess the influence of structural features on ion formation. Depending on the structural features, different ions were observed using mass spectrometry. Unsaturated hydrocarbons formed mostly [M - 1]+ and [(M - 1)2H]+ ions while mainly [M - 3]+ and [(M - 3)H2O]+ ions were found for saturated cis/trans isomers using photoionization and 63Ni ionization. These ionization methods and corona discharge ionization were used for ion mobility measurements of these compounds. Different ions were detected for compounds with different structural features. 63Ni ionization and photoionization provide comparable ions for every set of isomers. The product ions formed can be clearly attributed to the structures identified. However, differences in relative abundance of product ions were found. Although corona discharge ionization permits the most sensitive detection of non-polar hydrocarbons, the spectra detected are complex and differ from those obtained with 63Ni ionization and photoionization. c. 2002 American Society for Mass Spectrometry.

  2. Growth of polar and non-polar nitride semiconductor quasi-substrates by hydride vapor phase epitaxy for the development of optoelectronic devices by molecular beam epitaxy

    Science.gov (United States)

    Moldawer, Adam Lyle

    The family of nitride semiconductors has had a profound influence on the development of optoelectronics for a large variety of applications. However, as of yet there are no native substrates commercially available that are grown by liquid phase methods as with Si and GaAs. As a result, the majority of electronic and optoelectronic devices are grown heteroepitaxially on sapphire and SiC. This PhD research addresses both the development of polar and non-polar GaN and AIN templates by Hydride Vapor Phase Epitaxy (HVPE) on sapphire and SiC substrates, as well as the growth and characterization of optoelectronic devices on these templates by molecular beam epitaxy (MBE). Polar and non-polar GaN templates have been grown in a vertical HVPE reactor on the C- and R-planes of sapphire respectively. The growth conditions have been optimized to allow the formation for thick (50um) GaN templates without cracks. These templates were characterized structurally by studying their surface morphologies by SEM and AFM, and their structure through XRD and TEM. The polar C-plane GaN templates were found to be atomically smooth. However, the surface morphology of the non-polar GaN films grown on the R-plane of sapphire were found to have a facetted surface morphology, with the facets intersecting at 120° angles. This surface morphology reflects an equilibrium growth, since the A-plane of GaN grows faster than the M-planes of GaN due to the lower atomic density of the plane. For the development of deep-UV optoelectronics, it is required to grow AIGaN quantum wells on AIN templates. However, since AIN is a high melting point material, such templates have to be grown at higher temperatures, close to half the melting point of the material (1500 °C). As these temperatures cannot be easily obtained by traditional furnace heating, an HVPE reactor has been designed to heat the substrate inductively to these temperatures. This apparatus has been used to grow high-quality, transparent AIN films

  3. Doping dependent blue shift and linewidth broadening of intersubband absorption in non-polar m-plane AlGaN/GaN multiple quantum wells

    Energy Technology Data Exchange (ETDEWEB)

    Kotani, Teruhisa, E-mail: tkotani@iis.u-tokyo.ac.jp [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Advanced Technology Research Laboratories, Sharp Corporation, 2613-1 Ichinomoto-cho, Tenri, Nara 632-8567 (Japan); Arita, Munetaka [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Arakawa, Yasuhiko [Institute for Nano Quantum Information Electronics, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan); Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505 (Japan)

    2015-09-14

    Blue shift and broadening of the absorption spectra of mid-infrared intersubband transition in non-polar m-plane AlGaN/GaN 10 quantum wells were observed with increasing doping density. As the doping density was increased from 6.6 × 10{sup 11} to 6.0 × 10{sup 12 }cm{sup −2} per a quantum well, the intersubband absorption peak energy shifted from 274.0 meV to 302.9 meV, and the full width at half maximum increased from 56.4 meV to 112.4 meV. Theoretical calculations reveal that the blue shift is due to many body effects, and the intersubband linewidth in doped AlGaN/GaN QW is mainly determined by scattering due to interface roughness, LO phonons, and ionized impurities.

  4. An absorbing microwave micro-solid-phase extraction device used in non-polar solvent microwave-assisted extraction for the determination of organophosphorus pesticides

    Energy Technology Data Exchange (ETDEWEB)

    Wang Ziming, E-mail: wangziming@jlu.edu.cn [College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); College of Environment and Resources, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Zhao Xin; Xu Xu; Wu Lijie; Su Rui; Zhao Yajing; Jiang Chengfei; Zhang Hanqi [College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012 (China); Ma Qiang [Chinese Academy of Inspection and Quarantine, Beijing 100123 (China); Lu Chunmei [College of Technology Center, Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun 130062 (China); Dong Deming [College of Environment and Resources, Jilin University, 2699 Qianjin Street, Changchun 130012 (China)

    2013-01-14

    Highlights: Black-Right-Pointing-Pointer An absorbing microwave {mu}-SPE device packed with activated carbon was used. Black-Right-Pointing-Pointer Absorbing microwave {mu}-SPE device was made and used to enrich the analytes. Black-Right-Pointing-Pointer Absorbing microwave {mu}-SPE device was made and used to heat samples directly. Black-Right-Pointing-Pointer MAE-{mu}-SPE was applied to the extraction of OPPs with non-polar solvent only. - Abstract: A single-step extraction-cleanup method, including microwave-assisted extraction (MAE) and micro-solid-phase extraction ({mu}-SPE), was developed for the extraction of ten organophosphorus pesticides in vegetable and fruit samples. Without adding any polar solvent, only one kind of non-polar solvent (hexane) was used as extraction solvent in the whole extraction step. Absorbing microwave {mu}-SPE device, was prepared by packing activated carbon with microporous polypropylene membrane envelope, and used as not only the sorbent in {mu}-SPE, but also the microwave absorption medium. Some experimental parameters effecting on extraction efficiency was investigated and optimized. 1.0 g of sample, 8 mL of hexane and three absorbing microwave {mu}-SPE devices were added in the microwave extraction vessel, the extraction was carried out under 400 W irradiation power at 60 Degree-Sign C for 10 min. The extracts obtained by MAE-{mu}-SPE were directly analyzed by GC-MS without any clean-up process. The recoveries were in the range of 93.5-104.6%, and the relative standard deviations were lower than 8.7%.

  5. Impact of water dilution and cation tail length on ionic liquid characteristics: Interplay between polar and non-polar interactions

    Science.gov (United States)

    Hegde, Govind A.; Bharadwaj, Vivek S.; Kinsinger, Corey L.; Schutt, Timothy C.; Pisierra, Nichole R.; Maupin, C. Mark

    2016-08-01

    The recalcitrance of lignocellulosic biomass poses a major challenge that hinders the economical utilization of biomass for the production of biofuel, plastics, and chemicals. Ionic liquids have become a promising solvent that addresses many issues in both the pretreatment process and the hydrolysis of the glycosidic bond for the deconstruction of cellulosic materials. However, to make the use of ionic liquids economically viable, either the cost of ionic liquids must be reduced, or a less expensive solvent (e.g., water) may be added to reduce the overall amount of ionic liquid used in addition to reducing the viscosity of the binary liquid mixture. In this work, we employ atomistic molecular dynamics simulations to investigate the impact of water dilution on the overall liquid structure and properties of three imidazolium based ionic liquids. It is found that ionic liquid-water mixtures exhibit characteristics that can be grouped into two distinct regions, which are a function of the ionic liquid concentration. The trends observed in each region are found to correlate with the ordering in the local structure of the ionic liquid that arises from the dynamic interactions between the ion pairs. Simulation results suggest that there is a high level of local ordering in the molecular structure at high concentrations of ionic liquids that is driven by the aggregation of the cationic tails and the anion-water interactions. It is found that as the concentration of ionic liquids in the binary mixture is decreased, there is a point at which the competing self and cross interaction energies between the ionic liquid and water shifts away from a cation-anion dominated regime, which results in a significant change in the mixture properties. This break point, which occurs around 75% w/w ionic liquids, corresponds to the point at which water molecules percolate into the ionic liquid network disrupting the ionic liquids' nanostructure. It is observed that as the cationic alkyl

  6. Atkins' molecules

    CERN Document Server

    Atkins, Peters

    2003-01-01

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

  7. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); 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.

  8. A HIGH SENSITIVE MICROWAVE MEASURING DEVICE OF THE MOISTURE CONTENT IN THE NON-POLAR DIELECTRIC LIQUIDS BASED ON AN INHOMOGENEOUS STEP COAXIAL RESONATOR

    Directory of Open Access Journals (Sweden)

    V. V. Rudakov

    2016-11-01

    Full Text Available Purpose. Objective is to create a moisture meter for non-polar liquid dielectrics with low volumetric moisture content of more than 10‑3 %. Methodology. Moisture measuring is based on dielcometric method. It is implemented as a resonant method of determining a capacitance measuring transducer. Measuring transducer capacitive type has a working and parasitic capacitance. It was suggested the definition of moisture on four of resonance frequencies: when the measuring transducer is turned off, one by one filled with air, «dry» and investigated liquid, to determine the parasitic capacitance of the measuring generator, and the parasitic capacitance of the measuring transducer and humidity. Measurement frequency was increased up to microwave range to increase the sensitivity. Measuring transducer with distributed parameters representing a step heterogeneous coaxial resonator is used by. This measuring transducer has a zero stray capacitance, because the potential electrode has a galvanic connection with an external coaxial electrode. Inductive ties loop is used to neglect parasitic capacitance of the measuring generator, and to increase the quality factor of the system. Measuring moisture is reduced to measuring the two frequencies of resonance frequency and «dry» and investigated liquid. Resonant characteristics transducer in a step inhomogeneous coaxial resonator have been investigated to determine the quality factor of filled with air and transformer oil, and experiments to measure the moisture content in transformer oil have been conducted. Results. Measuring transducer of distributed type is developed and researched – it is step inhomogeneous coaxial resonator. It has a smaller geometric length and larger scatter of the first and second resonant frequencies. Expression is obtained for determination of moisture on the basis of two resonant frequencies. The formula of the two frequencies to determine the moisture is correct. Resonant

  9. Thermodynamic description of equilibria in mixed fluids (H 2O-non-polar gas) over a wide range of temperature (25-700°C) and pressure (1-5000 bars)

    Science.gov (United States)

    Akinfiev, Nikolai; Zotov, Alexander

    1999-07-01

    A new method for computing complicated equilibria in hydrothermal mixed fluids, H 2O-non-polar gas, is proposed. The computation algorithm is based on the electrostatic approach for the interaction between aqueous species and H 2O. The approach uses the SUPCRT92 database and the HKF format and may be considered as an application of the revised HKF model for mixed H 2O-non-polar gas fluids. Thermodynamic properties of dissolved gases at high temperatures and pressures are calculated using the Redlich-Kwong approach. Dielectric permittivity of the mixed solvent is estimated by the modified Kirkwood equation. The proposed approach is validated using available experimental data on the dissociation constants of H 2O and NaCl and the solubility of both covalent and ion crystals (SiO 2, AgCl, Ag 2SO 4, Ca(OH) 2, CaCO 3) in H 2O-non-polar component (dioxane, Ar, CO 2) mixtures. Predicted and experimental data are in close agreement over a wide range of P- T- xgas conditions (up to 500°C, 4 kbar and 0.25-0.3 mole fraction of non-polar gas). It is also shown how the computation method can be applied to estimate the Born parameters of aqueous species. The proposed approach enables not only examination of isolated reactions, but the study of equilibria of whole systems. Thus, it allows modelling of mixed natural fluids.

  10. Cathodoluminescence study of Mg activation in non-polar and semi-polar faces of undoped/Mg-doped GaN core-shell nanorods

    Science.gov (United States)

    Hortelano, V.; Martínez, O.; Cuscó, R.; Artús, L.; Jiménez, J.

    2016-03-01

    Spectrally and spatially resolved cathodoluminescence (CL) measurements were carried out at 80 K on undoped/Mg-doped GaN core-shell nanorods grown by selective area growth metalorganic vapor phase epitaxy in order to investigate locally the optical activity of the Mg dopants. A study of the luminescence emission distribution over the different regions of the nanorods is presented. We have investigated the CL fingerprints of the Mg incorporation into the non-polar lateral prismatic facets and the semi-polar facets of the pyramidal tips. The amount of Mg incorporation/activation was varied by using several Mg/Ga flow ratios and post-growth annealing treatment. For lower Mg/Ga flow ratios, the annealed nanorods clearly display a donor-acceptor pair band emission peaking at 3.26-3.27 eV and up to 4 LO phonon replicas, which can be considered as a reliable indicator of effective p-type Mg doping in the nanorod shell. For higher Mg/Ga flow ratios, a substantial enhancement of the yellow luminescence emission as well as several emission subbands are observed, which suggests an increase of disorder and the presence of defects as a consequence of the excess Mg doping.

  11. Uptake calibration of polymer-based passive samplers for monitoring priority and emerging organic non-polar pollutants in WWTP effluents.

    Science.gov (United States)

    Posada-Ureta, Oscar; Olivares, Maitane; Zatón, Leire; Delgado, Alejandra; Prieto, Ailette; Vallejo, Asier; Paschke, Albrecht; Etxebarria, Nestor

    2016-05-01

    The uptake calibration of more than 12 non-polar organic contaminants by 3 polymeric materials is shown: bare polydimetilsiloxane (PDMS, stir-bars), polyethersulfone tubes and membranes (PES) and polyoxymethylene membranes (POM), both in their free form and membrane-enclosed sorptive coating (MESCO). The calibration process was carried out exposing the samplers to a continuous flow of contaminated water at 100 ng mL(-1) for up to 28 days, and, consequently, the sampling rates (Rs, mL day(-1)) of several organic microcontaminants were provided for the first time. In situ Rs values were also determined disposing the samplers in the effluent of a wastewater treatment plant. Finally, these passive samplers were applied to monitor the effluents of two wastewater treatment plants. This application lead to the confirmation of the presence of galaxolide, tonalide and 4-tert-octylphenol at high ng mL(-1) levels, as well as the identification of compounds like some phthalates and alkylphenols at levels below the detection limits for active sampling methods.

  12. Fabrication of Schottky barrier diodes using H{sub 2}O{sub 2}-treated non-polar ZnO (101{sup ¯}0) substrates

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwaba, Yasuhiro, E-mail: kashi@sendai-nct.ac.jp [Sendai National College of Technology, Advanced Course of Information and Electronic System Engineering, 4-16-1 Ayashi-chuo, Sendai 989-3128 (Japan); Sakuma, Mio [Sendai National College of Technology, Advanced Course of Information and Electronic System Engineering, 4-16-1 Ayashi-chuo, Sendai 989-3128 (Japan); Abe, Takami; Nakagawa, Akira; Niikura, Ikuo; Kashiwaba, Yasube; Daibo, Masahiro; Osada, Hiroshi [Iwate University, 4-3-5 Ueda, Morioka 020-8551 (Japan)

    2013-12-01

    Non-polar single crystal ZnO (101{sup ¯}0) substrates with hydrogen peroxide (H{sub 2}O{sub 2}) treatment were characterized and applied to Schottky barrier diodes. Formation of a ZnO{sub 2} layer with a polycrystalline structure was confirmed by 2θ scans of X-ray diffraction (XRD) measurements. Tails of the X-ray rocking curve of ZnO (101{sup ¯}0) planes were broadened with increase in H{sub 2}O{sub 2} treatment time. Grain structures were clearly observed on the surfaces of ZnO (101{sup ¯}0) substrates with H{sub 2}O{sub 2} treatment by an atomic force microscope, and the root mean square roughness of the ZnO{sub 2} surface was about 5 nm. The current density–voltage (J–V) characteristics of Pd/ZnO/Al structures using ZnO (101{sup ¯}0) substrates without H{sub 2}O{sub 2} treatment were ohmic. The J–V characteristics of Pd/ZnO{sub 2}/ZnO/Al structures using ZnO (101{sup ¯}0) substrates with H{sub 2}O{sub 2} treatment time of 5 min showed good rectifying characteristics. The ideality factor n of this diode was 1.7 and the barrier height between Pd films and the ZnO{sub 2} layer on the ZnO (101{sup ¯}0) plane was estimated to be 0.92 eV.

  13. Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems.

    Science.gov (United States)

    Firaha, Dzmitry S; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara

    2016-11-28

    In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

  14. Can dispersion corrections annihilate the dispersion-driven nano-aggregation of non-polar groups? An ab initio molecular dynamics study of ionic liquid systems

    Science.gov (United States)

    Firaha, Dzmitry S.; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara

    2016-11-01

    In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.

  15. Hadron Molecules

    CERN Document Server

    Gutsche, Thomas; Faessler, Amand; Lee, Ian Woo; Lyubovitskij, Valery E

    2010-01-01

    We discuss a possible interpretation of the open charm mesons $D_{s0}^*(2317)$, $D_{s1}(2460)$ and the hidden charm mesons X(3872), Y(3940) and Y(4140) as hadron molecules. Using a phenomenological Lagrangian approach we review the strong and radiative decays of the $D_{s0}^* (2317)$ and $D_{s1}(2460)$ states. The X(3872) is assumed to consist dominantly of molecular hadronic components with an additional small admixture of a charmonium configuration. Determing the radiative ($\\gamma J/\\psi$ and $\\gamma \\psi(2s)$) and strong ($J/\\psi 2\\pi $ and $ J/\\psi 3\\pi$) decay modes we show that present experimental observation is consistent with the molecular structure assumption of the X(3872). Finally we give evidence for molecular interpretations of the Y(3940) and Y(4140) related to the observed strong decay modes $J/\\psi + \\omega$ or $J/\\psi + \\phi$, respectively.

  16. 一种二线制无极性数字称重传感器%A two-wire non-polarized digital weighing load cell

    Institute of Scientific and Technical Information of China (English)

    谭旗

    2015-01-01

    The present digital load cell is composed of 4 lines at least, which has 2 data lines and 2 power lines. The strict specialization and polarity make a wrong connection or a short circuit very dangerous. Once it happens, the equipment is prone to be damaged, and the installation and maintenance will become difficult for you; the data transmission encryption methods are not only limited, but also easy to be cracked. Our company's inventive patent"the two-wire data/ power collinear transmission device and technique with intelligent terminals and for complete machine power supply"(Patent No. 201510078098.7) can decrease the wires of digital loadcells to two Non-polarized wires. If a short circuit happens, it will not damage the equipment. Our patent product simplifies the system connection and improves the system reliability, thus making the installation and maintenance very simple. The special encryption method adopted by the data transmission is very hard to be cracked.%现有的数字传感器至少由2根数据线和2根电源线共4根线组成, 每根线均有明确的分工和极性, 不能接错和短路, 否则易损坏设备, 需专业人员才能安装和维护; 数据传输加密方式有限, 易破解. 利用本公司研发的"智能终端整机供电用二线制数据/电源共线传输装置及方法", 将数字传感器的连线减至2根, 且无极性、 可短路, 简化了系统的连接, 提高系统的可靠性, 使安装和维护变得极为简便. 数据传输采用特殊的加密方式, 极难破解.

  17. Energy efficiency for the removal of non-polar pollutants during ultraviolet irradiation, visible light photocatalysis and ozonation of a wastewater effluent.

    Science.gov (United States)

    Santiago-Morales, Javier; Gómez, María José; Herrera-López, Sonia; Fernández-Alba, Amadeo R; García-Calvo, Eloy; Rosal, Roberto

    2013-10-01

    This study aims to assess the removal of a set of non-polar pollutants in biologically treated wastewater using ozonation, ultraviolet (UV 254 nm low pressure mercury lamp) and visible light (Xe-arc lamp) irradiation as well as visible light photocatalysis using Ce-doped TiO2. The compounds tracked include UV filters, synthetic musks, herbicides, insecticides, antiseptics and polyaromatic hydrocarbons. Raw wastewater and treated samples were analyzed using stir-bar sorptive extraction coupled with comprehensive two-dimensional gas chromatography (SBSE-CG × GC-TOF-MS). Ozone treatment could remove most pollutants with a global efficiency of over 95% for 209 μM ozone dosage. UV irradiation reduced the total concentration of the sixteen pollutants tested by an average of 63% with high removal of the sunscreen 2-ethylhexyl trans-4-methoxycinnamate (EHMC), the synthetic musk 7-acetyl-1,1,3,4,4,6-hexamethyltetrahydronaphthalene (tonalide, AHTN) and several herbicides. Visible light Ce-TiO2 photocatalysis reached ~70% overall removal with particularly high efficiency for synthetic musks. In terms of power usage efficiency expressed as nmol kJ(-1), the results showed that ozonation was by far the most efficient process, ten-fold over Xe/Ce-TiO2 visible light photocatalysis, the latter being in turn considerably more efficient than UV irradiation. In all cases the efficiency decreased along the treatments due to the lower reaction rate at lower pollutant concentration. The use of photocatalysis greatly improved the efficiency of visible light irradiation. The collector area per order decreased from 9.14 ± 5.11 m(2) m(-3) order(-1) for visible light irradiation to 0.16 ± 0.03 m(2) m(-3) order(-1) for Ce-TiO2 photocatalysis. The toxicity of treated wastewater was assessed using the green alga Pseudokirchneriella subcapitata. Ozonation reduced the toxicity of treated wastewater, while UV irradiation and visible light photocatalysis limited by 20-25% the algal growth due to

  18. Electrically Dressed Ultralong-Range Polar Rydberg Molecules

    CERN Document Server

    Kurz, Markus

    2013-01-01

    We investigate the impact of an electric field on the structure of ultralong-range polar diatomic Rydberg molecules. Both the s-wave and p-wave interactions of the Rydberg electron and the neutral ground state atom are taken into account. In the presence of the electric field the angular degree of freedom between the electric field and the internuclear axis acquires vibrational character and we encounter two-dimensional oscillatory adiabatic potential energy surfaces with an antiparallel equilibrium configuration. The electric field allows to shift the corresponding potential wells in such a manner that the importance of the p-wave interaction can be controlled and the individual wells are energetically lowered at different rates. As a consequence the equilibrium configuration and corresponding energetically lowest well move to larger internuclear distances for increasing field strength. For strong fields the admixture of non-polar molecular Rydberg states leads to the possibility of exciting the large angula...

  19. Study on Surface Properties for Non-polar Fluids with Density Functional Theory%密度泛函理论在非极性纯流体表面性质研究中的应用

    Institute of Scientific and Technical Information of China (English)

    吴畏; 陆九芳; 付东; 刘金晨; 李以圭

    2004-01-01

    The density functional theory, simplified by the local density approximation and mean-field approximation, is applied to study the surface properties of pure non-polar fluids. A reasonable long rang correction is adopted to avoid the truncation of the potential. The perturbation theory is applied to establish the equation for the phase equilibrium, in which the hard-core chain fluid is as the reference fluid and the Yukawa potential is used as the perturbation term. Three parameters, ε/k, d and ms, are regressed from the vapor-liquid equilibria, and the surface properties, including density profile, surface tension and local surface tension profile are predicted with these parameters.

  20. Inclusion of poly-aromatic hydrocarbon (PAH) molecules in a functionalized layered double hydroxide

    Indian Academy of Sciences (India)

    L Mohanambe; S Vasudevan

    2006-01-01

    The internal surface of an Mg-Al layered double hydroxide has been functionalized by anchoring carboxy-methyl derivatized -cyclodextrin cavities to the gallery walls. Neutral polyaromatic hydrocarbon (PAH) molecules have been included within the functionalized solid by driving the hydrophobic aromatic molecules from a polar solvent into the less polar interior of the anchored cyclodextrin cavities by a partitioning process. The optical (absorption and emission) properties of the PAH molecules included within the functionalized Mg-Al layered double hydroxide solid are similar to that of dilute solutions of the PAH in non-polar solvents. The unique feature of these hybrid materials is that they are thermally stable over a wide temperature range with their emission properties practically unaltered.

  1. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    Directory of Open Access Journals (Sweden)

    Gregory A Ross

    Full Text Available Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  2. The importance of oxygen-containing defects on carbon nanotubes for the detection of polar and non-polar vapours through hydrogen bond formation

    Energy Technology Data Exchange (ETDEWEB)

    Watts, Paul C P; Mureau, Natacha; Tang, Zhenni; Miyajima, Yoji; Carey, J David; Silva, S Ravi P [Nano-Electronics Centre, Advanced Technology Institute, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom)

    2007-05-02

    We report the electrical responses of water vapour and O{sub 2} adsorption onto macroscopic multi-walled carbon nanotube (MWCNT) ropes, and compare the results with mats of acid-treated MWCNTs on SiO{sub 2} substrates in order to investigate the importance of oxygen-containing defects on CNTs. In the outgassed state both carbon nanotube (CNT) materials exhibit rapid changes in electrical resistance when exposed to dry air, humid air or water vapour at standard temperature and pressure (STP). The measured electrical responses are highly reversible at STP when cycled between humid air, vacuum and dry air. We report a decrease in resistance for the CNT materials in dry air, attributed to O{sub 2} p-type doping of the CNTs, whereas there is an increase in resistance when exposed to a humid environment. This latter effect is attributed to the formation of hydrogen bonding from the polar water molecules with the oxygen-containing defects on the CNTs. Our observations indicate that the increase in electrical resistance upon water absorption affects a reduction of the electron-withdrawing power of the oxygen-containing defect groups, thus leading to a reduced hole carrier concentration in the p-type nanotubes.

  3. Fluorescence enhancement of photoswitchable metal ion sensors

    Science.gov (United States)

    Sylvia, Georgina; Heng, Sabrina; Abell, Andrew D.

    2016-12-01

    Spiropyran-based fluorescence sensors are an ideal target for intracellular metal ion sensing, due to their biocompatibility, red emission frequency and photo-controlled reversible analyte binding for continuous signal monitoring. However, increasing the brightness of spiropyran-based sensors would extend their sensing capability for live-cell imaging. In this work we look to enhance the fluorescence of spiropyran-based sensors, by incorporating an additional fluorophore into the sensor design. We report a 5-membered monoazacrown bearing spiropyran with metal ion specificity, modified to incorporate the pyrene fluorophore. The effect of N-indole pyrene modification on the behavior of the spiropyran molecule is explored, with absorbance and fluorescence emission characterization. This first generation sensor provides an insight into fluorescence-enhancement of spiropyran molecules.

  4. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

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

  5. Spectral and photochromic study of spiropyran

    Energy Technology Data Exchange (ETDEWEB)

    Nordin, Rumaisa; Lazim, Azwani Mat; Hasbullah, Siti Aishah [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan (Malaysia)

    2013-11-27

    A new class of benzospiropyran has been synthesized by the condensation of the precursor, Fisher basespiropyran with substituted salicyaldehydes in 1:1 mole ratios. This photochromic compound, spiro [2H-1-benzopyran-2, 2’-(8’-hydroxy-1’, 3’, 3’-trimethylindoline)] was able to undergo convertion into its merocyanine form (colored) after being induced by irradiation of UV light. Both open and closed form of benzospiropyran were characterized and distinguished based on Infrared vibracional spectroscopy in Attenuated Total Reflexion mode (ATR) and UV-vis spectroscopy. In addition, association of ten different metal ions to ethanol solution of SP (A) leads to metal-ion binding by the MC isomer. The coupled reaction of all metal ions, MC-M{sup 2+} underwent a hypsochromic and bathochromic shift in the absorption bands.

  6. TNF-α decreases VEGF secretion in highly polarized RPE cells but increases it in non-polarized RPE cells related to crosstalk between JNK and NF-κB pathways.

    Directory of Open Access Journals (Sweden)

    Hiroto Terasaki

    Full Text Available Asymmetrical secretion of vascular endothelial growth factor (VEGF by retinal pigment epithelial (RPE cells in situ is critical for maintaining the homeostasis of the retina and choroid. VEGF is also involved in the development and progression of age-related macular degeneration (AMD. We studied the effect of tumor necrosis factor-α (TNF-α on the secretion of VEGF in polarized and non-polarized RPE cells (P-RPE cells and N-RPE cells, respectively in culture and in situ in rats. A subretinal injection of TNF-α caused a decrease in VEGF expression and choroidal atrophy. Porcine RPE cells were seeded on Transwell™ filters, and their maturation and polarization were confirmed by the asymmetrical VEGF secretion and trans electrical resistance. Exposure to TNF-α decreased the VEGF secretion in P-RPE cells but increased it in N-RPE cells in culture. TNF-α inactivated JNK in P-RPE cells but activated it in N-RPE cells, and TNF-α activated NF-κB in P-RPE cells but not in N-RPE cells. Inhibition of NF-κB activated JNK in both types of RPE cells indicating crosstalk between JNK and NF-κB. TNF-α induced the inhibitory effects of NF-κB on JNK in P-RPE cells because NF-κB is continuously inactivated. In N-RPE cells, however, it was not evident because NF-κB was already activated. The basic activation pattern of JNK and NF-κB and their crosstalk led to opposing responses of RPE cells to TNF-α. These results suggest that VEGF secretion under inflammatory conditions depends on cellular polarization, and the TNF-α-induced VEGF down-regulation may result in choroidal atrophy in polarized physiological RPE cells. TNF-α-induced VEGF up-regulation may cause neovascularization by non-polarized or non-physiological RPE cells.

  7. First-principles investigation of the size-dependent structural stability and electronic properties of O-vacancies at the ZnO polar and non-polar surfaces

    Science.gov (United States)

    Mun Wong, Kin; Alay-e-Abbas, S. M.; Shaukat, A.; Fang, Yaoguo; Lei, Yong

    2013-01-01

    In this paper, all electron full-potential linearized augmented plane wave plus local orbitals method has been used to investigate the structural and electronic properties of polar (0001) and non-polar (101¯0) surfaces of ZnO in terms of the defect formation energy (DFE), charge density, and electronic band structure with the supercell-slab (SS) models. Our calculations support the size-dependent structural phase transformation of wurzite lattice to graphite-like structure which is a result of the termination of hexagonal ZnO at the (0001) basal plane, when the stacking of ZnO primitive cell along the hexagonal principle c-axis is less than 16 atomic layers of Zn and O atoms. This structural phase transformation has been studied in terms of Coulomb energy, nature of the bond, energy due to macroscopic electric field in the [0001] direction, and the surface to volume ratio for the smaller SS. We show that the size-dependent phase transformation is completely absent for surfaces with a non-basal plane termination, and the resulting structure is less stable. Similarly, elimination of this size-dependent graphite-like structural phase transformation also occurs on the creation of O-vacancy which is investigated in terms of Coulomb attraction at the surface. Furthermore, the DFE at the (101¯0)/(1¯010) and (0001)/(0001¯) surfaces is correlated with the slab-like structures elongation in the hexagonal a- and c-axis. Electronic structure of the neutral O-vacancy at the (0001)/(0001¯) surfaces has been calculated and the effect of charge transfer between the two sides of the polar surfaces (0001)/(0001¯) on the mixing of conduction band through the 4s orbitals of the surface Zn atoms is elaborated. An insulating band structure profile for the non-polar (101¯0)/(1¯010) surfaces and for the smaller polar (0001)/(0001¯) SS without O-vacancy is also discussed. The results in this paper will be useful for the tuning of the structural and electronic properties of the

  8. [Endothelial cell adhesion molecules].

    Science.gov (United States)

    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.

  9. Trapping molecules on chips

    CERN Document Server

    Santambrogio, Gabriele

    2015-01-01

    In the last years, it was demonstrated that neutral molecules can be loaded on a microchip directly from a supersonic beam. The molecules are confined in microscopic traps that can be moved smoothly over the surface of the chip. Once the molecules are trapped, they can be decelerated to a standstill, for instance, or pumped into selected quantum states by laser light or microwaves. Molecules are detected on the chip by time-resolved spatial imaging, which allows for the study of the distribution in the phase space of the molecular ensemble.

  10. 出口压减压下非极性薄涂气相色谱柱的特性及应用%Performance and Application of Decompression and Low Coated Non-polar Liquid Phases in Gas Chromatographic Column

    Institute of Scientific and Technical Information of China (English)

    袁晓燕; 陈贻文

    2001-01-01

    In this paper,performance of decompression and low coated gas chromatographic column of non-polar liquid phases is described. Chromatographic parameters of a column packed with 0.5% OV-101 on glazing support (φ0.18~0.25mm) 302 was studied for C、C7、C8、C9 n-alkanes samples. The results showed that the column pressure 0.068 MPa was best,the column temperature for n-octane could be decreased to 52°C,column efficiency was four time as high as ordinary pressure detection.%以甲基硅油0V-101、210为固定液,研究了出口压减压下薄涂气相色谱柱的特性,从柱压、柱温、保留值、柱效、柱的稳定性等方面进行了探讨。应用于烷烃及几种农药的分离,效果良好。

  11. Progress of Multi Functional Properties of Organic-Inorganic Hybrid System, A[FeIIFeIIIX3] (A = (n-CnH2n+14N, Spiropyran; X = C2O2S2, C2OS3, C2O3S

    Directory of Open Access Journals (Sweden)

    Norimichi Kojima

    2010-05-01

    Full Text Available In the case of mixed-valence systems whose spin states are situated in the spin crossover region, new types of conjugated phenomena coupled with spin and charge are expected. From this viewpoint, we have investigated the multifunctional properties coupled with spin, charge and photon for the organic-inorganic hybrid system, A[FeIIFeIIIX3](A = (n-CnH2n+14N, spiropyran; X = dto(C2O2S2, tto(C2OS3, mto(C2O3S. A[FeIIFeIII(dto3] and A[FeIIFeIII(tto3] undergo the ferromagnetic phase transitions, while A[FeIIFeIII(mto3] undergoes a ferrimagnetic transition. In (n-CnH2n+14N [FeIIFeIII(dto3](n = 3,4, a new type of phase transition called charge transfer phase transition (CTPT takes place around 120 K, where the thermally induced charge transfer between FeII and FeIII occurs reversibly. At the CTPT, the iron valence state dynamically fluctuated with a frequency of about 0.1 MHz, which was confirmed by means of muon spin relaxation. The charge transfer phase transition and the ferromagnetic transition for (n-CnH2n+14N[FeIIFeIII(dto3] remarkably depend on the size of intercalated cation. In the case of (SP[FeIIFeIII(dto3](SP = spiropyran, the photoinduced isomerization of SP under UV irradiation induces the charge transfer phase transition in the [FeIIFeIII(dto3] layer and the remarkable change of the ferromagnetic transition temperature. In the case of (n-CnH2n+14N[FeIIFeIII(mto3](mto = C2O3S, a rapid spin equilibrium between the high-spin state (S = 5/2 and the low-spin state (S = 1/2 at the FeIIIO3S3 site takes place in a wide temperature range, which induces the valence fluctuation of the FeS3O3 and FeO6 sites through the ferromagnetic coupling between the low spin state (S = 1/2 of the FeIIIS3O3 site and the high spin state (S = 2 of the FeIIO6 site.

  12. Algebraic theory of molecules

    CERN Document Server

    Iachello, F

    1995-01-01

    1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters

  13. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  14. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  15. Molecules in galaxies

    CERN Document Server

    Omont, Alain

    2007-01-01

    The main achievements, current developments and prospects of molecular studies in external galaxies are reviewed. They are put in the context of the results of several decades of studies of molecules in local interstellar medium, their chemistry and their importance for star formation. CO observations have revealed the gross structure of molecular gas in galaxies. Together with other molecules, they are among the best tracers of star formation at galactic scales. Our knowledge about molecular abundances in various local galactic environments is progressing. They trace physical conditions and metallicity, and they are closely related to dust processes and large aromatic molecules. Major recent developments include mega-masers, and molecules in Active Galactic Nuclei; millimetre emission of molecules at very high redshift; and infrared H2 emission as tracer of warm molecular gas, shocks and photodissociation regions. The advent of sensitive giant interferometers from the centimetre to sub-millimetre range, espe...

  16. [Polar and non polar notations of refraction].

    Science.gov (United States)

    Touzeau, O; Gaujoux, T; Costantini, E; Borderie, V; Laroche, L

    2010-01-01

    Refraction can be expressed by four polar notations which correspond to four different combinations of spherical or cylindrical lenses. Conventional expressions of refraction (plus and minus cylinder notation) are described by sphere, cylinder, and axis. In the plus cylinder notation, the axis visualizes the most powerful meridian. The axis usually corresponds to the bow tie axis in curvature maps. Plus cylinder notation is also valuable for all relaxing procedures (i.e., selective suture ablation, arcuate keratotomy, etc.). In the cross-cylinder notation, two orthogonal cylinders can describe (without the sphere component) the actual refraction of both the principal meridians. This notation must be made before performing the vertex calculation. Using an association of a Jackson cross-cylinder and a spherical equivalent, refraction can be broken down into two pure components: astigmatism and sphere. All polar notations of refraction may perfectly characterize a single refraction but are not suitable for statistical analysis, which requires nonpolar expression. After doubling the axis, a rectangular projection breaks down the Jackson cross-cylinder, which has a polar axis, into two Jackson cross-cylinders on the 0 degrees /90 degrees and 45 degrees /135 degrees axis. This procedure results in the loss of the directional nature of the data. Refraction can be written in a nonpolar notation by three rectangular coordinates (x,y,z), which can also represent the spherocylinder by one point in a dioptric space. These three independent (orthogonal) variables have a concrete optical significance: a spherical component, a direct/inverse (WTR/ATR) component, and an oblique component of the astigmatism. Finally, nonpolar notations are useful for statistical analysis and graphical representation of refraction.

  17. The Origins and Evolution of Molecules in Icy Solids

    Science.gov (United States)

    Hudson, Reggie L.; Moore, Marla H.

    2010-01-01

    Astronomical observations of the past few decades have revealed the existence of a variety of molecules in extraterrestrial ices. These molecules include H2O, CO, and CO2, and organics such as CH4, CH30H, and C2H6. Some ices are dominated by polar molecules, while non-polar species appear to dominate others. Observations, mainly in the radio and IR regions, have allowed the inference of other solid-phase molecules whose formation remains difficult to explain by gas-phase chemistry alone. Several laboratory research groups have reported on extensive experiments on the solid-phase reaction chemistry of icy materials, generally as initiated by either ionizing radiation or vacuum-UV photons. These experiments not only permit molecular identifications to be made from astronomical observations, but also allow predictions of yet unidentified molecules. This laboratory approach has evolved over more than 30 years with much of the earliest work focusing on complex mixtures thought to represent either cometary or interstellar ices. Although those early experiments documented a rich solid-state photo- and radiation chemistry, they revealed few details of reactions for particular molecules, partly due to the multi-component nature of the samples. Since then, model systems have been examined that allow the chemistry of individual species and specific reactions to be probed. Reactions involving most of the smaller astronomical molecules have now been studied and specific processes identified. Current laboratory work suggests that a variety of reactions occur in extraterrestrial ices, including acid-base processes, radical dimerizations, proton transfers, oxidations, reductions, and isomerizations. This workshop presentation will focus on chemical reactions relevant to solar system and interstellar ices. While most of the work will be drawn from that to which the speaker has contributed, results from other laboratories also will be included. Suggestions for future studies will be

  18. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

    2016-11-16

    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  19. Heavy Exotic Molecules

    CERN Document Server

    Liu, Yizhuang

    2016-01-01

    We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general strictures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. The bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, and is identified as a mixed state of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound bottom isosinglet molecule with $J^{PC}=1^{++}$ is a possible neutral $X_b(10532)$ to be observed.

  20. Heavy exotic molecules

    Science.gov (United States)

    Liu, Yizhuang; Zahed, Ismail

    We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general structures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with JPC = 1++ binds, which we identify as the reported neutral X(3872). The bottom isotriplet exotic with JPC = 1+1 binds, and is identified as a mixed state of the reported charged exotics Zb+(10610) and Zb-(10650). The bound bottom isosinglet molecule with JPC = 1++ is a possible neutral Xb(10532) to be observed.

  1. Electron correlation in molecules

    CERN Document Server

    Wilson, S

    2007-01-01

    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  2. Ionization Study of Isomeric Molecules in Strong-field Laser Pulses

    Science.gov (United States)

    Zigo, Stefan; Le, Anh-Thu; Timilsina, Pratap; Trallero-Herrero, Carlos A.

    2017-01-01

    Through the use of the technique of time-of-flight mass spectroscopy, we obtain strong-field ionization yields for randomly oriented 1,2-dichloroethylene (1,2-DCE) (C2H2Cl2) and 2-butene (C4H8). We are interested in studying the effect of conformal structure in strong-field ionization and, in particular, the role of molecular polarity. That is, we can perform strong-field ionization studies in polar vs non-polar molecules that have the same chemical composition. We report our findings through the ionization yields and the ratio (trans/cis) of each stereoisomer pair as a function of intensity. PMID:28186110

  3. 光学相干断层扫描成像系统中消偏振分光膜的研制%Design and Fabrication of the Non-polarizing Beam Splitter Used in Optical Coherence Tomography Imaging System

    Institute of Scientific and Technical Information of China (English)

    陈童; 侯习平; 付秀华

    2015-01-01

    消偏振分束镜能够将光学相干断层扫描干涉成像系统中的信号光进行分束,是光学相干断层扫描成像系统中重要的组成器件。为了减小45度角入射时P光和S光造成的偏振分离,针对成像系统中分光棱镜的参数要求,选择Ti3O5、Al2O3和MgF2薄膜材料,借助Macleod膜系设计软件,结合Compact Design功能,运用Optimac和Needle Synthesis两种优化方法进行优化设计,选择电子束加热蒸发和离子源辅助沉积的方式镀制薄膜。根据实际镀膜结果,运用Independent Sensitivity功能对膜层敏感度进行分析,并采用Reverse Engineering模块进行逆向模拟分析,判断镀膜误差主要来源于不同监控波长的光控tooling值有细微的差距以及膜层的Final Swing值过大。通过改变不同监控波长的光控tooling值以及对敏感度较高的膜层进行重点监控,制备的消偏振分光膜经过测试,1310±50nm处P光平均透射比为51.47%,S光平均透射比为49.11%,偏振度为4.59%,满足成像系统的使用要求,并通过了环境测试。%Non-polarizing beam splitter is an important component which used in achieves optical coherence tomography Interference imaging system. It is able to split the light beam. In order to reduce the polarization separation between the P polarized light and the S polarized light in the incident angle of 45 degrees, analyses the parameters requirement in the beam splitter of imaging system,choose the Ti3O5,Al2O3 and MgF2 as the film materials,optimize the film de-sign by selecting the appropriate film materials and using Macleod coating design software. Choose electron beam heat-ing evaporation and ion assisted system for the thin film deposition. By using the function of independent sensitivity to analyses the layer sensitivities, and using the Reverse Engineer module simulate the coating result. Combined with the film sensitivities,analyze the causes of the monitoring error

  4. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst

    2007-01-01

    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  5. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo

    1984-01-01

    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  6. Quantum dot molecules

    CERN Document Server

    Wu, Jiang

    2014-01-01

    This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.

  7. Encaged molecules in external electric fields: A molecular "tug-of-war"

    Science.gov (United States)

    Gurav, Nalini D.; Gejji, Shridhar P.; Bartolotti, Libero J.; Pathak, Rajeev K.

    2016-08-01

    Response of polar molecules CH3OH and H2O2 and a non-polar molecule, CO2, as "guests" encapsulated in the dodecahedral water cage (H2O)20 "host," to an external, perturbative electric field is investigated theoretically. We employ the hybrid density-functionals M06-2X and ωB97X-D incorporating the effects of damped dispersion, in conjunction with the maug-cc-pVTZ basis set, amenable for a hydrogen bonding description. While the host cluster (cage) tends to confine the embedded guest molecule through cooperative hydrogen bonding, the applied electric field tends to rupture the cluster-composite by stretching it; these two competitive effects leading to a molecular "tug-of-war." The composite remains stable up to a maximal sustainable threshold electric field, beyond which, concomitant with the vanishing of the HOMO-LUMO gap, the field wins over and the cluster breaks down. The electric-field effects are gauged in terms of the changes in the molecular geometry of the confined species, interaction energy, molecular electrostatic potential surfaces, and frequency shifts of characteristic normal vibrations in the IR regime. Interestingly, beyond the characteristic threshold electric field, the labile, distorted host cluster fragmentizes, and the guest molecule still tethered to a remnant fragment, an effect attributed to the underlying hydrogen-bonded networks.

  8. Molecules as Automata

    Science.gov (United States)

    Cardelli, Luca

    Molecular biology investigates the structure and function of biochemical systems starting from their basic building blocks: macromolecules. A macromolecule is a large, complex molecule (a protein or a nucleic acid) that usually has inner mutable state and external activity. Informal explanations of biochemical events trace individual macromolecules through their state changes and their interaction histories: a macromolecule is endowed with an identity that is retained through its transformations, even through changes in molecular energy and mass. A macromolecule, therefore, is qualitatively different from the small molecules of inorganic chemistry. Such molecules are stateless: in the standard notation for chemical reactions they are seemingly created and destroyed, and their atomic structure is used mainly for the bookkeeping required by the conservation of mass.

  9. Molecules in supernova ejecta

    CERN Document Server

    Cherchneff, Isabelle

    2011-01-01

    The first molecules detected at infrared wavelengths in the ejecta of a Type II supernova, namely SN1987A, consisted of CO and SiO. Since then, confirmation of the formation of these two species in several other supernovae a few hundred days after explosion has been obtained. However, supernova environments appear to hamper the synthesis of large, complex species due to the lack of microscopically-mixed hydrogen deep in supernova cores. Because these environments also form carbon and silicate dust, it is of importance to understand the role played by molecules in the depletion of elements and how chemical species get incorporated into dust grains. In the present paper, we review our current knowledge of the molecular component of supernova ejecta, and present new trends and results on the synthesis of molecules in these harsh, explosive events.

  10. MOLECULES IN {eta} CARINAE

    Energy Technology Data Exchange (ETDEWEB)

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)

    2012-04-10

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

  11. Molecules in \\eta\\ Carinae

    CERN Document Server

    Loinard, Laurent; Guesten, Rolf; Zapata, Luis A; Rodriguez, Luis F

    2012-01-01

    We report the detection toward \\eta\\ Carinae of six new molecules, CO, CN, HCO+, HCN, HNC, and N2H+, and of two of their less abundant isotopic counterparts, 13CO and H13CN. The line profiles are moderately broad (about 100 km /s) indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO+ do not appear to be under-abundant in \\eta\\ Carinae. On the other hand, molecules containing nitrogen or the 13C 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.

  12. Enzyme molecules as nanomotors.

    Science.gov (United States)

    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.

  13. Multicolor Bound Soliton Molecule

    CERN Document Server

    Luo, Rui; Lin, Qiang

    2015-01-01

    We show a new class of bound soliton molecule that exists in a parametrically driven nonlinear optical cavity with appropriate dispersion characteristics. The composed solitons exhibit distinctive colors but coincide in time and share a common phase, bound together via strong inter-soliton four-wave mixing and Cherenkov radiation. The multicolor bound soliton molecule shows intriguing spectral locking characteristics and remarkable capability of spectrum management to tailor soliton frequencies, which may open up a great avenue towards versatile generation and manipulation of multi-octave spanning phase-locked Kerr frequency combs, with great potential for applications in frequency metrology, optical frequency synthesis, and spectroscopy.

  14. Gated container molecules

    Institute of Scientific and Technical Information of China (English)

    LIU Fang; WANG Hao; HOUK K. N.

    2011-01-01

    Donald J.Cram,the great UCLA chemist,received the Nobel Prize for his discoveries about host-guest complexes [1].Both theoretical and experimental studies have been conducted about the nature and strength of interactions between the host and guest molecules.The concepts of constrictive binding (the activation energy of the binding process) and intrinsic binding (the free energy difference between the complex and the free host and guest molecules) were introduced to characterize different binding properties (Figure 1)[2].

  15. Synthesis beyond the molecule

    NARCIS (Netherlands)

    Reinhoudt, D.N.; Crego-Calama, M.

    2002-01-01

    Weak, noncovalent interactions between molecules control many biological functions. In chemistry, noncovalent interactions are now exploited for the synthesis in solution of large supramolecular aggregates. The aim of these syntheses is not only the creation of a particular structure, but also the i

  16. Disentangling DNA molecules.

    Science.gov (United States)

    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.

  17. Disentangling DNA molecules

    Science.gov (United States)

    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.

  18. Diversity in Biological Molecules

    Science.gov (United States)

    Newbury, H. John

    2010-01-01

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

  19. Diversity in Biological Molecules

    Science.gov (United States)

    Newbury, H. John

    2010-01-01

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

  20. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  1. Properties of entanglement molecules

    Energy Technology Data Exchange (ETDEWEB)

    Huang Yanxia [Department of Physics, Hubei Normal University, Huangshi 435002 (China); Zhan Mingsheng [State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China)

    2004-09-14

    We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules {rho}{sub I} introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules vertical bar {psi}{sub N}){sub {alpha}} in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZ), vertical bar W{sub N}) and vertical bar {phi}{sub N}). We show that the maximal value N - 1 of the persistency of the state vertical bar {psi}{sub N}){sub {alpha}} corresponds to the case that all atoms are pairwise entangled. If any pair of atoms {rho}{sub ij} is disentangled, the entanglement of the state vertical bar {psi}{sub N}){sub {alpha}} is very easy to destroy by a single local measurement.

  2. Properties of entanglement molecules

    Science.gov (United States)

    Huang, Yan-Xia; Zhan, Ming-Sheng

    2004-09-01

    We propose a scheme to prepare a certain kind of N-atom entangled state that allows us to construct some possible types of entanglement molecules via cavity QED. The entanglement properties of entanglement molecules |psgrNrangagr are studied with respect to bipartite entanglement that is robust against the disposal of particles and are compared with entanglement molecules rgrI introduced in Dur (2001 Phys. Rev. A 63 020303). We also give the maximal amount of entanglement achievable for two particular situations in two possible configurations. Meanwhile, we investigate the entanglement properties of entanglement molecules |psgrNrangagr in terms of local measurement using the maximum connectedness and persistency and compare them with other kinds of N-atom entangled states such as |GHZrang, |WNrang and |phgrNrang. We show that the maximal value N - 1 of the persistency of the state |psgrNrangagr corresponds to the case that all atoms are pairwise entangled. If any pair of atoms rgrij is disentangled, the entanglement of the state |psgrNrangagr is very easy to destroy by a single local measurement.

  3. Bacterial invasion reconstructed molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory

    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

  4. Molecules in Magnetic Fields

    Science.gov (United States)

    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.

  5. Atoms, molecules & elements

    CERN Document Server

    Graybill, George

    2007-01-01

    Young scientists will be thrilled to explore the invisible world of atoms, molecules and elements. Our resource provides ready-to-use information and activities for remedial students using simplified language and vocabulary. Students will label each part of the atom, learn what compounds are, and explore the patterns in the periodic table of elements to find calcium (Ca), chlorine (Cl), and helium (He) through hands-on activities.

  6. Model molecules mimicking asphaltenes.

    Science.gov (United States)

    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.

  7. Hydrogen molecules in semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Joerg [Technische Universitaet Dresden, 01062 Dresden (Germany)], E-mail: joerg.weber@tu-dresden.de; Hiller, Martin; Lavrov, Edward V. [Technische Universitaet Dresden, 01062 Dresden (Germany)

    2007-12-15

    Molecular hydrogen, the simplest of all molecules, allows a direct insight into the fundamental properties of quantum mechanics. In the case of H{sub 2}, the Pauli principle leads to two different species, para-H{sub 2} and ortho-H{sub 2}. A conversion between these species is prohibited. Vibrational mode spectra reflect the fundamental properties and allow an unambiguous identification of the H{sub 2} molecules. Today, we have experimental evidence for the trapping of hydrogen molecules in the semiconductors Si, Ge and GaAs at the interstitial sites, within hydrogen-induced platelets, in voids and at impurities (interstitial oxygen in Si). Interstitial H{sub 2} is a nearly free rotor with a surprisingly simple behavior. We review on interstitial H{sub 2} in semiconductors and report on the unexpected preferential disappearance of the para-H{sub 2} or ortho-D{sub 2} species. The origin of the detected ortho-para conversion will be discussed.

  8. Photonic Molecule Lasers Revisited

    Science.gov (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.

    2014-05-01

    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  9. Molecules in crystals

    Science.gov (United States)

    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.

  10. Ultra-cold molecule production.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Passing Current through Touching Molecules

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  12. Molecules Best Paper Award 2013.

    Science.gov (United States)

    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.

  13. Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules.

    Science.gov (United States)

    Huggins, David J

    2012-11-21

    The structures of biomolecules and the strengths of association between them depend critically on interactions with water molecules. Thus, understanding these interactions is a prerequisite for understanding the structure and function of all biomolecules. Inhomogeneous fluid solvation theory provides a framework to derive thermodynamic properties of individual water molecules from a statistical mechanical analysis. In this work, two biomolecules are analysed to probe the distribution and thermodynamics of surrounding water molecules. The great majority of hydration sites are predicted to contribute favourably to the total free energy with respect to bulk water, though hydration sites close to non-polar regions of the solute do not contribute significantly. Analysis of a biomolecule with a positively and negatively charged functional group predicts that a charged species perturbs the free energy of water molecules to a distance of approximately 6.0 Å. Interestingly, short simulations are found to provide converged predictions if samples are taken with sufficient frequency, a finding that has the potential to significantly reduce the required computational cost of such analysis. In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models. This study provides important information on how inhomogeneous fluid solvation theory can be employed to understand the structures and intermolecular interactions of biomolecules.

  14. Lanthanide single molecule magnets

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jinkui; Zhang, Peng [Chinese Academy of Sciences, Changchun (China). Changchun Inst. of Applied Chemistry

    2015-10-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures - an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and explore new directions.

  15. Astrochemistry and Interstellar Molecules

    Science.gov (United States)

    Minh, Y. C.

    2010-03-01

    Astrochemistry provides powerful tools to understand various cosmic phenomena, including those in our solar system to the large-scale structure of the universe. In addition, the chemical property of an astronomical body is a crucial factor which governs the evolution of the system. Recent progress in astrophysical theories, computational modelings, and observational techniques requires a detailed understanding of the interactions between the constituents of an astronomical system, which are atoms and molecules within the system. Especially the far-infrared/sub-millimeter wave range, which is called as the last frontier in astronomical observations, contains numerous molecular lines, which may provide a huge amount of new information. However, we need an astrochemical understanding to use this information fully. Although this review is very limited, I would like to stress the importance of astrochemical approach in this overview for the field, which is getting much more attention than ever before.

  16. Lanthanide single molecule magnets

    CERN Document Server

    Tang, Jinkui

    2015-01-01

    This book begins by providing basic information on single-molecule magnets (SMMs), covering the magnetism of lanthanide, the characterization and relaxation dynamics of SMMs, and advanced means of studying lanthanide SMMs. It then systematically introduces lanthanide SMMs ranging from mononuclear and dinuclear to polynuclear complexes, classifying them and highlighting those SMMs with high barrier and blocking temperatures – an approach that provides some very valuable indicators for the structural features needed to optimize the contribution of an Ising type spin to a molecular magnet. The final chapter presents some of the newest developments in the lanthanide SMM field, such as the design of multifunctional and stimuli-responsive magnetic materials as well as the anchoring and organization of the SMMs on surfaces. In addition, the crystal structure and magnetic data are clearly presented with a wealth of illustrations in each chapter, helping newcomers and experts alike to better grasp ongoing trends and...

  17. Forces in molecules.

    Science.gov (United States)

    Hernández-Trujillo, Jesús; Cortés-Guzmán, Fernando; Fang, De-Chai; Bader, Richard F W

    2007-01-01

    Chemistry is determined by the electrostatic forces acting within a collection of nuclei and electrons. The attraction of the nuclei for the electrons is the only attractive force in a molecule and is the force responsible for the bonding between atoms. This is the attractive force acting on the electrons in the Ehrenfest force and on the nuclei in the Feynman force, one that is countered by the repulsion between the electrons in the former and by the repulsion between the nuclei in the latter. The virial theorem relates these forces to the energy changes resulting from interactions between atoms. All bonding, as signified by the presence of a bond path, has a common origin in terms of the mechanics determined by the Ehrenfest, Feynman and virial theorems. This paper is concerned in particular with the mechanics of interaction encountered in what are classically described as 'nonbonded interactions'--are atoms that 'touch' bonded or repelling one another?

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

    Science.gov (United States)

    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.

  19. Molecule-based magnets

    Indian Academy of Sciences (India)

    J V Yakhmi

    2009-06-01

    The conventional magnetic materials used in current technology, such as, Fe, Fe2O3, Cr2O3, SmCo5, Nd2Fe14B etc are all atom-based, and their preparation/processing require high temperature routes. Employing self-assembly methods, it is possible to engineer a bulk molecular material with long-range magnetic order, mainly because one can play with the weak intermolecular interactions. Since the first successful synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be categorized on the basis of the chemical nature of the magnetic units involved: organic-, metal-based systems, heterobimetallic assemblies, or mixed organic–inorganic systems. The design of molecule-based magnets has also been extended to the design of poly-functional molecular magnets, such as those exhibiting second-order optical nonlinearity, liquid crystallinity, or chirality simultaneously with long-range magnetic order. Solubility, low density and biocompatibility are attractive features of molecular magnets. Being weakly coloured, unlike their opaque classical magnet ‘cousins’ listed above, possibilities of photomagnetic switching exist. Persistent efforts also continue to design the ever-elusive polymer magnets towards applications in industry. While providing a brief overview of the field of molecular magnetism, this article highlights some recent developments in it, with emphasis on a few studies from the author’s own lab.

  20. Strongly interacting ultracold polar molecules

    CERN Document Server

    Gadway, Bryce

    2016-01-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole-dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  1. Theoretical Investigations Regarding Single Molecules

    DEFF Research Database (Denmark)

    Pedersen, Kim Georg Lind

    Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...... interfere destructively or constructively. Destructive interference effects in electron transport could potentially improve thermo-electrics, organic logic circuits and energy harvesting. We have investigated destructive interference in off-resonant transport through organic molecules, and have found a set...

  2. STM investigation of surfactant molecules

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Adsorption and self-organization of sodium alkyl sulfonates (STS and SHS) have been studied on HOPG by using the in situ scanning tunneling microscopy (STM). Both SHS and STS molecules adsorb on the HOPG surface and form long-range well-ordered monolayers. The neighboring molecules in different rows form a "head to head" configuration. In the high-resolution images of STS and SHS molecules, one end of the molecules shows bright spots which are attributed to the SO3- groups.

  3. Biofuels: from microbes to molecules

    National Research Council Canada - National Science Library

    Lu, Xuefeng

    2014-01-01

    .... The production of different biofuel molecules including hydrogen, methane, ethanol, butanol, higher chain alcohols, isoprenoids and fatty acid derivatives, from genetically engineered microbes...

  4. High Efficient Loading of Hydrophobic Molecules in Layer-by-Layer Assembled Microgel Films with the Assistance of Surfactant Micelles%表面活性剂胶束实现疏水分子在聚合物微凝胶层层组装膜中的高效负载

    Institute of Scientific and Technical Information of China (English)

    陈栋栋; 王林; 孙俊奇

    2012-01-01

    Layer-by-layer(LbL) assembly enables the fabrication of various kinds of functional films by sequential deposition of building blocks of polyelectrolytes,biomacromolecules,oligo-charged dyes,colloids,nanoparticles,polymeric complexes and so forth.However,water-insoluble organic species without necessary functional groups are difficult to be incorporated into multilayer films by conventional LbL assembly method.The present work aims to develop a facile method for efficient loading of hydrophobic molecules into LbL assembled films.To do so,PAH-D microgels,which are chemically cross-linked poly(allylamine hydrochloride)(PAH) and dextran,are LbL assembled with hyaluronic sodium(HA) to produce PAH-D/HA microgel films.Sodium dodecylsulfate(SDS) micelles are used as carriers to incorporate hydrophobic molecules of pyrene and spiropyran.The negatively charged SDS micelles loaded with hydrophobic molecules are successfully incorporated into the PAH-D/HA microgel films by a post-diffusion process,which produces transparent PAH-D microgel films with a large number of loaded pyrene and spiropyran molecules.Fluorescence emission spectra support that the hydrophobic molecules in PAH-D/HA films locate in the hydrophobic cores of SDS micelles.Stable loading of SDS micelles into PAH-D/HA films is achieved because of the strong electrostatic interaction between SDS micelles and protonated amine groups of PAH-D microgels.The high loading capacity of PAH-D/HA films toward SDS micelles encapsulated with hydrophobic molecules originates from the high swellability of the PAH-D/HA films and the abundance of unpaired amine groups in the PAH-D layers for binding of SDS micelles.The amount of hydrophobic molecules loaded into PAH-D/HA microgel films can be conveniently controlled by varying the deposition cycles of PAH-D/HA films and the concentration of hydrophobic molecules encapsulated in SDS micelles.The spiropyran-loaded PAH-D/HA microgel films show reversible

  5. Micro-Kelvin cold molecules.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  6. Theoretical Investigations Regarding Single Molecules

    DEFF Research Database (Denmark)

    Pedersen, Kim Georg Lind

    Neoclassical Valence Bond Theory, Quantum Transport, Quantum Interference, Kondo Effect, and Electron Pumping. Trap a single organic molecule between two electrodes and apply a bias voltage across this "molecular junction". When electrons pass through the molecule, the different electron paths can...

  7. Triatomic molecules laser-cooled

    Science.gov (United States)

    2017-06-01

    Molecules containing three atoms have been laser-cooled to ultracold temperatures for the first time. John Doyle and colleagues at Harvard University in the US used a technique called Sisyphus cooling to chill an ensemble of about a million strontium-monohydroxide molecules to 750 μK.

  8. Enzyme molecules in solitary confinement.

    Science.gov (United States)

    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.

  9. Enzyme Molecules in Solitary Confinement

    Directory of Open Access Journals (Sweden)

    Raphaela B. Liebherr

    2014-09-01

    Full Text Available Large arrays of homogeneous microwells each defining a femtoliter volume are a versatile platform for monitoring the substrate turnover of many individual enzyme molecules in parallel. The high degree of parallelization enables the analysis of a statistically representative enzyme population. Enclosing individual enzyme molecules in microwells does not require any surface immobilization step and enables the kinetic investigation of enzymes free in solution. This review describes various microwell array formats and explores their applications for the detection and investigation of single enzyme molecules. The development of new fabrication techniques and sensitive detection methods drives the field of single molecule enzymology. Here, we introduce recent progress in single enzyme molecule analysis in microwell arrays and discuss the challenges and opportunities.

  10. Single Molecule Electronics and Devices

    Directory of Open Access Journals (Sweden)

    Makusu Tsutsui

    2012-05-01

    Full Text Available 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.

  11. When water molecules meet air

    OpenAIRE

    Hsie, Cho-Shuen; Campen, R. Kramer; Verde, Ana Vila; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa

    2012-01-01

    About 70% of our planet is covered in water. Most of that water exists as water in the bulk – the neighbors of water molecules are other water molecules – and only a small fraction of molecules are at the air-water interface. Despite the small relative abundance of interfacial water, it is of the utmost importance: it governs the chemistry involving the surface of oceans and seawater aerosols, or the small water droplets forming clouds. Reactions at the air-water interface are directly releva...

  12. 应用石墨为微波吸收介质非极性溶剂微波提取孜然挥发油成分%Application of graphite Powder for Non-polar Solvent Microwave Extraction of Essential Oils Cumimm Cyminum L.

    Institute of Scientific and Technical Information of China (English)

    于永; 王玉堂; 汪子明; 李铁纯; 张寒琦

    2008-01-01

    1引言微波加热效率高低主要取决于体系中物质吸收微波的能力大小,由于非极性溶剂不吸收微波因而通常不能单独作为微波辅助提取的提取溶剂。乙醚是一种常用的非极性溶剂,在蒸馏-提取法(simultaneous distillation and solvent extraction,SDE)中被用作提取溶剂,石墨是一种良好的微波吸收介质,本实验通过在乙醚中加入石墨建立了孜然中挥发油组分的非极性溶剂微波提取法(non-polar solvent microwave extraction,NPSME),

  13. Absorption characteristics of bacteriorhodopsin molecules

    Indian Academy of Sciences (India)

    H K T Kumar; K Appaji Gowda

    2000-03-01

    The bacteriorhodopsin molecule absorbs light and undergoes a series of structural transformation following a well-defined photocycle. The complex photocycle is transformed to an equivalent level diagram by considering the lifetime of the intermediate states. Assuming that only and states are appreciably populated at any instant of time, the level diagram is further simplified to two-level system. Based on the rate equations for two-level system, an analytic expression for the absorption coefficient of bacteriorhodopsin molecule is derived. It is applied to study the behaviour of absorption coefficient of bacteriorhodopsin film in the visible wavelength region of 514 nm. The dependence of absorption coefficient of bacteriorhodopsin film on the thickness of the film, total number density of active molecules and initial number density of molecules in -state is presented in the graphical form.

  14. Cell adhesion molecules and sleep.

    Science.gov (United States)

    O'Callaghan, Emma Kate; Ballester Roig, Maria Neus; Mongrain, Valérie

    2017-03-01

    Cell adhesion molecules (CAMs) play essential roles in the central nervous system, where some families are involved in synaptic development and function. These synaptic adhesion molecules (SAMs) are involved in the regulation of synaptic plasticity, and the formation of neuronal networks. Recent findings from studies examining the consequences of sleep loss suggest that these molecules are candidates to act in sleep regulation. This review highlights the experimental data that lead to the identification of SAMs as potential sleep regulators, and discusses results supporting that specific SAMs are involved in different aspects of sleep regulation. Further, some potential mechanisms by which SAMs may act to regulate sleep are outlined, and the proposition that these molecules may serve as molecular machinery in the two sleep regulatory processes, the circadian and homeostatic components, is presented. Together, the data argue that SAMs regulate the neuronal plasticity that underlies sleep and wakefulness. Copyright © 2016 Elsevier Ireland Ltd and Japan Neuroscience Society. All rights reserved.

  15. Special Issue: Single Molecule Techniques

    Directory of Open Access Journals (Sweden)

    Hans H. Gorris

    2015-04-01

    Full Text Available Technological advances in the detection and manipulation of single molecules have enabled new insights into the function, structure and interactions of biomolecules. This Special Issue was launched to account for the rapid progress in the field of “Single Molecule Techniques”. Four original research articles and seven review articles provide an introduction, as well as an in-depth discussion, of technical developments that are indispensable for the characterization of individual biomolecules. Fluorescence microscopy takes center stage in this Special Issue because it is one of the most sensitive and flexible techniques, which has been adapted in many variations to the specific demands of single molecule analysis. Two additional articles are dedicated to single molecule detection based on atomic force microscopy.

  16. Quantum Transport Through Heterocyclic Molecules

    Science.gov (United States)

    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.

  17. Guidance molecules in lung cancer

    OpenAIRE

    Nasarre, Patrick; Potiron, Vincent; Drabkin, Harry; Roche, Joëlle

    2010-01-01

    Guidance molecules were first described in the nervous system to control axon outgrowth direction. They are also widely expressed outside the nervous system where they control cell migration, tissue development and establishment of the vascular network. In addition, they are involved in cancer development, tumor angiogenesis and metastasis. This review is primarily focused on their functions in lung cancer and their involvement in lung development is also presented. Five guidance molecule fam...

  18. Plasmonic atoms and plasmonic molecules

    CERN Document Server

    Klimov, V V

    2007-01-01

    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for a construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  19. Plasmonic atoms and plasmonic molecules

    Science.gov (United States)

    Klimov, V. V.; Guzatov, D. V.

    2007-11-01

    The proposed paradigm of plasmonic atoms and plasmonic molecules allows one to describe and predict the strongly localized plasmonic oscillations in the clusters of nanoparticles and some other nanostructures in uniform way. Strongly localized plasmonic molecules near the contacting surfaces might become the fundamental elements (by analogy with Lego bricks) for the construction of fully integrated opto-electronic nanodevices of any complexity and scale of integration.

  20. Optofluidic single molecule flow proteometry

    Science.gov (United States)

    Jing, Nan; Chou, Chao-Kai; Hung, Mien-Chie; Kameoka, Jun

    2009-02-01

    A microfluidic single molecule fluorescence-based detection scheme is developed to identify target protein direct from cell lysate by using polyclonal antibody. Relative concentration of target protein in solution is determined by twodimensional (2D) photon burst analysis. Compared to conventional ensemble measurement assays, this microfluidic single molecule approach combines the advantages of higher sensitivity, fast processing time, small sample consumption and high resolution quantitative analysis.

  1. Signaling Molecules and Pulp Regeneration.

    Science.gov (United States)

    Schmalz, Gottfried; Widbiller, Matthias; Galler, Kerstin M

    2017-09-01

    Signaling molecules play an essential role in tissue engineering because they regulate regenerative processes. Evidence exists from animal studies that single molecules such as members of the transforming growth factor beta superfamily and factors that induce the growth of blood vessels (vascular endothelial growth factor), nerves (brain-derived neurotrophic factor), or fibroblasts (fibroblast growth factor) may induce reparative dentin formation. Mainly the formation of atubular dentin (osteodentin) has been described after the application of single molecules or combinations of recombinant growth factors on healthy exposed pulps or in pulp regeneration. Generally, such preparations have not received regulatory approval on the market so far. Only the use of granulocyte colony-stimulating factors together with cell transplantation is presently tested clinically. Besides approaches with only 1 or few combined molecules, the exploitation of tissue-derived growth factors depicts a third promising way in dental pulp tissue engineering. Preparations such as platelet-rich plasma or platelet-rich fibrin provide a multitude of endogenous signaling molecules, and special regulatory approval for the market does not seem necessary. Furthermore, dentin is a perfect reservoir of signaling molecules that can be mobilized by treatment with demineralizing agents such as EDTA. This conditions the dentin surface and allows for contact differentiation of pulp stem cells into odontoblastlike cells, protects dentin from resorption, and enhances cell growth as well as attachment to dentin. By ultrasonic activation, signaling molecules can be further released from EDTA pretreated dentin into saline, thus avoiding cytotoxic EDTA in the final preparation. The use of dentin-derived growth factors offers a number of advantages because they are locally available and presumably are most fit to induce signaling processes in dental pulp. However, better characterization and standardization of the

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

    Science.gov (United States)

    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. The Molecule Cloud - compact visualization of large collections of molecules.

    Science.gov (United States)

    Ertl, Peter; Rohde, Bernhard

    2012-07-06

    Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach "Molecule Cloud". The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large data sets, including PubChem, ChEMBL and ZINC databases using

  4. The Molecule Cloud - compact visualization of large collections of molecules

    Directory of Open Access Journals (Sweden)

    Ertl Peter

    2012-07-01

    Full Text Available Abstract Background Analysis and visualization of large collections of molecules is one of the most frequent challenges cheminformatics experts in pharmaceutical industry are facing. Various sophisticated methods are available to perform this task, including clustering, dimensionality reduction or scaffold frequency analysis. In any case, however, viewing and analyzing large tables with molecular structures is necessary. We present a new visualization technique, providing basic information about the composition of molecular data sets at a single glance. Summary A method is presented here allowing visual representation of the most common structural features of chemical databases in a form of a cloud diagram. The frequency of molecules containing particular substructure is indicated by the size of respective structural image. The method is useful to quickly perceive the most prominent structural features present in the data set. This approach was inspired by popular word cloud diagrams that are used to visualize textual information in a compact form. Therefore we call this approach “Molecule Cloud”. The method also supports visualization of additional information, for example biological activity of molecules containing this scaffold or the protein target class typical for particular scaffolds, by color coding. Detailed description of the algorithm is provided, allowing easy implementation of the method by any cheminformatics toolkit. The layout algorithm is available as open source Java code. Conclusions Visualization of large molecular data sets using the Molecule Cloud approach allows scientists to get information about the composition of molecular databases and their most frequent structural features easily. The method may be used in the areas where analysis of large molecular collections is needed, for example processing of high throughput screening results, virtual screening or compound purchasing. Several example visualizations of large

  5. Molecule-by-Molecule Writing Using a Focused Electron Beam

    DEFF Research Database (Denmark)

    Van Dorp, Willem F.; Zhang, Xiaoyan; Feringa, Ben L.;

    2012-01-01

    on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...... atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor...

  6. Small molecule fluoride toxicity agonists.

    Science.gov (United States)

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

    2015-04-23

    Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here, we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Small Molecule Fluoride Toxicity Agonists

    Science.gov (United States)

    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

  8. Laser spectroscopy of cold molecules

    CERN Document Server

    Borri, Simone

    2016-01-01

    This paper reviews the recent results in high-resolution spectroscopy on cold molecules. Laser spectroscopy of cold molecules addresses issues of symmetry violation, like in the search for the electric dipole moment of the electron and the studies on energy differences in enantiomers of chiral species; tries to improve the precision to which fundamental physical constants are known and tests for their possible variation in time and space; tests quantum electrodynamics, and searches for a fifth force. Further, we briefly review the recent technological progresses in the fields of cold molecules and mid-infrared lasers, which are the tools that mainly set the limits for the resolution that is currently attainable in the measurements.

  9. Single-molecule magnet engineering

    DEFF Research Database (Denmark)

    Pedersen, Kasper Steen; Bendix, Jesper; Clérac, Rodolphe

    2014-01-01

    to delicately tune, for instance, the properties of molecules that behave as "magnets", the so-called single-molecule magnets (SMMs). Although many interesting SMMs have been prepared by a more or less serendipitous approach, the assembly of predesigned, isolatable molecular entities into higher nuclearity...... complexes constitutes an elegant and fascinating strategy. This Feature article focuses on the use of building blocks or modules (both terms being used indiscriminately) to direct the structure, and therefore also the magnetic properties, of metal ion complexes exhibiting SMM behaviour. This journal...

  10. Nonadiabatic reaction of energetic molecules.

    Science.gov (United States)

    Bhattacharya, Atanu; Guo, Yuanqing; Bernstein, Elliot R

    2010-12-21

    Energetic materials store a large amount of chemical energy that can be readily converted into mechanical energy via decomposition. A number of different ignition processes such as sparks, shocks, heat, or arcs can initiate the excited electronic state decomposition of energetic materials. Experiments have demonstrated the essential role of excited electronic state decomposition in the energy conversion process. A full understanding of the mechanisms for the decomposition of energetic materials from excited electronic states will require the investigation and analysis of the specific topography of the excited electronic potential energy surfaces (PESs) of these molecules. The crossing of multidimensional electronic PESs creates a funnel-like topography, known as conical intersections (CIs). CIs are well established as a controlling factor in the excited electronic state decomposition of polyatomic molecules. This Account summarizes our current understanding of the nonadiabatic unimolecular chemistry of energetic materials through CIs and presents the essential role of CIs in the determination of decomposition pathways of these energetic systems. Because of the involvement of more than one PES, a decomposition process involving CIs is an electronically nonadiabatic mechanism. Based on our experimental observations and theoretical calculations, we find that a nonadiabatic reaction through CIs dominates the initial decomposition process of energetic materials from excited electronic states. Although the nonadiabatic behavior of some polyatomic molecules has been well studied, the role of nonadiabatic reactions in the excited electronic state decomposition of energetic molecules has not been well investigated. We use both nanosecond energy-resolved and femtosecond time-resolved spectroscopic techniques to determine the decomposition mechanism and dynamics of energetic species experimentally. Subsequently, we employ multiconfigurational methodologies (such as, CASSCF

  11. Tunneling Ionization of Diatomic Molecules

    DEFF Research Database (Denmark)

    Svensmark, Jens Søren Sieg

    2016-01-01

    When a molecule is subject to a strong laser field, there is a probability that an electron can escape, even though the electrons are bound by a large potential barrier. This is possible because electrons are quantum mechanical in nature, and they are therefore able to tunnel through potential...... of tunneling ionizaion of molecules is presented and the results of numerical calculations are shown. One perhaps surprising result is, that the frequently used Born-Oppenheimer approximation breaks down for weak fields when describing tunneling ionization. An analytic theory applicable in the weak-field limit...

  12. Technetium-aspirin molecule complexes

    Energy Technology Data Exchange (ETDEWEB)

    El-Shahawy, A.S.; Mahfouz, R.M.; Aly, A.A.M.; El-Zohry, M. (Assiut Univ. (Egypt))

    1993-01-01

    Technetium-aspirin and technetium-aspirin-like molecule complexes were prepared. The structure of N-acetylanthranilic acid (NAA) has been decided through CNDO calculations. The ionization potential and electron affinity of the NAA molecule as well as the charge densities were calculated. The electronic absorption spectra of Tc(V)-Asp and Tc(V)-ATS complexes have two characteristic absorption bands at 450 and 600 nm, but the Tc(V)-NAA spectrum has one characteristic band at 450 nm. As a comparative study, Mo-ATS complex was prepared and its electronic absorption spectrum is comparable with the Tc-ATS complex spectrum. (author).

  13. Recoiling DNA Molecule Simulation & Experiment

    CERN Document Server

    Neto, J C; Mesquita, O N; Neto, Jose Coelho; Dickman, Ronald

    2002-01-01

    Many recent experiments with single DNA molecules are based on force versus extension measurements and involve tethering a microsphere to one of its extremities and the other to a microscope coverglass. In this work we show that similar results can also be obtained by studying the recoil dynamics of the tethered microspheres. Computer simulations of the corresponding Langevin equation indicate which assumptions are required for a reliable analysis of the experimental recoil curves. We have measured the persistence length A of single naked DNA molecules and DNA-Ethidium Bromide complexes using this approach.

  14. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M

    2007-12-15

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

  15. Small Molecule PET-Radiopharmaceuticals

    NARCIS (Netherlands)

    Elsinga, Philip H.; Dierckx, Rudi A. J. O.

    2014-01-01

    This review describes several aspects required for the development of small molecule PET-tracers. Design and selection criteria are important to consider before starting to develop novel PET-tracers. Principles and latest trends in C-11 and F-18-radiochemistry are summarized. In addition an update o

  16. Azobenzene-functionalized cascade molecules

    DEFF Research Database (Denmark)

    Archut, A.; Vogtle, F.; De Cola, L.;

    1998-01-01

    Cascade molecules bearing up to 32 azobenzene groups in the periphery have been prepared from poly(propylene imine) dendrimers and N-hydroxysuccinimide esters. The dendritic azobenzene species show similar isomerization properties as the corresponding azobenzene monomers. The all-E azobenzene...

  17. WHAT ARE THE MOLECULES DOING?

    African Journals Online (AJOL)

    Temechegn

    Johnstone's identification of teaching and learning difficulties derived from the three levels of description in .... and in aqueous solution the molecules (say HA) dissociate into a hydrogen ion, H+ (aq) and an anion, A-(aq). This is a chemical ...

  18. Small Molecules Target Carcinogenic Proteins

    Science.gov (United States)

    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.

  19. Pair Tunneling through Single Molecules

    Science.gov (United States)

    Raikh, Mikhail

    2007-03-01

    Coupling to molecular vibrations induces a polaronic shift, and can lead to a negative charging energy, U. For negative U, the occupation of the ground state of the molecule is even. In this situation, virtual pair transitions between the molecule and the leads can dominate electron transport. At low temperature, T, these transitions give rise to the charge-Kondo effect [1]. We developed the electron transport theory through the negative-U molecule [2] at relatively high T, when the Kondo correlations are suppressed. Two physical ingredients distinguish our theory from the transport through a superconducting grain coupled to the normal leads [3]: (i) in parallel with sequential pair-tunneling processes, single-particle cotunneling processes take place; (ii) the electron pair on the molecule can be created (or annihilated) by two electrons tunneling in from (or out to) opposite leads. We found that, even within the rate-equation description, the behavior of differential conductance through the negative-U molecule as function of the gate voltage is quite peculiar: the height of the peak near the degeneracy point is independent of temperature, while its width is proportional to T. This is in contrast to the ordinary Coulomb-blockade conductance peak, whose integral strength is T-independent. At finite source-drain bias, V>>T, the width of the conductance peak is ˜V, whereas the conventional Coulomb-blockade peak at finite V splits into two sharp peaks at detunings V/2, and -V/2. Possible applications to the gate-controlled current rectification and switching will be discussed. [1] A. Taraphder and P. Coleman, Phys. Rev. Lett. 66, 2814 (1991). [2] J. Koch, M. E. Raikh, and F. von Oppen, Phys. Rev. Lett. 96, 056803 (2006). [3] F. W. J. Hekking, L. I. Glazman, K. A. Matveev, and R. I. Shekhter, Phys. Rev. Lett. 70, 4138 (1993).

  20. Spectral Properties and Photochromic Characteristics of Spiropyran Dyes

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A bis-benzospiropyran(BBSP) and nitro-substituted indoline spirobenzopyrans(SBP) were prepared by following a simple procedure. The reaction mechanism of synthesizing bis-benzospiropyran is discussed. A comparative analysis of the spectral and photochromic properties between SBP and BBSP was carried out with the aid of a PMMA film. The results indicate that chemical structures and UV irradiation played an important role in the spectral and photochromic properties of SBP and BBSP, which would readily affect λmax of the colored forms and the reversibility. The IR spectra and 1H NMR spectra of these compounds are used to interpret the photochromic phenomena under different UV irradiation and determine the configurations of SBP and BBSP.

  1. Detection of cyanide anion by zinc porphyrin-spiropyran dyad

    Energy Technology Data Exchange (ETDEWEB)

    Kho, Young Min; Hur, Dae Young; Shin, Eun Ju [Dept. of Chemistry, Sunchon National University, Suncheon (Korea, Republic of)

    2016-10-15

    Versatile methods of the sensitive and selective detection for cyanide anion to monitor toxic cyanide have been developed. These include colorimetric, colorimetric, chromatographic, and electrochemical analyses. Among those methods for cyanide detection, optical methods based on absorption and fluorescence spectroscopy are relatively simple, inexpensive, and sensitive. A number of organic sensors for cyanide anion have been designed and synthesized. Absorption and/or fluorescence spectra of these sensors are changed by forming coordination complex or bonding covalently with cyanide. Compared with other anions, cyanide anion has some characteristic properties, such as its strong nucleophilicity and high binding affinity toward metal ions, and is superior and useful for the development of the sensors. Both covalent bond-based sensors and coordination complex-based sensors have been developed for cyanide detection. The results indicate that ZnP-SP plays a role as a CN{sup -} selective, colorimetric sensor either without or with UV irradiation.

  2. A versatile route to benzodiazocine and spiropyran derivatives through chalcones

    Indian Academy of Sciences (India)

    Johnson George; Saurabh Singh; Rahul Joshi; Ramchand T Pardasani

    2013-05-01

    Syntheses of 3-(phenyl)-benzo[b]thiophene [2, 3-d][1,2] benzodiazocine derivatives have been accomplished by the reaction of 3-phenacylidine-2-benzo[b]thiophene-2-ones with o-phenylene diamine. The photolytic reaction with trans-stilbene resulted in the exclusive formation of spiro{2',5',6'-triphenyl-2H-pyran-4',3}-benzo[b]thiophene-2-one derivatives. Theoretical calculations have been performed to study the mechanism and stereoselectivity of products. Good yield and broad scope of usable substrates of industrial relevance are other prominent features of the present methodologies.

  3. Structural Analysis of Spiropyran Polimers using ATR Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Delgado Macui, R; Rojas Lopez, M; Gayou, V L; Orduna Diaz, A [Centro de Investigacion en BiotecnologIa Aplicada del IPN, San Juan de los Molinos km. 1.5 Tepetitla de Lardizabal, A.P. 90700, Tlaxcala (Mexico)

    2006-01-01

    We have used infrared spectroscopy in attenuated total reflection (ATR) mode to analyze the interactions between the polymeric base and solvent with a photochromic material (spyropiran). We used cellulose acetate as polymeric base and the spyropiran; 1,3,3 trimethyl indoline-5-nitro benzopyrane. Thin films with different weight concentrations of SP were deposited in the polymeric base. The infrared spectra show bands whose frequencies are associated to several molecular bondings. It was observed a decreasing in intensity of absorbance for C = O stretching mode of the acetate group at 1720 cm{sup -1} and for C = C stretching mode for the main chain at 823 and 982 cm{sup -1} both associated to the presence of SP in polymeric films.

  4. Synthesis of spiropyrans: H-abstractions in 3-cycloalkenyloxybenzopyrans

    Directory of Open Access Journals (Sweden)

    Berar Urmila

    2007-03-01

    Full Text Available Abstract A photochemical route for the synthesis of some benzopyronospiropyrans from 2-furyl-3-cycloalkenyloxybenzopyrones involving H-abstraction is reported. How a methyl group on the furyl ring affects the product formation is also investigated.

  5. Ballonet String Model of Molecules

    Directory of Open Access Journals (Sweden)

    Gavril NIAC

    2008-06-01

    Full Text Available Strings of ballonets, modelling rows of orbitals, are assembled to molecule models by crossing them properly. The ballonets at the ends of the strings of 2, 3, 4 or 5 spheres represent bonding orbitals of hydrogen with other elements like C, N or O (the proton being inside the sphere, as well as nonbonding orbitals. The ballonets between them are modelling bonding orbitals among elements other than hydrogen - except the double bond in diborane, the atomic cores laying at the junction of two or more spheres.Advantages of elastic sphere models range from self-adjusting bond angles to resistance when closing cycles like cyclopropane or modeling double bonds.Examples comprise alkanes, including platonic hydrocarbons, ethene, acetylene, and some inorganic molecules.

  6. Electrondriven processes in polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    McKoy, Vincent [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2017-03-20

    This project developed and applied scalable computational methods to obtain information about low-energy electron collisions with larger polyatomic molecules. Such collisions are important in modeling radiation damage to living systems, in spark ignition and combustion, and in plasma processing of materials. The focus of the project was to develop efficient methods that could be used to obtain both fundamental scientific insights and data of practical value to applications.

  7. Small Molecules-Big Data.

    Science.gov (United States)

    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

  8. Physics of Atoms and Molecules

    CERN Document Server

    Bransden, B H

    2003-01-01

    New edition of a well-established second and third year textbook for Physics degree students, covering the physical structure and behaviour of atoms and molecules. The aim of this new edition is to provide a unified account of the subject within an undergraduate framework, taking the opportunity to make improvements based on the teaching experience of users of the first edition, and cover important new developments in the subject.

  9. Optical highlighter molecules in neurobiology.

    Science.gov (United States)

    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.

  10. Water molecules orientation in surface layer

    Science.gov (United States)

    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.

  11. Small Molecule Organic Optoelectronic Devices

    Science.gov (United States)

    Bakken, Nathan

    Organic optoelectronics include a class of devices synthesized from carbon containing 'small molecule' thin films without long range order crystalline or polymer structure. Novel properties such as low modulus and flexibility as well as excellent device performance such as photon emission approaching 100% internal quantum efficiency have accelerated research in this area substantially. While optoelectronic organic light emitting devices have already realized commercial application, challenges to obtain extended lifetime for the high energy visible spectrum and the ability to reproduce natural white light with a simple architecture have limited the value of this technology for some display and lighting applications. In this research, novel materials discovered from a systematic analysis of empirical device data are shown to produce high quality white light through combination of monomer and excimer emission from a single molecule: platinum(II) bis(methyl-imidazolyl)toluene chloride (Pt-17). Illumination quality achieved Commission Internationale de L'Eclairage (CIE) chromaticity coordinates (x = 0.31, y = 0.38) and color rendering index (CRI) > 75. Further optimization of a device containing Pt-17 resulted in a maximum forward viewing power efficiency of 37.8 lm/W on a plain glass substrate. In addition, accelerated aging tests suggest high energy blue emission from a halogen-free cyclometalated platinum complex could demonstrate degradation rates comparable to known stable emitters. Finally, a buckling based metrology is applied to characterize the mechanical properties of small molecule organic thin films towards understanding the deposition kinetics responsible for an elastic modulus that is both temperature and thickness dependent. These results could contribute to the viability of organic electronic technology in potentially flexible display and lighting applications. The results also provide insight to organic film growth kinetics responsible for optical

  12. Small molecules for big tasks

    Institute of Scientific and Technical Information of China (English)

    Jiarui Wu

    2011-01-01

    @@ One of the most important achievements in the post-genome era is discovery of microRNAs (miRNAs), which widely exist from simple-genome organisms such as viruses and bacteria to complexgenome organisms such as plants and animals.miRNAs are single-stranded non-coding RNAs of 18-25 nucleotides in length, which are generated from larger precursors that are transcribed from noncoding genes.As a new type of regulatory molecules, miRNAs present unique features in regulating gene and its products, including rapidly turning off protein production, reversibly, and compartmentalized regulating gene expression.

  13. Dissociation Energies of Diatomic Molecules

    Institute of Scientific and Technical Information of China (English)

    FAN Qun-Chao; SUN Wei-Guo

    2008-01-01

    Molecular dissociation energies of 10 electronic states of alkali molecules of KH, 7LID, 7LiH, 6LiH, NaK, NaLi and NaRb are studied using the highest three accurate vibrational energies of each electronic state, and an improved parameter-free analytical formula which is obtained starting from the LeRoy-Bernstein vibrational energy expression near the dissociation limit. The results show that as long as the highest three vibrational energies are accurate, the current analytical formula will give accurate theoretical dissociation energies Detheory, which are in excellent agreement with the experimental dissociation energies Dexpte.

  14. The neural cell adhesion molecule

    DEFF Research Database (Denmark)

    Berezin, V; Bock, E; Poulsen, F M

    2000-01-01

    During the past year, the understanding of the structure and function of neural cell adhesion has advanced considerably. The three-dimensional structures of several of the individual modules of the neural cell adhesion molecule (NCAM) have been determined, as well as the structure of the complex...... between two identical fragments of the NCAM. Also during the past year, a link between homophilic cell adhesion and several signal transduction pathways has been proposed, connecting the event of cell surface adhesion to cellular responses such as neurite outgrowth. Finally, the stimulation of neurite...

  15. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)

    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.

  16. The molecule-metal interface

    CERN Document Server

    Koch, Norbert; Wee, Andrew Thye Shen

    2013-01-01

    Reviewing recent progress in the fundamental understanding of the molecule-metal interface, this useful addition to the literature focuses on experimental studies and introduces the latest analytical techniques as applied to this interface.The first part covers basic theory and initial principle studies, while the second part introduces readers to photoemission, STM, and synchrotron techniques to examine the atomic structure of the interfaces. The third part presents photoelectron spectroscopy, high-resolution UV photoelectron spectroscopy and electron spin resonance to study the electroni

  17. Proteins Are the Body's Worker Molecules

    Science.gov (United States)

    ... PDF Chapter 1: Proteins are the Body's Worker Molecules You've probably heard that proteins are important ... are much more than that. Proteins are worker molecules that are necessary for virtually every activity in ...

  18. Molecules in Studio v. 1.0

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Similarity of atoms in molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cioslowski, J.; Nanayakkara, A. (Florida State Univ., Tallahassee, FL (United States))

    1993-12-01

    Similarity of atoms in molecules is quantitatively assessed with a measure that employs electron densities within respective atomic basins. This atomic similarity measure does not rely on arbitrary assumptions concerning basis functions or 'atomic orbitals', is relatively inexpensive to compute, and has straightforward interpretation. Inspection of similarities between pairs of carbon, hydrogen, and fluorine atoms in the CH[sub 4], CH[sub 3]F, CH[sub 2]F[sub 2], CHF[sub 3], CF[sub 4], C[sub 2]H[sub 2], C[sub 2]H[sub 4], and C[sub 2]H[sub 6] molecules, calculated at the MP2/6-311G[sup **] level of theory, reveals that the atomic similarity is greatly reduced by a change in the number or the character of ligands (i.e. the atoms with nuclei linked through bond paths to the nucleus of the atom in question). On the other hand, atoms with formally identical (i.e. having the same nuclei and numbers of ligands) ligands resemble each other to a large degree, with the similarity indices greater than 0.95 for hydrogens and 0.99 for non-hydrogens. 19 refs., 6 tabs.

  20. Characterization of Interstellar Organic Molecules

    Science.gov (United States)

    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.

  1. Is JPC = 3-+ molecule possible?

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  3. How Is a Protein Molecule Nearsighted?

    Institute of Scientific and Technical Information of China (English)

    GAO De; JI Qing; L(U) Gang

    2005-01-01

    @@ The effect range of a local change of a protein molecule is calculated using a cluster method developed in this work based on the Gaussian software. This range is found to be about 8 A, which gives a concrete estimation on the "nearsightedness" by Kohn for protein molecules. The cluster method can be applied to calculation of the electronic density of a large molecule such as a motor protein and can provide a basis for the dynamical analysis of a single protein molecule.

  4. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    Science.gov (United States)

    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.

  5. Faddeev Random Phase Approximation applied to molecules

    CERN Document Server

    Degroote, Matthias

    2012-01-01

    This Ph.D. thesis derives the equations of the Faddeev Random Phase Approximation (FRPA) and applies the method to a set of small atoms and molecules. The occurence of RPA instabilities in the dissociation limit is addressed in molecules and by the study of the Hubbard molecule as a test system with reduced dimensionality.

  6. Visualization of large elongated DNA molecules.

    Science.gov (United States)

    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.

  7. Three-cluster nuclear molecules

    CERN Document Server

    Poenaru, D N; Greiner, W

    2000-01-01

    A three-center phenomenological model able to explain, at least from a qualitative point of view, the difference in the observed yield of a particle-accompanied fission and that of binary fission was developed. It is derived from the liquid drop model under the assumption that the aligned configuration, with the emitted particle between the light and heavy fragment is obtained by increasing continuously the separation distance, while the radii of the light fragment and of the light particle are kept constant. During the first stage of the deformation one has a two-center evolution until the neck radius becomes equal to the radius of the emitted particle. Then the three center starts developing by decreasing with the same amount the two tip distances. In such a way a second minimum, typical for a cluster molecule, appears in the deformation energy. Examples are presented for $^{240}$Pu parent nucleus emitting $\\alpha$-particles and $^{14}$C in a ternary process.

  8. Molecule Formation on Interstellar Grains

    Science.gov (United States)

    Vidali, G.

    2011-05-01

    The first experiments that were expressively designed to be applicable to hydrogen formation reactions in the ISM measured the efficiency of formation of molecular hydrogen on a polycrystalline olivine (Pirronello et al. (1997a)). It soon turned out that more was needed, and research began on the mechanism of reaction, on the in uence of the surface morphology, and on the excitation of the just- ormed molecule. In this review, I summarize what we learned from these and other experiments, and where more work is needed: in the elementary steps of reaction, in the bridging of the laboratory-ISM gap (large ux/large surface - small ux/small grain) using simulations, and in using realistic samples of dust grains. Understanding what experiments can and cannot deliver will help in designing and targeting observations, and vice-versa.

  9. Photoluminescence of a Plasmonic Molecule.

    Science.gov (United States)

    Huang, Da; Byers, Chad P; Wang, Lin-Yung; Hoggard, Anneli; Hoener, Ben; Dominguez-Medina, Sergio; Chen, Sishan; Chang, Wei-Shun; Landes, Christy F; Link, Stephan

    2015-07-28

    Photoluminescent Au nanoparticles are appealing for biosensing and bioimaging applications because of their non-photobleaching and non-photoblinking emission. The mechanism of one-photon photoluminescence from plasmonic nanostructures is still heavily debated though. Here, we report on the one-photon photoluminescence of strongly coupled 50 nm Au nanosphere dimers, the simplest plasmonic molecule. We observe emission from coupled plasmonic modes as revealed by single-particle photoluminescence spectra in comparison to correlated dark-field scattering spectroscopy. The photoluminescence quantum yield of the dimers is found to be surprisingly similar to the constituent monomers, suggesting that the increased local electric field of the dimer plays a minor role, in contradiction to several proposed mechanisms. Aided by electromagnetic simulations of scattering and absorption spectra, we conclude that our data are instead consistent with a multistep mechanism that involves the emission due to radiative decay of surface plasmons generated from excited electron-hole pairs following interband absorption.

  10. Special Issue: "Molecules against Alzheimer".

    Science.gov (United States)

    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.

  11. Anti-cancer Lead Molecule

    KAUST Repository

    Sagar, Sunil

    2014-04-17

    Derivatives of plumbagin can be selectively cytotoxic to breast cancer cells. Derivative `A` (Acetyl Plumbagin) has emerged as a lead molecule for testing against estrogen positive breast cancer and has shown low hepatotoxicity as well as overall lower toxicity in nude mice model. The toxicity of derivative `A` was determined to be even lower than vehicle control (ALT and AST markers). The possible mechanism of action identified based on the microarray experiments and pathway mapping shows that derivative `A` could be acting by altering the cholesterol-related mechanisms. The low toxicity profile of derivative `A` highlights its possible role\\'as future anti-cancer drug and/or as an adjuvant drug to reduce the toxicity of highly toxic chemotherapeutic\\'drugs

  12. Optoelectronics of Molecules and Polymers

    CERN Document Server

    Moliton, André

    2006-01-01

    Optoelectronic devices are being developed at an extraordinary rate. Organic light emitting diodes, photovoltaic devices and electro-optical modulators are pivotal to the future of displays, photosensors and solar cells, and communication technologies. This book details the theories underlying the relevant mechanisms in organic materials and covers, at a basic level, how the organic components are made. The first part of this book introduces the fundamental theories used to detail ordered solids and localised energy levels. The methods used to determine energy levels in perfectly ordered molecular and macromolecular systems are discussed, making sure that the effects of quasi-particles are not missed. The function of excitons and their transfer between two molecules are studied, and the problems associated with interfaces and charge injection into resistive media are presented. The second part details technological aspects such as the fabrication of devices based on organic materials by dry etching. The princ...

  13. High-harmonic spectroscopy of aligned molecules

    Science.gov (United States)

    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.

  14. Observation of pendular butterfly Rydberg molecules.

    Science.gov (United States)

    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.

  15. Spin polarization effect for Cr2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying

    2008-01-01

    Density functional theory (DFT) (B3P86) of Ganssian 03 has been used to optimize the structure of the Cr2 molecule, a transition metal element molecule. The result shows that the ground state for the Cr2 molecule is a 13-multiple state, indicating that there exists a spin polarization effect in the Cr2 molecule. Meanwhile, we have not found any spin pollution because the wave function of the ground state does not mingle with wave functions of higher-energy states. So the ground state for Cr2 molecule being a 13-multiple state is indicative of spin polarization effect of the Cr2 molecule among transition metal elements, that is, there are 12 parallel spin electrons in the Cr2 molecule. The number of non-conjugated electrons is greatest. These electrons occupy different spatial orbitals so that the energy of the Cr2 molecule is minimized. It can be concluded that the effect of parallel spin in the Cr2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition,the Murrell-Sorbie potential functions with the parameters for the ground state and other states of the Cr2 molecule are derived. The dissociation energy De for the ground state of the Cr2 molecule is 0.1034eV, equilibrium bond length Re is 0.3396nm, and vibration frequency ωe is 73.81cm-1. Its force constants f2, f3 and f4 are 0.0835, -0.2831 and 0.3535 aJ·nm-4 respectively. The other spectroscopic data for the ground state of the Cr2 molecule ωeχe, Be and αe are 1.2105, 0.0562 and 7.2938 × 10-4cm-1 respectively.

  16. Spin polarization effect of Ni2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He

    2008-01-01

    The density functional theory (DFT) method (b3p86) of Gaussian 03 is used to optimize the structure of the Ni2 molecule. The result shows that the ground state for the Ni2 molecule is a 5-multiple state, symbolizing a spin polarization effect existing in the Ni2 molecule, a transition metal molecule, but no spin pollution is found because the wavefunction of the ground state does not mingle with wavefunctions of higher-energy states. So the ground state for Ni2 molecule, which is a 5-multiple state, is indicative of spin polarization effect of the Ni2 molecule, that is, there exist 4 parallel spin electrons in Ni2 molecule. The number of non-conjugated electrons is greatest. These electrons occupy different spatial orbitals so that the energy of the Ni2 molecule is minimized. It can be concluded that the effect of parallel spin in the Ni2 molecule is larger than that of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters of the ground state and other states of the Ni2 molecule are derived. The dissociation energy De for the ground state of the Ni2 molecule is 1.835 eV, equilibrium bond length Re is 0.2243 nm, vibration frequency ωe is 262.35 cm-1. Its force constants f2, f3 and f4 are 1.1901 aJ.nm-2, 5.8723 aJ.nm-3, and 21.2505 aJ.nm-4 respectively. The other spectroscopic data for the ground state of the Ni2 molecule ωexe, Be and αe are 1.6315cm-1, 0.1141 cm-1, and 8.0145×10-4 cm-1 respectively.

  17. Spin squeezing an ultracold molecule

    CERN Document Server

    Bhattacharya, M

    2015-01-01

    Most research on spin squeezing thus far has focused on realizations involving either atomic or nuclear degrees of freedom. In this article we discuss a concrete proposal for spin squeezing the ultracold ground state polar paramagnetic molecule OH, a system currently under fine control in the laboratory. Starting from an experimentally relevant effective Hamiltonian, we identify a parameter regime where different combinations of static electric and magnetic fields can be used to realize the single-axis twisting Hamiltonian of Kitagawa and Ueda [M. Kitagawa and M. Ueda, Phys. Rev. A 47, 5138 (1993)], the uniform field Hamiltonian proposed by Law et al. [C. K. Law, H. T Ng and P. T. Leung, Phys. Rev. A 63, 055601 (2001)], and a model of field propagation in a Kerr medium considered by Agarwal and Puri [G. S. Agarwal and R. R. Puri, Phys. Rev. A 39, 2969 (1989)]. To support our conclusions, we provide analytical expressions as well as numerical calculations, including optimization of field strengths and accounti...

  18. Geochemical Origin of Biological Molecules

    Science.gov (United States)

    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

  19. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Coordination Programming of Photofunctional Molecules

    Directory of Open Access Journals (Sweden)

    Hiroshi Nishihara

    2013-04-01

    Full Text Available 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(dipyrrinatozinc(II complexes. Conventional homoleptic bis(dipyrrinatozinc(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(arylethynylfumarate 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. Cochleates bridged by drug molecules.

    Science.gov (United States)

    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.

  2. Coordination programming of photofunctional molecules.

    Science.gov (United States)

    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.

  3. Single-Molecule Stochastic Resonance

    Directory of Open Access Journals (Sweden)

    K. Hayashi

    2012-08-01

    Full Text Available Stochastic resonance (SR is a well-known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic (random or probabilistic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively transitions from folded to unfolded configurations under the action of an oscillating mechanical force applied with optical tweezers. By varying the frequency of the force oscillation, we investigate the folding and unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measure several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that a good quantifier of the SR is the signal-to-noise ratio (SNR of the spectral density of measured fluctuations in molecular extension of the DNA hairpins. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance-matching condition. Finally, we carry out experiments on short hairpins that show how SR might be useful for enhancing the detection of conformational molecular transitions of low SNR.

  4. Single-molecule stochastic resonance

    CERN Document Server

    Hayashi, K; Manosas, M; Huguet, J M; Ritort, F; 10.1103/PhysRevX.2.031012

    2012-01-01

    Stochastic resonance (SR) is a well known phenomenon in dynamical systems. It consists of the amplification and optimization of the response of a system assisted by stochastic noise. Here we carry out the first experimental study of SR in single DNA hairpins which exhibit cooperatively folding/unfolding transitions under the action of an applied oscillating mechanical force with optical tweezers. By varying the frequency of the force oscillation, we investigated the folding/unfolding kinetics of DNA hairpins in a periodically driven bistable free-energy potential. We measured several SR quantifiers under varied conditions of the experimental setup such as trap stiffness and length of the molecular handles used for single-molecule manipulation. We find that the signal-to-noise ratio (SNR) of the spectral density of measured fluctuations in molecular extension of the DNA hairpins is a good quantifier of the SR. The frequency dependence of the SNR exhibits a peak at a frequency value given by the resonance match...

  5. Observation of pendular butterfly Rydberg molecules

    CERN Document Server

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

    2016-01-01

    Obtaining full control over the internal and external quantum states of molecules is the central goal of ultracold chemistry and allows for the study of coherent molecular dynamics, collisions and tests of fundamental laws of physics. When the molecules additionally have a permanent electric dipole moment, the study of dipolar quantum gases and spin-systems with long-range interactions as well as applications in quantum information processing are possible. Rydberg molecules constitute a class of exotic molecules, which are bound by the interaction between the Rydberg electron and the ground state atom. They exhibit extreme bond lengths of hundreds of Bohr radii and giant permanent dipole moments in the kilo-Debye range. A special type with exceptional properties are the so-called butterfly molecules, whose electron density resembles the shape of a butterfly. Here, we report on the photoassociation of butterfly Rydberg molecules and their orientation in a weak electric field. Starting from a Bose-Einstein cond...

  6. Rotational cooling of trapped polyatomic molecules

    CERN Document Server

    Glöckner, Rosa; Englert, Barbara G U; Rempe, Gerhard; Zeppenfeld, Martin

    2015-01-01

    Controlling the internal degrees of freedom is a key challenge for applications of cold and ultracold molecules. Here, we demonstrate rotational-state cooling of trapped methyl fluoride molecules (CH3F) by optically pumping the population of 16 M-sublevels in the rotational states J=3,4,5, and 6 into a single level. By combining rotational-state cooling with motional cooling, we increase the relative number of molecules in the state J=4, K=3, M=4 from a few percent to over 70%, thereby generating a translationally cold (~30mK) and nearly pure state ensemble of about 10^6 molecules. Our scheme is extendable to larger sets of initial states, other final states and a variety of molecule species, thus paving the way for internal-state control of ever larger molecules.

  7. Laser cooling of a diatomic molecule

    CERN Document Server

    Shuman, E S; DeMille, D

    2011-01-01

    It has been roughly three decades since laser cooling techniques produced ultracold atoms, leading to rapid advances in a vast array of fields. Unfortunately laser cooling has not yet been extended to molecules because of their complex internal structure. However, this complexity makes molecules potentially useful for many applications. For example, heteronuclear molecules possess permanent electric dipole moments which lead to long-range, tunable, anisotropic dipole-dipole interactions. The combination of the dipole-dipole interaction and the precise control over molecular degrees of freedom possible at ultracold temperatures make ultracold molecules attractive candidates for use in quantum simulation of condensed matter systems and quantum computation. Also ultracold molecules may provide unique opportunities for studying chemical dynamics and for tests of fundamental symmetries. Here we experimentally demonstrate laser cooling of the molecule strontium monofluoride (SrF). Using an optical cycling scheme re...

  8. Small-Molecule Carbohydrate-Based Immunostimulants.

    Science.gov (United States)

    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.

  9. Making "Operations" inside a Single Molecule

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ Free and delicate manipulation of single molecules has long been expected by scientists so as to realize specific functions. In the 1990s, the laboratory led by Prof. Wison Ho from the University of California was successful in inducing chemical reactions at the single molecule level with scanning tunneling microscopy (STM), revealing the extensive potentials of "single molecule operation." However, until recently, researchers have failed to utilize the reaction to give rise to special physical properties.

  10. Negative refraction in Möbius molecules

    Science.gov (United States)

    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.

  11. Ultracold Molecules: Physics in the Quantum Regime

    Energy Technology Data Exchange (ETDEWEB)

    Doyle, John [Harvard Univ., Cambridge, MA (United States). Dept. of Physics

    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.

  12. Electron-molecule interactions and their applications

    CERN Document Server

    Christophorou, L G

    1984-01-01

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

  13. Submillimeter Spectroscopy of Hydride Molecules

    Science.gov (United States)

    Phillips, T. G.

    1998-05-01

    Simple hydride molecules are of great importance in astrophysics and astrochemistry. Physically they dominate the cooling of dense, warm phases of the ISM, such as the cores and disks of YSOs. Chemically they are often stable end points of chemical reactions, or may represent important intermediate stages of the reaction chains, which can be used to test the validity of the process. Through the efforts of astronomers, physicists, chemists, and laboratory spectroscopists we have an approximate knowledge of the abundance of some of the important species, but a great deal of new effort will be required to achieve the comprehensive and accurate data set needed to determine the energy balance and firmly establish the chemical pathways. Due to the low moment of inertia, the hydrides rotate rapidly and so have their fundamental spectral lines in the submillimeter. Depending on the cloud geometry and temperature profile they may be observed in emission or absorption. Species such as HCl, HF, OH, CH, CH(+) , NH_2, NH_3, H_2O, H_2S, H_3O(+) and even H_3(+) have been detected, but this is just a fraction of the available set. Also, most deduced abundances are not nearly sufficiently well known to draw definitive conclusions about the chemical processes. For example, the most important coolant for many regions, H_2O, has a possible range of deduced abundance of a factor of 1000. The very low submillimeter opacity at the South Pole site will be a significant factor in providing a new capabilty for interstellar hydride spectroscopy. The new species and lines made available in this way will be discussed.

  14. Theoretical spectra of floppy molecules

    Science.gov (United States)

    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

  15. Spin polarization effect for Tc2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He

    2004-01-01

    Density functional method (DFT) (B3p86) of Gaussian98 has been used to optimize the structure of the Tc2 molecule. The result shows that the ground state for Tc2 molecule is an 11-multiple state and its electronic configuration is 11∑- g, which shows the spin polarization effect of Tc2 molecule of a transition metal element for the first time.Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions of higher energy states. So, that the ground state for Tc2 molecule is an 11-multiple state is indicative of the spin polarization effect of Tc2 molecule of a transition metal element: that is, there exist 10 parallel spin electrons. The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of Tc2 molecule is minimized. It can be concluded that the effect of parallel spin of the Tc2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization.In addition, the Murrell-Sorbie potential functions with the parameters for the ground state 11∑- g and other states of Tc2 molecule are derived. Dissociation energy De for the ground state of Tc2 molecule is 2.266eV, equilibrium bond length Re is 0.2841nm, vibration frequency ωe is 178.52cm-1. Its force constants f2, f3, and f4 are 0.9200aJ.nm-2,-3.5700aJ.nm-3, 11.2748aJ.nm-4 respectively. The other spectroscopic data for the ground state of Tc2 molecule ωexe,Be, αe are 0.5523cm- 1, 0.0426cm- 1, 1.6331 × 10-4cm- 1 respectively.

  16. Spin polarization effect for Fe2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Zhu Zheng-He

    2006-01-01

    This paper uses the density functional theory (DFT)(B3p86) of Gaussian03 to optimize the structure of Fe2 molecule. The result shows that the ground state for Fe2 molecule is a 9-multiple state, which shows spin polarization effect of Fe2 molecule of transition metal elements for the first time. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions with higher energy states. So, that the ground state for Fe2 molecule is a 9-multiple state is indicative of the spin polarization effect of Fe2 molecule of transition metal elements. That is, there exist 8 parallel spin electrons. The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of the Fe2 molecule is minimized. It can be concluded that the effect of parallel spin of the Fe2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state and other states of Fe2 molecule are derived. Dissociation energy De for the ground state of Fe2 molecule is 2.8586ev, equilibrium bond length Re is 0.2124nm, vibration frequency ωe is 336.38 cm-1. Its force constants f2, f3, and f4 are 1.8615aJ·nm-2, -8.6704a J·nm-3, 29.1676aJ·nm-4 respectively. The other spectroscopic data for the ground state of Fe2 moleculeωeχe, Be, αe are 1.5461 cm-1, 0.1339 cm-1, 7.3428×10-4 cm-1 respectively.

  17. Laser cooling of a diatomic molecule.

    Science.gov (United States)

    Shuman, E S; Barry, J F; Demille, D

    2010-10-14

    It has been roughly three decades since laser cooling techniques produced ultracold atoms, leading to rapid advances in a wide array of fields. Laser cooling has not yet been extended to molecules because of their complex internal structure. However, this complexity makes molecules potentially useful for a wide range of applications. For example, heteronuclear molecules possess permanent electric dipole moments that lead to long-range, tunable, anisotropic dipole-dipole interactions. The combination of the dipole-dipole interaction and the precise control over molecular degrees of freedom possible at ultracold temperatures makes ultracold molecules attractive candidates for use in quantum simulations of condensed-matter systems and in quantum computation. Also, ultracold molecules could provide unique opportunities for studying chemical dynamics and for tests of fundamental symmetries. Here we experimentally demonstrate laser cooling of the polar molecule strontium monofluoride (SrF). Using an optical cycling scheme requiring only three lasers, we have observed both Sisyphus and Doppler cooling forces that reduce the transverse temperature of a SrF molecular beam substantially, to a few millikelvin or less. At present, the only technique for producing ultracold molecules is to bind together ultracold alkali atoms through Feshbach resonance or photoassociation. However, proposed applications for ultracold molecules require a variety of molecular energy-level structures (for example unpaired electronic spin, Omega doublets and so on). Our method provides an alternative route to ultracold molecules. In particular, it bridges the gap between ultracold (submillikelvin) temperatures and the ∼1-K temperatures attainable with directly cooled molecules (for example with cryogenic buffer-gas cooling or decelerated supersonic beams). Ultimately, our technique should allow the production of large samples of molecules at ultracold temperatures for species that are chemically

  18. Controlled contact to a C-60 molecule

    DEFF Research Database (Denmark)

    Neel, N.; Kröger, J.; Limot, L.;

    2007-01-01

    The tip of a low-temperature scanning tunneling microscope is approached towards a C-60 molecule adsorbed at a pentagon-hexagon bond on Cu(100) to form a tip-molecule contact. The conductance rapidly increases to approximate to 0.25 conductance quanta in the transition region from tunneling...

  19. Spectrum Generating Algebra for X$_{3}$ Molecules

    CERN Document Server

    Bijker, R; Leviatan, A

    1995-01-01

    A new spectrum generating algebra for a unified description of rotations and vibrations in polyatomic molecules is introduced. An application to nonlinear X$_3$ molecules shows that this model (i) incorporates exactly the relevant point group, (ii) provides a complete classification of oblate top states, and (iii) treats properly both degenerate and nondegenerate vibrations.

  20. Tumor suppressor molecules and methods of use

    Science.gov (United States)

    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.

  1. Molecule-oriented programming in Java

    NARCIS (Netherlands)

    Bergstra, J.A.

    2002-01-01

    Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation

  2. The MHC molecules of nonmammalian vertebrates

    DEFF Research Database (Denmark)

    Kaufman, J; Skjoedt, K; Salomonsen, J

    1990-01-01

    There is very little known about the long-term evolution of the MHC and MHC-like molecules. This is because both the theory (the evolutionary questions and models) and the practice (the animals systems, functional assays and reagents to identify and characterize these molecules) have been difficu...

  3. Molecule-oriented programming in Java

    NARCIS (Netherlands)

    Bergstra, J.A.

    2002-01-01

    Molecule-oriented programming is introduced as a programming style carrying some perspective for Java. A sequence of examples is provided. Supporting the development of the molecule-oriented programming style several matters are introduced and developed: profile classes allowing the representation o

  4. Small Molecules in the Cone Snail Arsenal.

    Science.gov (United States)

    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.

  5. Decelerating and Trapping Large Polar Molecules.

    Science.gov (United States)

    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.

  6. A storage ring for neutral molecules

    NARCIS (Netherlands)

    Crompvoets, F.M.H.

    2005-01-01

    Time-varying inhomogeneous electric fields can be used to manipulate the motion of neutral molecules in phase-space, i.e., position-momentum space, via their electric dipole moment. A theoretical background is given on the motion of the molecules in phase-space. As the forces exerted on the

  7. Hydrogen storage by polylithiated molecules and nanostructures

    NARCIS (Netherlands)

    Er, S.; de Wijs, Gilles A.; Brocks, G.

    2009-01-01

    We study polylithiated molecules as building blocks for hydrogen storage materials, using first-principles calculations. CLi4 and OLi2 bind 12 and 10 hydrogen molecules, respectively, with an average binding energy of 0.10 and 0.13 eV, leading to gravimetric densities of 37.8 and 40.3 wt % of H2.

  8. Single-molecule dynamics at variable temperatures

    NARCIS (Netherlands)

    Zondervan, Rob

    2006-01-01

    Single-molecule optics has evolved from a specialized variety of optical spectroscopy at low temperatures into a versatile tool to address questions in physics, chemistry, biology, and materials science. In this thesis, the potential of single-molecule (and ensemble) optical microscopy at variable t

  9. Near-field single molecule spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Matter-Wave Optics of Diatomic Molecules

    Science.gov (United States)

    2012-10-23

    Lima , Peru (2010). S. Singh and P. Meystre, "Atomic probe Wigner tomography of a nanomechanical system," contributed paper, APS DAMOP Annual Meeting...Triangle Park , NC 27709-2211 15. SUBJECT TERMS matter-wave optics, ultracold molecules, polar molecules, quantum optomechanics, quantum-degenerate

  11. Nanoscience: Single-molecule instant replay

    Science.gov (United States)

    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

  12. Spin polarization effect for Co2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Bao Wen-Sheng

    2007-01-01

    The density functional theory (DFT)(b3p86) of Gaussian 03 has been used to optimize the structure of the Co2molecule, a transition metal element molecule. The result shows that the ground state for the Co2 molecule is a 7-multiple state, indicating a spin polarization effect in the Co2 molecule. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state is not mingled with wavefunctions of higher-energy states. So for the ground state of Co2 molecule to be a 7-multiple state is the indicative of spin polarization effect of the Co2molecule, that is, there exist 6 parallel spin electrons in a Co2 molecule. The number of non-conjugated electrons is the greatest. These electrons occupy different spacial orbitals so that the energy of the Co2 molecule is minimized. It can be concluded that the effect of parallel spin in the Co2 molecule is larger than the effect of the conjugated molecule,which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state and the other states of the Co2 molecule are derived. The dissociation energy De for the ground state of Co2 molecule is 4.0489eV, equilibrium bond length Re is 0.2061 nm, and vibration frequency 11.2222 aJ.nm-4respectively(1 a.J=10-18 J). The other spectroscopic data for the ground state of Co2 molecule ωexe,Be, and αe are 0.7202 cm-1, 0.1347 cm-1, and 2.9120× 10-1 cm-1 respectively. And ωexe is the non-syntonic part of frequency, Be is the rotational constant, αe is revised constant of rotational constant for non-rigid part of Co2 molecule.

  13. Quantum transport of the single metallocene molecule

    Science.gov (United States)

    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.

  14. The symmetry of single-molecule conduction.

    Science.gov (United States)

    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.

  15. Electronic and thermal properties of Biphenyl molecules

    Science.gov (United States)

    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.

  16. Small azomethine molecules and their use in photovoltaic devices

    NARCIS (Netherlands)

    Dingemans, T.J.; Petrus, M.L.

    2015-01-01

    The present invention is in the field of a small azomethine molecule having photovoltaic characteristics, a method of synthesizing said molecule, use of said molecule in a photovoltaic device, a solar cell comprising said molecule, and a film comprising said molecule. The present molecules may find

  17. Novel Applications of Buffer-Gas Cooling to Cold Atoms, Diatomic Molecules, and Large Molecules

    OpenAIRE

    Drayna, Garrett Korda

    2016-01-01

    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 thi...

  18. Search for complex organic molecules in space

    Science.gov (United States)

    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.

  19. Spin polarization effect for Mn2 molecule

    Institute of Scientific and Technical Information of China (English)

    Yan Shi-Ying; Xu Guo-Liang

    2007-01-01

    The density functional theory method (DFT) (b3p86) of Gaussian 03 has been used to optimize the structure of the Mn2 molecule.The result shows that the ground state of the Mn2 molecule is an 11-multiple state,indicating a spin polarization effect in the Mn2 molecule,a transition metal element molecule.Meanwhile,we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions of higher-energy states.So the ground state for Mn2 molecule being of an 11-multiple state is the indicative of spin polarization effect of the Mn2 molecule among those in the transition metal elements:that is,there are 10 parallel spin electrons in a Mn2 molecule.The number of non-conjugated electrons is the greatest.These electrons occupy different spacious orbitals so that the energy of the Mn2 molecule is minimized.It can be concluded that the effect of parallel spin in the Mn2 molecule is larger than the effect of the conjugated molecule,which is obviously related to the effect of electron d delocalization.In addition,the Murrell-Sorbie potential functions with the parameters for the ground state and other states of the Mn2 molecule are derived.The dissociation energy De for the ground state of the Mn2 molecule is 1.4477eV,equilibrium bond length Re is 0.2506 nm,vibration frequency ωe is 211.51 cm-1.Its force constants,f2,f3,and f4 are 0.7240 aJ·nm-2,-3.35574 aJ·nm-3,11.4813 aJ·nm-4 respectively. The other spectroscopic data for the ground state of the Mn2 molecule ωeχe,Be,αe are 1.5301 cm-1,0.0978 cm-1,7.7825×10-4 cm-1 respectively.

  20. Trapping and manipulating single molecules of DNA

    Science.gov (United States)

    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.

  1. Optically active quantum-dot molecules.

    Science.gov (United States)

    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.

  2. Molecular Wring Resonances in Chain Molecules

    DEFF Research Database (Denmark)

    Bohr, Henrik; Brunak, Søren; Bohr, Jakob

    1997-01-01

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

  3. Nanopore analytics: sensing of single molecules.

    Science.gov (United States)

    Howorka, Stefan; Siwy, Zuzanna

    2009-08-01

    In nanopore analytics, individual molecules pass through a single nanopore giving rise to detectable temporary blockades in ionic pore current. Reflecting its simplicity, nanopore analytics has gained popularity and can be conducted with natural protein as well as man-made polymeric and inorganic pores. The spectrum of detectable analytes ranges from nucleic acids, peptides, proteins, and biomolecular complexes to organic polymers and small molecules. Apart from being an analytical tool, nanopores have developed into a general platform technology to investigate the biophysics, physicochemistry, and chemistry of individual molecules (critical review, 310 references).

  4. Nano-manipulation of single DNA molecules

    Institute of Scientific and Technical Information of China (English)

    HU Jun; L(U) Jun-Hong; LI Hai-Kuo; AN Hong-Jie; WANG Guo-Hua; WANG Ying; LI Min-Qian; ZHANG Yi; LI Bin

    2004-01-01

    Nano-manipulation of single atoms and molecules is a critical technique in nanoscience and nanotechnology. This review paper will focus on the recent development of the manipulation of single DNA molecules based on atomic force microscopy (AFM). Precise manipulation has been realized including varied manipulating modes such as "cutting", "pushing", "folding", "kneading", "picking up", "dipping", etc. The cutting accuracy is dominated by the size of the AFM tip, which is usually 10nm or less. Single DNA fragments can be cut and picked up and then amplified by single molecule PCR. Thus positioning isolation and sequencing can be performed.

  5. Formation of ultracold LiCs molecules

    CERN Document Server

    Kraft, S D; Lange, J; Vogel, L; Wester, R; Weidemüller, M; Kraft, Stephan D.; Staanum, Peter; Lange, Joerg; Vogel, Leif; Wester, Roland; Weidemueller, Matthias

    2006-01-01

    We present the first observation of ultracold LiCs molecules. The molecules are formed in a two-species magneto-optical trap and detected by two-photon ionization and time-of-flight mass spectrometry. The production rate coefficient is found to be in the range $10^{-18}\\unit{cm^3s^{-1}}$ to $10^{-16}\\unit{cm^3s^{-1}}$, at least an order of magnitude smaller than for other heteronuclear diatomic molecules directly formed in a magneto-optical trap.

  6. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

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

    1999-01-01

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

  7. Multichannel long-range Rydberg molecules

    CERN Document Server

    Eiles, Matthew T

    2015-01-01

    A generalized class of ultra-long-range Rydberg molecules is proposed which consist of a multichannel Rydberg atom whose outermost electron creates a chemical bond with a distant ground state atom. Such multichannel Rydberg molecules exhibit favorable properties for laser excitation, because states exist where the quantum defect varies strongly with the principal quantum number. The resulting occurrence of near degeneracies with states of high orbital angular momentum promotes the admixture of low $l$ into the high $l$ deeply bound `trilobite' molecule states, thereby circumventing the usual difficulty posed by electric dipole selection rules. Such states also can exhibit multi-scale binding possibilities that could present novel options for quantum manipulation.

  8. Kondo effect in molecules with strong correlations

    Energy Technology Data Exchange (ETDEWEB)

    Kuzmenko, Tetyana [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel)]. E-mail: tetyana@bgumail.bgu.ac.il; Kikoin, Konstantin [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel); Avishai, Yshai [Department of Physics, Ben-Gurion University, P.O. Box 653, Beer-Sheva 84105 (Israel)

    2005-04-30

    A theory of Kondo tunneling through molecules adsorbed on metallic substrate is constructed and the underlying physics is exposed. It is shown that in the case of weak chemisorption the sandwich-type molecules manifest a novel type of Kondo effect that has not been observed in magnetically doped bulk metals. The exchange Hamiltonian of these molecules unveils unusual dynamical SO(n) symmetries instead of conventional SU(2) symmetry. These symmetries can be experimentally realized and the specific value of n can be controlled by gate voltage.

  9. Population redistribution in optically trapped polar molecules

    CERN Document Server

    Deiglmayr, J; Dulieu, O; Wester, R; Weidemüller, M

    2011-01-01

    We investigate the rovibrational population redistribution of polar molecules in the electronic ground state induced by spontaneous emission and blackbody radiation. As a model system we use optically trapped LiCs molecules formed by photoassociation in an ultracold two-species gas. The population dynamics of vibrational and rotational states is modeled using an ab-initio electric dipole moment function and experimental potential energy curves. Comparison with the evolution of the v"=3 electronic ground state yields good qualitative agreement. The analysis provides important input to assess applications of ultracold LiCs molecules in quantum simulation and ultracold chemistry.

  10. Imaging Cold Molecules on a Chip

    CERN Document Server

    Marx, S; Abel, M J; Zehentbauer, T; Meijer, G; Santambrogio, G

    2013-01-01

    We present the integrated imaging of cold molecules in a microchip environment. The on-chip de- tection is based on REMPI, which is quantum-state-selective and generally applicable. We demon- strate and characterize time-resolved spatial imaging and subsequently use it to analyze the effect of a phase-space manipulation sequence aimed at compressing the velocity distribution of a molec- ular ensemble with a view to future high-resolution spectroscopic studies. The realization of such on-chip measurements adds the final fundamental component to the molecule chip, offering a new and promising route for investigating cold molecules.

  11. Tunable optical absorption in silicene molecules

    KAUST Repository

    Mokkath, Junais Habeeb

    2016-07-13

    Two-dimensional materials with a tunable band gap that covers a wide range of the solar spectrum hold great promise for sunlight harvesting. For this reason, we investigate the structural, electronic, and optical properties of silicene molecules using time dependent density functional theory. We address the influence of the molecular size, buckling, and charge state as well as that of a dielectric environment. Unlike planar graphene molecules, silicene molecules prefer to form low-buckled structures with strong visible to ultraviolet optical response. We also identify molecular plasmons.

  12. Single Molecule Biophysics Experiments and Theory

    CERN Document Server

    Komatsuzaki, Tamiki; Takahashi, Satoshi; Yang, Haw; Silbey, Robert J; Rice, Stuart A; Dinner, Aaron R

    2011-01-01

    Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches

  13. Stochastic Models of Molecule Formation on Dust

    Science.gov (United States)

    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

  14. Stretching p -wave molecules by transverse confinements

    Science.gov (United States)

    Zhou, Lihong; Cui, Xiaoling

    2017-09-01

    We revisit the confinement-induced p -wave resonance in quasi-one-dimensional (quasi-1D) atomic gases and study the induced molecules near resonance. We derive the reduced 1D interaction parameters and show that they can well predict the binding energy of shallow molecules in quasi-1D system. Importantly, these shallow molecules are found to be much more spatially extended compared to those in three dimensions (3D) without transverse confinement. Our results strongly indicate that a p -wave interacting atomic gas can be much more stable in quasi-1D near the induced p -wave resonance, where most weight of the molecule lies outside the short-range regime and thus the atom loss could be suppressed.

  15. Large molecules in diffuse interstellar clouds

    Science.gov (United States)

    Lepp, S.; Dalgarno, A.; Van Dishoeck, E. F.; Black, J. H.

    1988-01-01

    The effects of the presence of a substantial component of large molecules on the chemistry of diffuse molecular clouds are explored, and detailed models of the zeta Persei and zeta Ophiuchi clouds are constructed. The major consequence is a reduction in the abundances of singly charged atomic species. The long-standing discrepancy between cloud densities inferred from rotational and fine-structure level populations and from the ionization balance can be resolved by postulating a fractional abundance of large molecules of 1 x 10 to the -7th for zeta Persei and 6 x 10 to the -7th for zeta Ophiuchi. If the large molecules are polycyclic aromatic hydrocarbons (PAH) containing about 50 carbon atoms, they contain 1 percent of the carbon in zeta Persei and 7 percent in zeta Ophiuchi. Other consequences of the possible presence of PAH molecules are discussed.

  16. SINGLE MOLECULE ENZYMOLOGY FINDS ITS STRIDE.

    Science.gov (United States)

    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.

  17. Single-Molecule Studies in Live Cells

    Science.gov (United States)

    Yu, Ji

    2016-05-01

    Live-cell single-molecule experiments are now widely used to study complex biological processes such as signal transduction, self-assembly, active trafficking, and gene regulation. These experiments' increased popularity results in part from rapid methodological developments that have significantly lowered the technical barriers to performing them. Another important advance is the development of novel statistical algorithms, which, by modeling the stochastic behaviors of single molecules, can be used to extract systemic parameters describing the in vivo biochemistry or super-resolution localization of biological molecules within their physiological environment. This review discusses recent advances in experimental and computational strategies for live-cell single-molecule studies, as well as a selected subset of biological studies that have utilized these new technologies.

  18. The evolution of polymorphic compatibility molecules

    NARCIS (Netherlands)

    Boer, R.J. de

    1995-01-01

    Several primitive colonial organisms distinguish self from nonself by means of polymorphic compatibility molecules bearing similarity to the major histocompatibility complex (MHC). The evolution of such polymorphisms is generally explained in terms of resistance to parasites. Ignoring parasites, I d

  19. Spin polarization effect for Os2 molecule

    Institute of Scientific and Technical Information of China (English)

    Xie An-Dong; Yan Shi-Ying; Zhu Zheng-He; Fu Yi-Bei

    2005-01-01

    Density functional Theory (DFT) (B3p86) of Gaussian03 has been used to optimize the structure of Os2 molecule.The result shows that the ground state for Os2 molecule is 9-multiple state and its electronic configuration is 9∑+g,which shows spin polarization effect of Os2 molecule of transition metal elements for the first time. Meanwhile, we have not found any spin pollution because the wavefunction of the ground state does not mingle with wavefunctions with higher energy states. So, the fact that the ground state for Os2 molecule is a 9-multiple state is indicative of spin polarization effect of Os2 molecule of transition metal elements. That is, there exist 8 parallel spin electrons.The non-conjugated electron is greatest in number. These electrons occupy different spacious tracks, so that the energy of Os2 molecule is minimized. It can be concluded that the effect of parallel spin of Os2 molecule is larger than the effect of the conjugated molecule, which is obviously related to the effect of electron d delocalization. In addition, the Murrell-Sorbie potential functions with the parameters for the ground state 9∑+g and other states of Os2 molecule are derived. Dissociation energy De for the ground state of Os2 molecule is 3.3971eV, equilibrium bond length Re is 0.2403nm, vibration frequency ωe is 235.32cm-1. Its force constants f2, f3, and f4 are 3.1032×102aJ.nm-2,-14.3425×103aJ.nm-3 and 50.5792×104aJ.nm-4 respectively. The other spectroscopic data for the ground state of Os2 molecule ωeχe, Be and αe are 0.4277cm-1, 0.0307cm-1 and 0.6491× 10-4cm-1 respectively.

  20. Electron Transfer for Large Molecules through Delocalization

    Energy Technology Data Exchange (ETDEWEB)

    Neuhauser, D.; Reslan, R.; Hernandez, S.; Arnsen, C.; Lopata, K.; Govind, N.; Gao, Y.; Tolbert, S.; Schwartz, B.; Rubin, Y.; Nardes, A.; Kopidakis, N.

    2012-01-01

    Electron transfer for large molecules lies in between a Marcus-Theory two-state transfer and a Landauer description. We discuss a delocalization formalism which,through the introduction of artificial electric fields which emulate bulk dipole fields, allows calculation between a pair of identical molecules (A+A- (R)A-+A) with several open states. Dynamical electron polarization effects can be inserted with TDDFT and are crucial for large separations.

  1. New issues in zero dimensions: magnetic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Luban, M. E-mail: luban@ameslab.gov

    2004-05-01

    We discuss some major features of isolated magnetic molecules where intermolecular magnetic interactions are negligible and the magnetic properties are determined using a Heisenberg model of intramolecular exchange between a relatively small number of diverse paramagnetic ions. We survey some of the more challenging issues and results that have emerged to date, including the spectrum of excitations, effects of geometric frustration, and critical slowing down of the spin dynamics at low temperatures. Primary attention is given to realizable magnetic molecules.

  2. Novel Small-Molecule Antibacterial Agents

    Science.gov (United States)

    2014-07-01

    of Papers published in peer-reviewed journals: Number of Papers published in non peer-reviewed journals: Novel Small-Molecule Antibacterial Agents...Release; Distribution Unlimited Novel Small-Molecule Antibacterial Agents The views, opinions and/or findings contained in this report are those of...half life of ~31 days. (a) Papers published in peer-reviewed journals (N/A for none) Enter List of papers submitted or published that acknowledge ARO

  3. Probing halo molecules with nonresonant light

    CERN Document Server

    Lemeshko, Mikhail

    2009-01-01

    We show that halo molecules can be probed by "shaking" in a pulsed nonresonant laser field. The field introduces a centrifugal term which expels the highest vibrational level from the potential that binds it. Our numerical simulations as well as an analytic model applied to the Rb$_2$ and KRb Feshbach molecules indicate that shaking by feasible laser pulses can be used to accurately recover the square of the vibrational wavefunction and, by inversion, also the molecular potential.

  4. On Chiral Space Groups and Chiral Molecules

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    This note explains the relationship (as well as the absence of a relationship) between chiral space groups and chiral molecules (which have absolute configurations). For a chiral molecule, which must crystallize in a chiral space group, the outcome of the absolute configuration determination must be linked to some other properties of the chiral crystal such as its optical activity for the observation to the relevant.

  5. On Chiral Space Groups and Chiral Molecules

    Institute of Scientific and Technical Information of China (English)

    NgSeikWng; HUSheng-Zhi

    2003-01-01

    This note explains the relationship (as well as the absence of a relationship) between chiral space groups and chiral molecules (which have absolute configurations).For a chiral molecule,which must crystallize in a chiral space group,the outcome of the absolute configuration determination must be linked to some other properties of the chiral crystal such as its optical activity for the observation to the relevant.

  6. (pro)renin receptor: A stable molecule

    OpenAIRE

    Wiwanitkit, Viroj

    2011-01-01

    Background: Basically, (pro)renin acts via a specific receptor, (pro)renin receptor (PRR) binding between renin and prorenin, its inactive proenzyme form. The study on the molecular level of PRR can give useful knowledge to help understand many renal disorders. Method: Here, the author focuses on the stability of the PRR molecule. The mutation prone positions within the PRR molecule was assessed using standard reference technique. Result: The study showed there is no identified mutation prone...

  7. Allosteric small-molecule kinase inhibitors

    DEFF Research Database (Denmark)

    Wu, Peng; Clausen, Mads Hartvig; Nielsen, Thomas E.

    2015-01-01

    -molecule allosteric inhibitor trametinib in 2013, the progress of more than 10 other allosteric inhibitors in clinical trials, and the emergence of a pipeline of highly selective and potent preclinical molecules, have been reported in the past decade. In this article, we present the current knowledge on allosteric...... inhibition in terms of conception, classification, potential advantages, and summarized debatable topics in the field. Recent progress and allosteric inhibitors that were identified in the past three years are highlighted in this paper....

  8. Recollision induced superradiance of ionized nitrogen molecules

    CERN Document Server

    Liu, Yi; Lambert, Guillaume; Houard, Aurelien; Tikhonchuk, Vladimir; Mysyrowicz, Andre

    2015-01-01

    We propose a new mechanism to explain the origin of optical gain in the transitions between excited and ground state of the ionized nitrogen molecule following irradiation of neutral nitrogen molecules with an intense ultra short laser pulse. An efficient transfer of population to the excited state is achieved via field-induced multiple recollisions. We show that the proposed excitation mechanism must lead to a super-radiant emission, a feature that we confirm experimentally.

  9. Hadronic molecules in the heavy baryon spectrum

    Science.gov (United States)

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

    2016-01-01

    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 Λc(2940) as a D*N molecule with JP = 3/2- quantum numbers. We also find D(*)Δ candidates for the recently discovered Xc(3250) resonance.

  10. Molecules on si: electronics with chemistry.

    Science.gov (United States)

    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.

  11. Sol-gel method for encapsulating molecules

    Science.gov (United States)

    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.

  12. Vibrational Cooling of Photoassociated Homonuclear Cold Molecules

    Science.gov (United States)

    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.

  13. Chapter 3: Small molecules and disease.

    Directory of Open Access Journals (Sweden)

    David S Wishart

    Full Text Available "Big" molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. "Small" molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called "chemical bioinformatics"--a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules--either as the treatment, symptom or cause--to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.

  14. Analysis of acid-base interactions at Al2O3 (11-20) interfaces by means of single molecule force spectroscopy

    Science.gov (United States)

    Mosebach, Bastian; Ozkaya, Berkem; Giner, Ignacio; Keller, Adrian; Grundmeier, Guido

    2017-10-01

    Single molecule force spectroscopy (SMFS) was employed to investigate the interaction forces between aliphatic amino, hydroxyl and ether groups and aluminum oxide single crystal surfaces in an aqueous electrolyte at pH = 6. The force studies were based on the variation of the terminal group of polyethylene glycol which was bound via a Ssbnd Au bond to the gold coated AFM tip. X-ray Photoelectron Spectroscopy (XPS) was performed to characterize the surface chemistry of the substrate. Force distance curves were measured between the PEG-NH2, sbnd OH and sbnd OCH3 functionalized atomic force microscope (AFM) tip and the non-polar single crystalline Al2O3(11-20) surface. The experimental results exhibit non-equilibrium desorption events which hint at acid-base interactions of the electron donating hydroxyl and amino groups with Al-ions in the surface of the oxide. The observed desorption forces for the sbnd NH2, sbnd OH/Al2O3(11-20) were in the range of 100-200 pN.

  15. Spin polarization effect for molecule Ta2

    Institute of Scientific and Technical Information of China (English)

    Xie An-Dong

    2006-01-01

    Density functional theory (DFT) (B3p86) has been used to optimize the structure of the molecule Taa- The result shows that the ground state of molecule Ta,2 is a 7- multiple state and its electronic configuration is 7∑+u which shows the spin polarization effect for molecule Ta2 of transition metal elements for the first time. Meanwhile, spin pollution has not been found because the wavefunction of the ground state does not mix with those of higher states. So, the fact that the ground state of molecule Ta2 is a 7-multiple state indicates a spin polarization effect of molecule Ta2 of the transition metal elements, i.e. there exist 6 parallel spin electrons and the non-conjugated electrons are greatest in number. These electrons occupy different space orbitals so that the energy of molecule Ta2 is minimized. It can be concluded that the effect of parallel spin of the molecule Ta2 is larger than the effect of the conjugated molecule, which is obviously related to the effect of d-electron delocalization. In addition, the Murrell-Sorbie potential functions with parameters for the ground state 7∑+u and other states of the molecule Ta2 are derived. The dissociation energy De, equilibrium bond length Re and vibration frequency ωe for the ground state of molecule Ta2 are 4.5513eV, 0.2433nm and 173.06cm-1, respectively. Its force constants f2,f3 and f4 are 1.5965×l02aJ·nm-2,-6.4722×l03aJ·nm-3 and 29.4851×04aJ·nm-4, respectively. Other spectroscopic data ωe χe, Be and αe for the ground state of Ta2 are 0.2078cm-1, 0.0315cm-1 and 0.7858×104 cm-1, respectively.

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

    DEFF Research Database (Denmark)

    Jørgensen, Jacob Lykkebo

    , which is characterised by destructive quantum interference. The molecules are cross-conjugated, which means that the two parts of the molecules are conjugated to a third part, but not to each other. This gives rise to an anti-resonance in the trans- mission. In the low bias and low temperature regime......, the electrons can tunnel in- elastically from the left to the right electrode. This is the process behind inelastic electron tunnelling spectroscopy (IETS), which is a single-molecule spectroscopic method, where the vibrational ngerprint of a molecule is di- rectly observed by the tunnelling current......-conjugated molecules. We nd that the vibrational modes that would be expected to dominate, following the propensity, rules are very weak. Instead, other modes are found to be the dominant ones. We study this phenomenon for a number of cross-conjugated molecules, and link these ndings to the anti...

  17. Universal deceleration of highly polar molecules

    Science.gov (United States)

    Hamamda, Mehdi; Pillet, Pierre; Lignier, Hans; Comparat, Daniel

    2015-04-01

    We propose a method to produce, in a pulsed or continuous way, cold samples of highly polar molecules. Using a pulsed or continuous standard (supersonic) beam of these molecules, our idea consists of transforming the molecules into their anionic counterparts, which are decelerated to a standstill by a well-controlled external electric field and ultimately neutralized. The neutral-to-anion transformation occurs through collisions with Rydberg atoms coming from an additional atomic beam. This Rydberg electron transfer process is possible provided that the molecular species has a sufficiently strong electric dipole (\\gt 2.5 D, i.e., \\gt 8.3× {{10}-30} cm). Whatever the mass of the species, the deceleration stage is realized by a temporally and spatially controlled electric field within a range of less than one centimeter, which is much shorter than in current deceleration experiments of neutral molecules. Once stopped, the molecular anions are neutralized by laser photodetachment or a pulsed electric field process. The resulting molecules might be held and accumulated, for instance, in a magnetic trap.

  18. Classical interaction model for the water molecule.

    Science.gov (United States)

    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.

  19. Direct laser cooling of the BH molecule

    Science.gov (United States)

    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. Quantum Computer Using Coupled Quantum Dot Molecules

    CERN Document Server

    Wu, N J; Natori, A; Yasunaga, H; Wu*, Nan-Jian

    1999-01-01

    We propose a method for implementation of a quantum computer using artificial molecules. The artificial molecule consists of two coupled quantum dots stacked along z direction and one single electron. One-qubit and two-qubit gates are constructed by one molecule and two coupled molecules, respectively.The ground state and the first excited state of the molecule are used to encode the |0> and |1> states of a qubit. The qubit is manipulated by a resonant electromagnetic wave that is applied directly to the qubit through a microstrip line. The coupling between two qubits in a quantum controlled NOT gate is switched on (off) by floating (grounding) the metal film electrodes. We study the operations of the gates by using a box-shaped quantum dot model and numerically solving a time-dependent Schridinger equation, and demonstrate that the quantum gates can perform the quantum computation. The operating speed of the gates is about one operation per 4ps. The reading operation of the output of the quantum computer can...

  1. Capillary condensation of short-chain molecules.

    Science.gov (United States)

    Bryk, Paweł; Pizio, Orest; Sokolowski, Stefan

    2005-05-15

    A density-functional study of capillary condensation of fluids of short-chain molecules confined to slitlike pores is presented. The molecules are modeled as freely jointed tangent spherical segments with a hard core and with short-range attractive interaction between all the segments. We investigate how the critical parameters of capillary condensation of the fluid change when the pore width decreases and eventually becomes smaller than the nominal linear dimension of the single-chain molecule. We find that the dependence of critical parameters for a fluid of dimers and of tetramers on pore width is similar to that of the monomer fluid. On the other hand, for a fluid of chains consisting of a larger number of segments we observe an inversion effect. Namely, the critical temperature of capillary condensation decreases with increasing pore width for a certain interval of values of the pore width. This anomalous behavior is also influenced by the interaction between molecules and pore walls. We attribute this behavior to the effect of conformational changes of molecules upon confinement.

  2. Half-lives of trinuclear molecules

    Science.gov (United States)

    Carstoiu, F.; Bulboacă, I.; Săndulescu, A.; Greiner, W.

    2000-04-01

    Recent discoveries of 10Be and 12C accompanied cold fission in the spontaneous fission of 252Cf lead to the surprising result that long living trinuclear molecules may exists. For the description of the dynamics and decay of such molecules, we used a coplanar three body cluster model (two deformed fragments and an α particle) with a three body potential computed by a double folding potential generated by M3Y effective interaction. A repulsive compression term was included. The computed α ternary cold fission yields are in agreement with the experiment. The energy and angular distributions of the three clusters at infinity and the half-lives are strongly dependent of the initial positions of the α particle relative to the two fragments and of mass asymmetry of the fragments. The evaluated lifetimes of such trinuclear molecules are quite large, of the order of one second.

  3. Protein Scaffolding for Small Molecule Catalysts

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-09-14

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

  4. Diamond based single molecule magnetic resonance spectroscopy

    CERN Document Server

    Cai, J -M; Plenio, M B; Retzker, A

    2011-01-01

    The detection of a nuclear spin in an individual molecule represents a key challenge in physics and biology whose solution has been pursued for many years. The small magnetic moment of a single nucleus and the unavoidable environmental noise present the key obstacles for its realization. Here, we theoretically demonstrate that a single nitrogen-vacancy (NV) center in diamond can be used to construct a nano-scale single molecule spectrometer that is capable of detecting the position and spin state of a single nucleus and can determine the distance and alignment of a nuclear or electron spin pair. In combination with organic spin labels, this device will find applications in single molecule spectroscopy in chemistry and biology, such as in determining protein structure or monitoring macromolecular motions and can thus provide a tool to help unravelling the microscopic mechanisms underlying bio-molecular function.

  5. Adhesion molecules in experimental phacoanaphylactic endophthalmitis.

    Science.gov (United States)

    Till, G O; Lee, S; Mulligan, M S; Wolter, J R; Smith, C W; Ward, P A; Marak, G E

    1992-11-01

    Intraocular accumulation of inflammatory neutrophils is an important feature of experimental phacoanaphylactic endophthalmitis (EPE). Increasing evidence suggests that localization of neutrophils to the site of inflammation requires the participation of neutrophil and endothelial adhesion molecules. These studies were undertaken to determine if blocking of adhesion molecules on neutrophils (CD18) or endothelium (ELAM-1) could attenuate EPE in Lewis rats. Treatment of experimental animals with anti-CD18 or anti-ELAM-1 significantly suppressed intraocular neutrophil accumulation, retinal hemorrhage, and vasculitis, and attenuated retinal edema formation by 48% and 70%, respectively. These observations demonstrate that antibodies directed against adhesion molecules on the neutrophil (CD18) or the vascular endothelial cell (ELAM-1) exhibit potent anti-inflammatory effects, resulting in a striking amelioration of injury in EPE in rats.

  6. Single Molecule Sensitive FRET in Attoliter Droplets

    CERN Document Server

    Milas, Peker; Gamari, Ben D; Goldner, Lori S

    2013-01-01

    Single molecular-pair fluorescence resonance energy transfer (spFRET) has become an cross-disciplinary tool for understanding molecular folding and interactions. While providing detailed information about the individual members of a molecular ensemble, this technique is always limited by fluorophore brightness and stability. In the case of diffusing molecules, the experiment is further limited by the number of photons that can be collected during the time it takes for a molecule to diffuse across the detection volume. To maximize the number of photons it is common to either increase the detection volume at the expense of increased background, or increase the diffusion time by adding glycerol or sucrose to increase viscosity. Here we demonstrate that FRET from attoliter volume (100 nm radius) aqueous droplets in perfluorinated oil has significantly higher signal-to-noise and a much wider dynamic range than FRET from molecules diffusing in solution. However, our measurements also reveal a droplet environment th...

  7. Single molecule transcription profiling with AFM

    Energy Technology Data Exchange (ETDEWEB)

    Reed, Jason [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States); Mishra, Bud [Departments of Computer Science and Mathematics, Courant Institute of Mathematical Sciences, New York University, New York, NY 10012 (United States); Pittenger, Bede [Veeco Instruments, Santa Barbara, CA 93117 (United States); Magonov, Sergei [Veeco Instruments, Santa Barbara, CA 93117 (United States); Troke, Joshua [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Teitell, Michael A [Department of Pathology and Center for Cell Control, an NIH Nanomedicine Development Center, UCLA, Los Angeles, CA 90095 (United States); Gimzewski, James K [Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 (United States)

    2007-01-31

    Established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. Due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. Here, we examine the use of single molecule, ordered restriction mapping, combined with AFM, to measure gene transcription levels from very low abundance samples. We frame the problem mathematically, using coding theory, and present an analysis of the critical error sources that may serve as a guide to designing future studies. We follow with experiments detailing the construction of high density, single molecule, ordered restriction maps from plasmids and from cDNA molecules, using two different enzymes, a result not previously reported. We discuss these results in the context of our calculations.

  8. Observational astrochemistry: The quest for interstellar molecules

    Directory of Open Access Journals (Sweden)

    Guélin M.

    2012-01-01

    Full Text Available Over 160 molecular species, not counting isotopologues, have been identified in circumstellar envelopes and interstellar clouds. These species have revealed a wealth of familiar, as much as exotic molecules and in complex organic (and silicon compounds, that was fully unexpected in view of the harshness of surrounding conditions: vanishingly low densities, extreme temperatures and intense embedding UV radiation. They illustrate the diversity of astrochemistry and show robust prebiotic molecules may be. In this lecture, we review the quest for interstellar molecules and show how tributary it is from theoretical ideas and technology developments. A. A. Penzias, who discovered interstellar CO and the 2.7 K Cosmic Background radiation, used to joke that astronomical research is easy: the great questions have largely been formulated; one only has to wait until technological progress makes it possible to answer.

  9. Complex Organic Molecules in Protoplanetary Disks

    Science.gov (United States)

    Walsh, Catherine; Millar, T. J.; Nomura, H.; Herbst, E.; Widicus-Weaver, S.

    2013-06-01

    Protoplanetary disks are vital objects in star and planet formation. In addition to aiding mass accretion onto the central star and angular momentum dissipation, they also contain all material which may form an orbiting planetary system. Of great interest to the astrochemistry and astrobiology communities is the origin of prebiotic molecules, considered the "building blocks" of Life. Is it possible for complex molecules to form in protoplanetary disks and survive assimilation into planets and other planetary system objects, such as, comets? We explore the synthesis of large complex organic molecules (COMs) in protoplanetary disks which encompass young stars. We use a chemical network primarily developed for use in hot core models to calculate the abundance and distribution of gas-phase and grain-mantle (ice) COMs and discuss the potential of observing the gas-phase form of these species with new facilities, such as, ALMA.

  10. Prebiotically Important Molecules in Orion KL

    Science.gov (United States)

    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.

  11. Enlarged Molecules from Excited Atoms in Nanochannels

    CERN Document Server

    Boström, Mathias; Sernelius, Bo E; Dou, Maofeng; Persson, Clas; Ninham, Barry W

    2012-01-01

    The resonance interaction that takes place in planar nanochannels between pairs of excited state atoms is explored. We consider interactions in channels of silica, zinc oxide and gold. The nanosized channels induce a dramatically different interaction from that in free space. Illustrative calculations for two lithium and cesium atoms, demonstrate that there is a short range repulsion followed by long range attraction. The binding energy is strongest near the surfaces. The size of the enlarged molecule is biggest at the center of the cavity and increases with channel width. Since the interaction is generic, we predict that enlarged molecules are formed in porous structures, and that the molecule size depends on the size of the nanochannels

  12. Relativistic Scott correction for atoms and molecules

    DEFF Research Database (Denmark)

    Solovej, Jan Philip; Sørensen, Thomas Østergaard; Spitzer, Wolfgang Ludwig

    2010-01-01

    We prove the first correction to the leading Thomas-Fermi energy for the ground state energy of atoms and molecules in a model where the kinetic energy of the electrons is treated relativistically. The leading Thomas-Fermi energy, established in [25], as well as the correction given here, are of ......We prove the first correction to the leading Thomas-Fermi energy for the ground state energy of atoms and molecules in a model where the kinetic energy of the electrons is treated relativistically. The leading Thomas-Fermi energy, established in [25], as well as the correction given here......, are of semiclassical nature. Our result on atoms and molecules is proved from a general semiclassical estimate for relativistic operators with potentials with Coulomb-like singularities. This semiclassical estimate is obtained using the coherent state calculus introduced in [36]. The paper contains a unified treatment...

  13. Theoretical study on single-molecule spectroscopy

    Institute of Scientific and Technical Information of China (English)

    SHAN Guang-cun; HUANG Wei

    2006-01-01

    The photon-by-photon approach for single molecule spectroscopy experiments utilizes the information carried by each detected photon and allows the measurements of conformational fluctuation with time resolution on a vast range of time scales,where each photon represents a data point.Here,we theoretically simulate the photon emission dynamics of a single molecule spectroscopy using the kinetic Monte Carlo algorithm to understand the underlying complex photon dynamic process of a single molecule.In addition,by following the molecular process in real time,the mechanism of complex biochemical reactions can be revealed.We hope that this theoretical study will serve as an introduction and a guideline into this exciting new field.

  14. Molecule capture by olfactory antennules: mantis shrimp.

    Science.gov (United States)

    Stacey, Mark T; Mead, Kristina S; Koehl, Mimi A R

    2002-01-01

    A critical step in the process of olfaction is the movement of odorant molecules from the environment to the surface of a chemosensory structure. Many marine crustaceans capture odorant molecules with arrays of chemosensory sensilla (aesthetascs) on antennules that they flick through the water. We developed a model to calculate molecule flux to the surfaces of aesthetascs in order to study how the size, aesthetasc spacing, and flick kinematics of olfactory antennules affect their performance in capturing molecules from the surrounding water. Since the three-dimensional geometry of an aesthetasc-bearing antennule is complex, dynamically-scaled physical models can often provide an efficient method of determining the fluid velocity field through the array. Here we present a method to optimize the incorporation of such measured velocity vector fields into a numerical simulation of the advection and diffusion of odorants to aesthetasc surfaces. Furthermore, unlike earlier models of odorant interception by antennae, our model incorporates odorant concentration distributions that have been measured in turbulent ambient flows. By applying our model to the example of the olfactory antennules of mantis shrimp, we learned that flicking velocity can have profound effects on odorant flux to the aesthetascs if they operate in the speed range in which the leakiness of the gaps between the aesthetascs to fluid movement is sensitive to velocity. This sensitivity creates an asymmetry in molecule fluxes between outstroke and return stroke, which results in an antennule taking discrete samples in space and time, i.e. "sniffing". As stomatopods grow and their aesthetasc Reynolds number increases, the aesthetasc arrangement on the antennule changes in a way that maintains these asymmetries in leakiness and molecule flux between the outstroke and return stroke, allowing the individual to continue to take discrete samples as it develops.

  15. Chiral Molecules Revisited by Broadband Microwave Spectroscopy

    Science.gov (United States)

    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

  16. Simple and advanced ferromagnet/molecule spinterfaces

    Science.gov (United States)

    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.

  17. Small Molecule Subgraph Detector (SMSD toolkit

    Directory of Open Access Journals (Sweden)

    Rahman Syed

    2009-08-01

    Full Text Available Abstract Background Finding one small molecule (query in a large target library is a challenging task in computational chemistry. Although several heuristic approaches are available using fragment-based chemical similarity searches, they fail to identify exact atom-bond equivalence between the query and target molecules and thus cannot be applied to complex chemical similarity searches, such as searching a complete or partial metabolic pathway. In this paper we present a new Maximum Common Subgraph (MCS tool: SMSD (Small Molecule Subgraph Detector to overcome the issues with current heuristic approaches to small molecule similarity searches. The MCS search implemented in SMSD incorporates chemical knowledge (atom type match with bond sensitive and insensitive information while searching molecular similarity. We also propose a novel method by which solutions obtained by each MCS run can be ranked using chemical filters such as stereochemistry, bond energy, etc. Results In order to benchmark and test the tool, we performed a 50,000 pair-wise comparison between KEGG ligands and PDB HET Group atoms. In both cases the SMSD was shown to be more efficient than the widely used MCS module implemented in the Chemistry Development Kit (CDK in generating MCS solutions from our test cases. Conclusion Presently this tool can be applied to various areas of bioinformatics and chemo-informatics for finding exhaustive MCS matches. For example, it can be used to analyse metabolic networks by mapping the atoms between reactants and products involved in reactions. It can also be used to detect the MCS/substructure searches in small molecules reported by metabolome experiments, as well as in the screening of drug-like compounds with similar substructures. Thus, we present a robust tool that can be used for multiple applications, including the discovery of new drug molecules. This tool is freely available on http://www.ebi.ac.uk/thornton-srv/software/SMSD/

  18. Hadronic molecules with hidden charm and bottom

    Directory of Open Access Journals (Sweden)

    Guo Feng-Kun

    2016-01-01

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

  19. Magneto-optical trap for polar molecules.

    Science.gov (United States)

    Stuhl, Benjamin K; Sawyer, Brian C; Wang, Dajun; Ye, Jun

    2008-12-12

    We propose a method for laser cooling and trapping a substantial class of polar molecules and, in particular, titanium (II) oxide (TiO). This method uses pulsed electric fields to nonadiabatically remix the ground-state magnetic sublevels of the molecule, allowing one to build a magneto-optical trap based on a quasicycling J' = J'' -1 transition. Monte Carlo simulations of this electrostatically remixed magneto-optical trap demonstrate the feasibility of cooling TiO to a temperature of 10 micrpK and trapping it with a radiation-pumping-limited lifetime on the order of 80 ms.

  20. Nanoscale methods for single-molecule electrochemistry.

    Science.gov (United States)

    Mathwig, Klaus; Aartsma, Thijs J; Canters, Gerard W; Lemay, Serge G

    2014-01-01

    The development of experiments capable of probing individual molecules has led to major breakthroughs in fields ranging from molecular electronics to biophysics, allowing direct tests of knowledge derived from macroscopic measurements and enabling new assays that probe population heterogeneities and internal molecular dynamics. Although still somewhat in their infancy, such methods are also being developed for probing molecular systems in solution using electrochemical transduction mechanisms. Here we outline the present status of this emerging field, concentrating in particular on optical methods, metal-molecule-metal junctions, and electrochemical nanofluidic devices.

  1. Extracellular Molecules Involved in Cancer Cell Invasion

    Energy Technology Data Exchange (ETDEWEB)

    Stivarou, Theodora; Patsavoudi, Evangelia, E-mail: epatsavoudi@pasteur.gr [Department of Biochemistry, Hellenic Pasteur Institute, Athens 11521 (Greece); Technological Educational Institute of Athens, Egaleo, Athens 12210 (Greece)

    2015-01-26

    Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion.

  2. Photoassociative production of ultracold heteronuclear ytterbium molecules

    Energy Technology Data Exchange (ETDEWEB)

    Borkowski, Mateusz; Ciurylo, Roman [Instytut Fizyki, Uniwersytet Mikolaja Kopernika, ul. Grudziadzka 5/7, PL-87-100 Torun (Poland); Julienne, Paul S. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, 100 Bureau Drive, Stop 8423, Gaithersburg, Maryland 20899-8423 (United States); Yamazaki, Rekishu; Takahashi, Yoshiro [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); CREST, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan); Hara, Hideaki; Taie, Shintaro; Sugawa, Seiji; Takasu, Yosuke [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Enomoto, Katsunari [Department of Physics, University of Toyama, Toyama 930-8555 (Japan)

    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.

  3. Extracellular Molecules Involved in Cancer Cell Invasion

    Directory of Open Access Journals (Sweden)

    Theodora Stivarou

    2015-01-01

    Full Text Available Nowadays it is perfectly clear that understanding and eradicating cancer cell invasion and metastasis represent the crucial, definitive points in cancer therapeutics. During the last two decades there has been a great interest in the understanding of the extracellular molecular mechanisms involved in cancer cell invasion. In this review, we highlight the findings concerning these processes, focusing in particular on extracellular molecules, including extracellular matrix proteins and their receptors, growth factors and their receptors, matrix metalloproteinases and extracellular chaperones. We report the molecular mechanisms underlying the important contribution of this pool of molecules to the complex, multi-step phenomenon of cancer cell invasion.

  4. A toy model for a diatomic molecule

    Science.gov (United States)

    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.

  5. Organic- and molecule-based magnets

    Indian Academy of Sciences (India)

    Joel S Miller

    2006-07-01

    The discovery of organic- and molecule-based magnets has led to design and synthesis of several families with magnetic ordering temperatures as high as ∼ 125° C. Examples of soft and hard magnets with coercivities as high as 27 kOe have also been reported. Examples from our laboratory of organic-based magnets using the tetracya- noethylene radical anion, [TCNE]$^{\\bullet -}$, are discussed. In addition, several molecule-based magnets based on Prussian Blue structured materials as well as dicyanamide are discussed.

  6. Watching single protein molecules in action

    DEFF Research Database (Denmark)

    Heiðarsson, Pétur Orri

    molecules in unprecedented detail. These methods can, in principle, detect rare folding or misfolding events, and ultimately lead to a reconstruction of the free energy landscape. In this thesis, the folding mechanism of both single- and double-domain proteins is unraveled using single-molecule optical...... tweezers. We first focused on the mechanical properties and unfolding pathway of the four-helix acyl-CoA binding protein (ACBP). Contrary to previous studies which have shown protein native states to be brittle, we observed extraordinary compliance for ACBP along two orthogonal pulling axis...

  7. Detecting gas molecules via atomic magnetization.

    Science.gov (United States)

    Choi, Heechae; Lee, Minho; Kim, Seungchul; Lee, Kwang-Ryeol; Chung, Yong-Chae

    2014-09-14

    Adsorptions of gas molecules were found to alter the directions and magnitudes of magnetic moments of transition metal (Co, Fe) atoms adsorbed on graphene. Using first-principles calculations, we demonstrated that magnetism of surface atoms can be used to identify the kind of existing gas molecules via spin-reorientation and/or demagnetizations caused by the reconfigurations of 3d electron energy levels of Co and Fe. We suggest for the first time that magnetic properties of transition metal-embedded nanostructures can be used in highly selective gas-sensing applications.

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

    Science.gov (United States)

    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.

  9. Evidence of disorder in biological molecules from single molecule pulling experiments

    CERN Document Server

    Hyeon, Changbong; Thirumalai, D

    2014-01-01

    Heterogeneity in biological molecules, resulting in molecule-to-molecule variations in their dynamics and function, is an emerging theme. To elucidate the consequences of heterogeneous behavior at the single molecule level, we propose an exactly solvable model in which the unfolding rate due to mechanical force depends parametrically on an auxiliary variable representing an entropy barrier arising from fluctuations in internal dynamics. When the rate of fluctuations, a measure of dynamical disorder, is comparable to or smaller than the rate of force-induced unbinding, we show that there are two experimentally observable consequences: non-exponential survival probability at constant force, and a heavy-tailed rupture force distribution at constant loading rate. By fitting our analytical expressions to data from single molecule pulling experiments on proteins and DNA, we quantify the extent of disorder. We show that only by analyzing data over a wide range of forces and loading rates can the role of disorder due...

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  12. The Molecules of the Cell Membrane.

    Science.gov (United States)

    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…

  13. Organic chemistry: Precision pruning of molecules

    Science.gov (United States)

    Yang, Kin S.; Engle, Keary M.

    2016-05-01

    If organic molecules were trees, then the numerous carbon-hydrogen bonds within them would be leaves. A catalyst that targets one 'leaf' out of many similar other ones looks set to be a huge leap for synthetic chemistry. See Letter p.230

  14. The formation of molecules in protostellar winds

    Energy Technology Data Exchange (ETDEWEB)

    Glassgold, A.E.; Mamon, G.A.; Huggins, P.J. (New York University, NY (USA))

    1991-05-01

    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. 57 refs.

  15. The formation of molecules in protostellar winds

    Science.gov (United States)

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

    1991-05-01

    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 highly 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.

  16. The formation of molecules in protostellar winds

    Science.gov (United States)

    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.

  17. Mathematics and Molecules: Exploring Connections via Programming.

    Science.gov (United States)

    Ploger, Don; Carlock, Margaret

    1996-01-01

    Examines the self-directed activity of two students who learned about molecular structure by writing computer programs. The programs displayed the solution of a mathematics problem, then the programs were extended to represent several classes of organic molecules. Different ways to enhance mathematical connections to chemistry education are…

  18. Single Molecule Conductance of Oligothiophene Derivatives

    Science.gov (United States)

    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

  19. Origin of organic molecules and biomolecular homochirality.

    Science.gov (United States)

    Podlech, J

    2001-01-01

    Theories about the origin of biomolecular homochirality, which seems to be a prerequisite for the creation of life, are discussed. First, possible terrestrial and extraterrestrial sources of organic molecules are outlined. Then, mechanisms for the formation of enantiomerically enriched compounds and for the amplification of their chirality are described.

  20. Predicting the Stability of Hypervalent Molecules

    Science.gov (United States)

    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.

  1. Writing with molecules on molecular printboards

    NARCIS (Netherlands)

    Crespo biel, O.; Ravoo, B.J.; Huskens, Jurriaan; Reinhoudt, David

    2006-01-01

    Nanotechnology aspires to create functional materials with characteristic dimensions of the order 1–100 nm. One requirement to make nanotechnology work is to precisely position molecules and nanoparticles on surfaces, so that they may be addressed and manipulated for bottom-up construction of

  2. Comprehensive Map of Molecules Implicated in Obesity.

    Directory of Open Access Journals (Sweden)

    Jaisri Jagannadham

    Full Text Available 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.

  3. Polypetide signaling molecules in plant development

    Science.gov (United States)

    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...

  4. Aging-From molecules to populations

    DEFF Research Database (Denmark)

    Sander, Miriam; Avlund, Kirsten; Lauritzen, Martin;

    2008-01-01

    -From Molecules to Populations. The following questions about human aging were discussed at the workshop: What is the limit of human life expectancy? What are the key indicators of human aging? What are the key drivers of human aging? Which genes have the greatest impact on human aging? How similar is aging...

  5. Field-free orientation of molecules

    DEFF Research Database (Denmark)

    Machholm, Mette; Henriksen, Niels Engholm

    2001-01-01

    The excitation of angular motion, in particular, the creation of a wave packet in the angular degrees of freedom via short-pulse, off-resonant excitation with respect to rotational transitions, was examined. The key result was that field-free time-dependent orientation for a molecule like LiH can...

  6. Tunneling ionization of vibrationally excited nitrogen molecules

    Science.gov (United States)

    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.

  7. Cluster ions and van der Waals molecules

    CERN Document Server

    Smirnov, Boris M

    1992-01-01

    This review discusses current ideas in the physics and chemistry of cluster ions and Van der Waals molecules as well as presenting numerical data on their parameters and the processes involving them. It is also a detailed reference on basic data relating to many species.

  8. Modified "DMC" technique for stretching DNA molecules

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A modified "dynamic molecular combing"(DMC)technique used for stretching double-strandedDNA is reported. DNA molecules were stretched on the silanized mica surface by thistechnique, its speed being precisely controlled with a computer. This approachcombinedthe precise DNA stretching method with high resolution AFM imaging at nanometer scale,thusmaking it useful for DNA alignment manipulation and subsequent gene research.

  9. Molecules during stellar formation and death

    NARCIS (Netherlands)

    Li, Xiaohu

    2015-01-01

    This thesis explores the chemistry of interstellar and circumstellar molecules during star formation and death. From the perspective of chemical physics, the most important outcome of this thesis lies in that the rates for two important reactions are determined accurately for the first time: N2 phot

  10. Chain-like molecules confined in nanopores

    Science.gov (United States)

    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).

  11. Photoelectron spectroscopy of heavy atoms and molecules

    Energy Technology Data Exchange (ETDEWEB)

    White, M.G.

    1979-07-01

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

  12. The MHC molecules of nonmammalian vertebrates

    DEFF Research Database (Denmark)

    Kaufman, J; Skjoedt, K; Salomonsen, J

    1990-01-01

    to develop. There is no molecular evidence yet to decide whether vertebrate immune systems (and particularly the MHC molecules) are evolutionarily related to invertebrate allorecognition systems, and the functional evidence can be interpreted either way. Even among the vertebrates, there is great...

  13. Chiral Sensitivity in Electron-Molecule Interactions

    Science.gov (United States)

    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.

  14. Single-molecule Michaelis-Menten equations.

    Science.gov (United States)

    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 )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.

  15. Molecules for Fluorescence Detection of Specific Chemicals

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  17. Synthesis of single-molecule nanocars.

    Science.gov (United States)

    Vives, Guillaume; Tour, James M

    2009-03-17

    The drive to miniaturize devices has led to a variety of molecular machines inspired by macroscopic counterparts such as molecular motors, switches, shuttles, turnstiles, barrows, elevators, and nanovehicles. Such nanomachines are designed for controlled mechanical motion and the transport of nanocargo. As researchers miniaturize devices, they can consider two complementary approaches: (1) the "top-down" approach, which reduces the size of macroscopic objects to reach an equivalent microscopic entity using photolithography and related techniques and (2) the "bottom-up" approach, which builds functional microscopic or nanoscopic entities from molecular building blocks. The top-down approach, extensively used by the semiconductor industry, is nearing its scaling limits. On the other hand, the bottom-up approach takes advantage of the self-assembly of smaller molecules into larger networks by exploiting typically weak molecular interactions. But self-assembly alone will not permit complex assembly. Using nanomachines, we hope to eventually consider complex, enzyme-like directed assembly. With that ultimate goal, we are currently exploring the control of nanomachines that would provide a basis for the future bottom-up construction of complex systems. This Account describes the synthesis of a class of molecular machines that resemble macroscopic vehicles. We designed these so-called nanocars for study at the single-molecule level by scanning probe microscopy (SPM). The vehicles have a chassis connected to wheel-terminated axles and convert energy inputs such as heat, electric fields, or light into controlled motion on a surface, ultimately leading to transport of nanocargo. At first, we used C(60) fullerenes as wheels, which allowed the demonstration of a directional rolling mechanism of a nanocar on a gold surface by STM. However, because of the low solubility of the fullerene nanocars and the incompatibility of fullerenes with photochemical processes, we developed new

  18. Nondestructive Detection of Polar Molecules via Rydberg Atoms

    OpenAIRE

    Zeppenfeld, Martin

    2016-01-01

    A highly sensitive, general, and preferably nondestructive technique to detect polar molecules would greatly advance a number of fields, in particular quantum science with cold and ultracold molecules. Here, we propose using resonant energy transfer between molecules and Rydberg atoms to detect molecules. Based on an energy transfer cross section of $>10^{-6}\\,$cm$^2$ for sufficiently low collision energies, a near unit efficiency non-destructive detection of basically any polar molecule spec...

  19. Molecule by molecule, the physics and chemistry of life: SMB 2007.

    Science.gov (United States)

    Block, Steven M; Larson, Matthew H; Greenleaf, William J; Herbert, Kristina M; Guydosh, Nicholas R; Anthony, Peter C

    2007-04-01

    Interdisciplinary work in the life sciences at the boundaries of biology, chemistry and physics is making enormous strides. This progress was showcased at the recent Single Molecule Biophysics conference.

  20. From the molecule to the mole: improving heterogeneous copper catalyzed click chemistry using single molecule spectroscopy.

    Science.gov (United States)

    Wang, Bowen; Durantini, Javier; Decan, Matthew R; Nie, Jun; Lanterna, Anabel E; Scaiano, Juan C

    2016-12-22

    Single molecule spectroscopy (SMS) inspired the optimization of a heterogeneous 'click' catalyst leading to enhanced yields of the Cu-catalyzed reaction of azides with terminal alkynes. Changes in SMS data after optimization confirm the improvements in catalyst performance.

  1. Adsorption. Cage molecules to pick up the pollutants; Adsorption. Des molecules cages pour capter les polluants

    Energy Technology Data Exchange (ETDEWEB)

    Anon.

    1999-12-01

    The cyclo-dextrins have the property to be cage molecules, that is to say they are able to shut up organic molecules in their structure. To use them in remedial action against pollution it is necessary to find a support on which they can be grafted. The Laboratory of organic chemistry and macromolecules from the University of Sciences and Technologies of Lilles is looking for this. The researchers have used a textile material in non weaved polypropylene, a support chemically steady that resists to aggressive media such polluted effluents. To graft the cage molecule, the technique of electrons bombing has been chosen. It produces a monomer (methacrylate of glycidyl) that allows to have a tissue bearer of epoxide functions susceptible to react with the cyclo-dextrin. The studies are continued in particular to valid the use of cage molecules on the dioxin and pesticides, and also to adapt the filter to gaseous media (volatile organic compounds, smells). (N.C.)

  2. Manifestation of the strong quadrupole light-molecule interaction in the SEHR spectra of symmetrical molecules

    CERN Document Server

    Polubotko, A M

    2009-01-01

    The paper demonstrates possibility of giant enhancement of Surface Enhanced Hyper Raman Scattering on the base of qualitative consideration of electromagnetic field near some models of rough metal surfaces and of some features of the dipole and quadrupole light-molecule interaction, such as it was made in the dipole-quadrupole SERS theory. Consideration of symmetrical molecules permits to obtain selection rules for their SEHR spectra and establish such regularity as appearance of the bands, caused by the totally symmetric vibrations, transforming after the unitary irreducible representation in molecules with C2h,D and higher symmetry groups, which are forbidden in usual HRS spectra. Analysis of literature data on trans-1,2-bis (4-pyridyle) ethylene and pyridine molecules demonstrates that their SEHR spectra can be explained by the SEHRS dipole-quadrupole theory, while analysis of the SEHR spectrum of pyrazine reveals appearance of the strong forbidden bands, caused by vibrations transforming after the unitary...

  3. Handbook of Single-Molecule Biophysics

    CERN Document Server

    Hinterdorfer, Peter

    2009-01-01

    The last decade has seen the development of a number of novel biophysical methods that allow the manipulation and study of individual biomolecules. The ability to monitor biological processes at this fundamental level of sensitivity has given rise to an improved understanding of the underlying molecular mechanisms. Through the removal of ensemble averaging, distributions and fluctuations of molecular properties can be characterized, transient intermediates identified, and catalytic mechanisms elucidated. By applying forces on biomolecules while monitoring their activity, important information can be obtained on how proteins couple function to structure. The Handbook of Single-Molecule Biophysics provides an introduction to these techniques and presents an extensive discussion of the new biological insights obtained from them. Coverage includes: Experimental techniques to monitor and manipulate individual biomolecules The use of single-molecule techniques in super-resolution and functional imaging Single-molec...

  4. Multiorbital tunneling ionization of the CO molecule

    CERN Document Server

    Wu, J; Kunitski, M; Meckel, M; Voss, S; Sann, H; Kim, H; Jahnke, T; Czasch, A; Dörner, R

    2012-01-01

    We coincidently measure the molecular frame photoelectron angular distribution and the ion sum-momentum distribution of single and double ionization of CO molecules by using circularly and elliptically polarized femtosecond laser pulses, respectively. The orientation dependent ionization rates for various kinetic energy releases allow us to individually identify the ionizations of multiple orbitals, ranging from the highest occupied to the next two lower-lying molecular orbitals for various channels observed in our experiments. Not only the emission of a single electron, but also the sequential tunneling dynamics of two electrons from multiple orbitals are traced step by step. Our results confirm that the shape of the ionizing orbitals determine the strong laser field tunneling ionization in the CO molecule, whereas the linear Stark effect plays a minor role.

  5. Optical slowing of calcium monofluoride molecules

    Science.gov (United States)

    Ravi, Aakash; Chae, Eunmi; Hemmerling, Boerge; Anderegg, Loic; Augenbraun, Benjamin; Drayna, Garrett; Hutzler, Nicholas; Collopy, Alejandra; Wu, Yewei; Ding, Shiqian; Ye, Jun; Ketterle, Wolfgang; Doyle, John

    2016-05-01

    We report white-light slowing of calcium monofluoride molecules. A single main laser (606 nm) plus two additional vibrational repump lasers (628 nm) are employed. The slowing lasers are spectrally broadened to address the molecules' velocity spread and hyperfine splittings. We use a background-free two-photon fluorescence detection scheme to make high signal-to-noise measurements of our molecular beam's longitudinal velocity distribution. This method is applied to slow CaF produced by a two-stage cryogenic buffer gas beam source by > 30 m/s to near the capture velocity of a molecular magneto-optical trap (MOT). Due to the presence of magnetic dark states which inhibit optical cycling, we will use an AC-MOT. We characterize the performance of this AC-MOT used in the trapping of Li and Yb.

  6. Interstellar molecules - Formation in solar nebulae

    Science.gov (United States)

    Anders, E.

    1973-01-01

    Herbig's (1970) hypothesis that solar nebulae might be the principal source of interstellar grains and molecules is investigated. The investigation includes the determination of physical and chemical conditions in the early solar system. The production of organic compounds in the solar nebula is studied, and the compounds in meteorites are compared with those obtained in Miller-Urey and Fischer-Tropsch-type (FTT) reactions, taking into consideration aliphatic hydrocarbons, aromatic hydrocarbons, purines, pyrimidines, amino acids, porphyrins, and aspects of carbon-isotope fractionation. It is found that FTT reactions account reasonably well for all well-established features of organic matter in meteorites investigated. The distribution of compounds produced by FTT reactions is compared with the distribution of interstellar molecules. Biological implications of the results are considered.

  7. Trace Molecules in Giant Planet Atmospheres

    Science.gov (United States)

    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.

  8. Diiododurene: four centrosymmetric molecules in general positions.

    Science.gov (United States)

    Britton, Doyle; Gleason, William B

    2003-08-01

    Diiododurene (1,4-diodo-2,3,5,6-tetramethylbenzene), C(10)H(12)I(2), packs with four molecules in the asymmetric unit. All four of these moleules violate Kitaigorodsky's suggestion that molecules with centers of symmetry will lie on crystallographic centers of symmetry. There is 5.6% disorder at one of the sites. Most of the I atoms are in contact with other I atoms, but only six of the I.I contacts are shorter than 4.2 A. Of these six contacts, one set of three contacts forms a triangular set in which all of the I.I distances are less than 3.9 A.

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

    Science.gov (United States)

    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.

  10. Automated imaging system for single molecules

    Science.gov (United States)

    Schwartz, David Charles; Runnheim, Rodney; Forrest, Daniel

    2012-09-18

    There is provided a high throughput automated single molecule image collection and processing system that requires minimal initial user input. The unique features embodied in the present disclosure allow automated collection and initial processing of optical images of single molecules and their assemblies. Correct focus may be automatically maintained while images are collected. Uneven illumination in fluorescence microscopy is accounted for, and an overall robust imaging operation is provided yielding individual images prepared for further processing in external systems. Embodiments described herein are useful in studies of any macromolecules such as DNA, RNA, peptides and proteins. The automated image collection and processing system and method of same may be implemented and deployed over a computer network, and may be ergonomically optimized to facilitate user interaction.

  11. Effective interaction between helical bio-molecules

    CERN Document Server

    Allahyarov, E

    1999-01-01

    The effective interaction between two parallel strands of helicalbio-molecules, such as deoxyribose nucleic acids (DNA), is calculated usingcomputer simulations of the "primitive" model of electrolytes. In particular westudy a simple model for B-DNA incorporating explicitly its charge pattern as adouble-helix structure. The effective force and the effective torque exertedonto the molecules depend on the central distance and on the relativeorientation. The contributions of nonlinear screening by monovalent counterionsto these forces and torques are analyzed and calculated for different saltconcentrations. As a result, we find that the sign of the force dependssensitively on the relative orientation. For intermolecular distances smallerthan $6\\AA$ it can be both attractive and repulsive. Furthermore we report anonmonotonic behaviour of the effective force for increasing saltconcentration. Both features cannot be described within linear screeningtheories. For large distances, on the other hand, the results agree...

  12. Multichannel quantum defect theory for polar molecules

    Science.gov (United States)

    Elfimov, Sergei V.; Dorofeev, Dmitrii L.; Zon, Boris A.

    2014-02-01

    Our work is devoted to developing a general approach for nonpenetrating Rydberg states of polar molecules. We propose a method to estimate the accuracy of calculation of their wave functions and quantum defects. Basing on this method we estimate the accuracy of Born-Oppenheimer (BO) and inverse Born-Oppenheimer (IBO) approximations for these states. This estimation enables us to determine the space and energy regions where BO and IBO approximations are valid. It depends on the interplay between l coupling (due to dipole potential of the core) and l uncoupling (due to rotation the core). Next we consider the intermediate region where both BO and IBO are not valid. For this intermediate region we propose a modification of Fano's multichannel quantum defect theory to match BO and IBO wave functions and show that it gives more reliable results. They are demonstrated on the example of SO molecule.

  13. Vibrational and coherence dynamics of molecules

    CERN Document Server

    Zhang, Zhedong

    2015-01-01

    We {\\it analytically} investigate the population and coherence dynamics and relaxations in the vibrational energy transport in molecules. The corresponding two time scales $t_1$ and $t_2$ are explored. Coherence-population entanglement is found to considerably promote the time scale $t_2$ for dephasing and the amplitude of coherence. This is attributed to the suppression of the environment-induced drift force by coherence. Moreover the population imbalance (magnetization) is shown to be significantly amplified with the coherence-population entanglement. Contrary to the previous studies, we exactly elucidate a coherent process by showing $t_1molecules dissolved in D$_2$O. Finally we explore the coherence effect on the heat current at the macroscopic level.

  14. Is the focus on "molecules" obsolete?

    Science.gov (United States)

    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.

  15. Rotational dynamics of simple asymmetric molecules

    Science.gov (United States)

    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.

  16. Modelling proton transfer in water molecule chains

    CERN Document Server

    Korzhimanov, Artem; Shutova, Tatiana; Samuelsson, Goran

    2011-01-01

    The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better understood in terms of simplified model problems. Here we have tested, analytically and numerically, a model describing the classical proton hopping process in molecular water chains. In order to capture the main features of the proton hopping process in such molecular chains, we use a simplified model for our analysis. In particular, our discrete model describes a 1D chain of water molecules situated in an external protein channel structure, and each water molecule is allowed to oscillate around its equilibrium point in this system, while the protons are allowed to move along the line of neighboring oxygen atoms. The occurrence and properties of nonlinear solitary transport structures, allowing for much faster proton transport, are discussed, and the possible implications of...

  17. Atomic Rydberg Reservoirs for Polar Molecules

    CERN Document Server

    Zhao, Bo; Pupillo, Guido; Zoller, Peter

    2011-01-01

    We discuss laser dressed dipolar and Van der Waals interactions between atoms and polar molecules, so that a cold atomic gas with laser admixed Rydberg levels acts as a designed reservoir for both elastic and inelastic collisional processes. The elastic scattering channel is characterized by large elastic scattering cross sections and repulsive shields to protect from close encounter collisions. In addition, we discuss a dissipative (inelastic) collision where a spontaneously emitted photon carries away (kinetic) energy of the collision partners, thus providing a significant energy loss in a single collision. This leads to the scenario of rapid thermalization and cooling of a molecule in the mK down to the \\mu K regime by cold atoms.

  18. Atomic Rydberg Reservoirs for Polar Molecules

    Science.gov (United States)

    Zhao, B.; Glaetzle, A. W.; Pupillo, G.; Zoller, P.

    2012-05-01

    We discuss laser-dressed dipolar and van der Waals interactions between atoms and polar molecules, so that a cold atomic gas with laser admixed Rydberg levels acts as a designed reservoir for both elastic and inelastic collisional processes. The elastic scattering channel is characterized by large elastic scattering cross sections and repulsive shields to protect from close encounter collisions. In addition, we discuss a dissipative (inelastic) collision where a spontaneously emitted photon carries away (kinetic) energy of the collision partners, thus providing a significant energy loss in a single collision. This leads to the scenario of rapid thermalization and cooling of a molecule in the mK down to the μK regime by cold atoms.

  19. Clinical review: Oxygen as a signaling molecule

    OpenAIRE

    2010-01-01

    Molecular oxygen is obviously essential for conserving energy in a form useable for aerobic life; however, its utilization comes at a cost - the production of reactive oxygen species (ROS). ROS can be highly damaging to a range of biological macromolecules, and in the past the overproduction of these short-lived molecules in a variety of disease states was thought to be exclusively toxic to cells and tissues such as the lung. Recent basic research, however, has indicated that ROS production -...

  20. Single Molecule Data Analysis: An Introduction

    CERN Document Server

    Tavakoli, Meysam; Li, Chun-Biu; Komatsuzaki, Tamiki; Pressé, Steve

    2016-01-01

    We review methods of data analysis for biophysical data with a special emphasis on single molecule applications. Our review is intended for anyone, from student to established researcher. For someone just getting started, we focus on exposing the logic, strength and limitations of each method and cite, as appropriate, the relevant literature for implementation details. We review traditional frequentist and Bayesian parametric approaches to data analysis and subsequently extend our discussion to recent non-parametric and information theoretic methods.

  1. DNA, the central molecule of aging.

    Science.gov (United States)

    Lenart, Peter; Krejci, Lumir

    2016-04-01

    Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.

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

    Science.gov (United States)

    Jakab, Cheryl

    2013-08-01

    This paper reports on 6-11-year-old children's `sayings and doings' (Harré 2002) as they explore molecule artefacts in dialectical-interactive teaching interviews (Fleer, Cultural Studies of Science Education 3:781-786, 2008; Hedegaard et al. 2008). This sociocultural study was designed to explore children's everyday awareness of and meaning-making with cultural molecular artefacts. Our everyday world is populated with an ever increasing range of molecular or nanoworld words, symbols, images, and games. What do children today say about these artefacts that are used to represent molecular world entities? What are the material and social resources that can influence a child's everyday and developing scientific ideas about `molecules'? How do children interact with these cognitive tools when given expert assistance? What meaning-making is afforded when children are socially and materially assisted in using molecular tools in early chemical and nanoworld thinking? Tool-dependent discursive studies show that provision of cultural artefacts can assist and direct developmental thinking across many domains of science (Schoultz et al., Human Development 44:103-118, 2001; Siegal 2008). Young children's use of molecular artefacts as cognitive tools has not received much attention to date (Jakab 2009a, b). This study shows 6-11-year-old children expressing everyday ideas of molecular artefacts and raising their own questions about the artefacts. They are seen beginning to domesticate (Erneling 2010) the words, symbols, and images to their own purposes when given the opportunity to interact with such artefacts in supported activity. Discursive analysis supports the notion that using `molecules' as cultural tools can help young children to begin `putting on molecular spectacles' (Kind 2004). Playing with an interactive game (ICT) is shown to be particularly helpful in assisting children's early meaning-making with representations of molecules, atoms, and their chemical symbols.

  3. Interstellar Molecules Their Laboratory and Interstellar Habitat

    CERN Document Server

    Yamada, Koichi M T

    2011-01-01

    This book deals with the astrophysics and spectroscopy of the interstellar molecules. In the introduction, overview and history of interstellar observations are described in order to help understanding how the modern astrophysics and molecular spectroscopy have been developed interactively. The recent progress in the study of this field, after the 4th Cologne-Bonn-Zermatt symposium 2003 is briefly summarized. Furthermore, the basic knowledge of molecular spectroscopy, which is essential to correctly comprehend the astrophysical observations, is presented in a compact form.

  4. Electron correlation in molecules and condensed phases

    CERN Document Server

    March, N H

    1996-01-01

    This reference describes the latest research on correlation effects in the multicenter problems of atoms, molecules, and solids The author utilizes first- and second-order matrices, including the important observable electron density rho(r), and the Green function for discussing quantum computer simulations With its focus on concepts and theories, this volume will benefit experimental physicists, materials scientists, and physical and inorganic chemists as well as graduate students

  5. Molecules as tracers of galaxy evolution

    DEFF Research Database (Denmark)

    Costagliola, F.; Aalto, S.; I. Rodriguez, M.;

    2011-01-01

    We investigate the molecular gas properties of a sample of 23 galaxies in order to find and test chemical signatures of galaxy evolution and to compare them to IR evolutionary tracers. Observation at 3 mm wavelengths were obtained with the EMIR broadband receiver, mounted on the IRAM 30 m telesco...... detect the molecule in its vibrationally excited state.We find low HNC/HCN line ratios (...

  6. Potential energy landscapes of tetragonal pyramid molecules

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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'.

  8. Soliton molecules for advanced optical telecommunications

    Science.gov (United States)

    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.

  9. Nuclear fusion in excited hydrogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    Bellini, M.; Casetti, L.; Rosa-Clot, M. (Florence Univ. (Italy). Dipt. di Fisica Istituto Nazionale di Fisica Nucleare, Florence (Italy))

    1990-10-01

    We evaluate the nuclear fusion rates in the excited vibrational states of molecules of hydrogen isotopes. The ground state fusion rate is increased by about eight order of magnitude but even in the most favorable situation it is out of any possible experimental test. We discuss the effects due to the nuclear potential in different hyperfine states, and the improvements attainable using coherent states and a solid phase. (orig.).

  10. Circular Intensity Differential Scattering of chiral molecules

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. Isatin, a versatile molecule: studies in Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Barbara, E-mail: barbara.iq@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil)

    2013-05-15

    Isatin is a small, versatile and widely applicable pharmacological molecule. These characteristics make isatin and its derivatives attractive to many research groups as resources for chemical and pharmacological studies. Although it has a relatively simple structure, isatin is a useful chemical scaffold for a variety of chemical transformations. This article discusses several studies performed by Brazilian groups, including investigations of its structural changes, biological assay designs and new methods for the synthesis of isatin. (author)

  12. Detecting electron motion in atoms and molecules.

    Science.gov (United States)

    Shao, Hua-Chieh; Starace, Anthony F

    2010-12-31

    The detection of spatial and temporal electronic motion by scattering of subfemtosecond pulses of 10 keV electrons from coherent superpositions of electronic states of both H and T2(+) is investigated. For the H atom, we predict changes in the diffraction images that reflect the time-dependent effective radius of the electronic charge density. For an aligned T2(+) molecule, the diffraction image changes reflect the time-dependent localization or delocalization of the electronic charge density.

  13. Origins of the handedness of biological molecules.

    Science.gov (United States)

    Mason, S F

    1991-01-01

    Pasteur (1860) showed that many organic molecules form enantiomeric pairs with non-superposable mirror-image shapes, characterized by their oppositely signed optical rotation but otherwise apparently identical. Equal numbers of left-handed and right-handed molecules resulted from laboratory synthesis, whereas biosynthetic processes afforded only one of the two enantiomers, leading Pasteur to conclude that biosynthesis involves a chiral force. Fischer demonstrated (1890-1919) that functional biomolecules are composed specifically of the D-sugars and the L-amino acids and that the laboratory synthetic reactions of such molecules propagate with chiral stereoselectivity. Given a primordial enantiomer, biomolecular homochirality follows without the intervention of a chiral natural force, except prebiotically. Chiral forces known at the time were found to be even handed on a time and space average, exemplifying parity conservation (1927). The weak nuclear force, shown to violate parity (1956), was unified with electro-magnetism in the electroweak force (1970). Ab initio estimations including the chiral electroweak force indicate that the L-amino acids and the D-sugars are more stable than the corresponding enantiomers. The small energy difference between these enantiomeric pairs, with Darwinian reaction kinetics in a flow reactor, account for the choice of biomolecular handedness made when life began.

  14. Physiological roles of small RNA molecules.

    Science.gov (United States)

    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.

  15. Partially dark optical molecule via phase control

    Science.gov (United States)

    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.

  16. Small molecule-guided thermoresponsive supramolecular assemblies

    KAUST Repository

    Rancatore, Benjamin J.

    2012-10-23

    Small organic molecules with strong intermolecular interactions have a wide range of desirable optical and electronic properties and rich phase behaviors. Incorporating them into block copolymer (BCP)-based supramolecules opens new routes to generate functional responsive materials. Using oligothiophene- containing supramolecules, we present systematic studies of critical thermodynamic parameters and kinetic pathway that govern the coassemblies of BCP and strongly interacting small molecules. A number of potentially useful morphologies for optoelectronic materials, including a nanoscopic network of oligothiophene and nanoscopic crystalline lamellae, were obtained by varying the assembly pathway. Hierarchical coassemblies of oligothiophene and BCP, rather than macrophase separation, can be obtained. Crystallization of the oligothiophene not only induces chain stretching of the BCP block the oligothiophene is hydrogen bonded to but also changes the conformation of the other BCP coil block. This leads to an over 70% change in the BCP periodicity (e.g., from 31 to 53 nm) as the oligothiophene changes from a melt to a crystalline state, which provides access to a large BCP periodicity using fairly low molecular weight BCP. The present studies have demonstrated the experimental feasibility of generating thermoresponsive materials that convert heat into mechanical energy. Incorporating strongly interacting small molecules into BCP supramolecules effectively increases the BCP periodicity and may also open new opportunities to tailor their optical properties without the need for high molecular weight BCP. © 2012 American Chemical Society.

  17. Heavy Exotic Molecules with Charm and Bottom

    CERN Document Server

    Liu, Yizhuang

    2016-01-01

    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 $(0^\\pm, 1^\\pm)$ cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for $J\\leq 1$. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. Also, the bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, which we identify as a mixture of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound isosinglet with $J^{PC}=1^{++}$ is suggested as a possible neutral $X_b(10532)$ not yet reported.

  18. Fixman compensating potential for general branched molecules

    Energy Technology Data Exchange (ETDEWEB)

    Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States); Kandel, Saugat; Wagner, Jeffrey; Larsen, Adrien; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States)

    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.

  19. Fluorescence Polarization Assays in Small Molecule Screening

    Science.gov (United States)

    Lea, Wendy A.; Simeonov, Anton

    2011-01-01

    Importance of the field Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field has been symbolized by the facile adoption of FP in high-throughput screening (HTS) and small molecule drug discovery of an increasing range of target classes. Areas covered in this review The article provides a brief overview on the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including G-protein coupled receptors (GPCRs), enzymes and protein-protein interactions (PPIs). The strengths and weaknesses of this method, practical considerations in assay design, novel applications, and future directions are also discussed. What the reader will gain The reader will be informed of the most recent advancements and future directions of FP application to small molecule screening. Take home message In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor binding studies. PMID:22328899

  20. Evaluating enzymatic synthesis of small molecule drugs.

    Science.gov (United States)

    Moura, Matthew; Finkle, Justin; Stainbrook, Sarah; Greene, Jennifer; Broadbelt, Linda J; Tyo, Keith E J

    2016-01-01

    There have been many achievements in applying biochemical synthetic routes to the synthesis of commodity chemicals. However, most of these endeavors have focused on optimizing and increasing the yields of naturally existing pathways. We sought to evaluate the potential for biosynthesis beyond the limits of known biochemistry towards the production of small molecule drugs that do not exist in nature. Because of the potential for improved yields compared to total synthesis, and therefore lower manufacturing costs, we focused on drugs for diseases endemic to many resource poor regions, like tuberculosis and HIV. Using generalized biochemical reaction rules, we were able to design biochemical pathways for the production of eight small molecule drugs or drug precursors and identify potential enzyme-substrate pairs for nearly every predicted reaction. All pathways begin from native metabolites, abrogating the need for specialized precursors. The simulated pathways showed several trends with the sequential ordering of reactions as well as the types of chemistries used. For some compounds, the main obstacles to finding feasible biochemical pathways were the lack of appropriate, natural starting compounds and a low diversity of biochemical coupling reactions necessary to synthesize molecules with larger molecular size.

  1. Rydberg States of Atoms and Molecules

    Science.gov (United States)

    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.

  2. Sorption of small molecules in polymeric media

    Science.gov (United States)

    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.

  3. Self and directed assembly: people and molecules

    Directory of Open Access Journals (Sweden)

    Tony D. James

    2016-03-01

    Full Text Available 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.

  4. Heavy exotic molecules with charm and bottom

    Science.gov (United States)

    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.

  5. Electron attachment to the phthalide molecule

    Energy Technology Data Exchange (ETDEWEB)

    Asfandiarov, N. L. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); Bashkir State Pedagogical University, Oktyabrskoy Revolutsii St., 3a, 450000 Ufa (Russian Federation); Pshenichnyuk, S. A. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); St.-Petersburg State University, Uljanovskaja, 1, 198504 St.-Petersburg (Russian Federation); Vorob’ev, A. S.; Nafikova, E. P. [Institute of Molecule and Crystal Physics, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 151, 450075 Ufa (Russian Federation); Lachinov, A. N. [Bashkir State Pedagogical University, Oktyabrskoy Revolutsii St., 3a, 450000 Ufa (Russian Federation); Kraikin, V. A. [Institute of Organic Chemistry, Ufa Research Centre, Russian Academy of Sciences, Prospect Oktyabrya 59, 450075 Ufa (Russian Federation); Modelli, A. [Dipartimento di Chimica “G. Ciamician,” Universitá di Bologna, Via Selmi 2, 40126 Bologna (Italy); Centro Interdipartimentale di Ricerca in Scienze Ambientali (CIRSA), Universitá di Bologna, Via S. Alberto 163, 48123 Ravenna (Italy)

    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.

  6. The origin of large molecules in primordial autocatalytic reaction networks

    CERN Document Server

    Giri, Varun

    2011-01-01

    Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we know that can accomplish this task consist of large molecules. Thus the origin of large molecules is a chicken and egg problem in chemistry. Here we present a mechanism, based on autocatalytic sets (ACSs), that is a possible solution to this problem. We discuss a mathematical model describing the population dynamics of molecules in a stylized but prebiotically plausible chemistry. Large molecules can be produced in this chemistry by the coalescing of smaller ones, with the smallest molecules, the `food set', being buffered. Some of the reactions can be catalyzed by molecules within the chemistry with varying catalytic strengths. Normally the concentrations of large molecules in such a scenario are very small, diminishing exponentially with their size. ACSs, if present in the c...

  7. Synthesis and characterization of lower generation broom molecules

    Institute of Scientific and Technical Information of China (English)

    Jun Wang; Cui Qin Li; Shu Yan Zhang; Fang Sun; Teng Jie Ge

    2008-01-01

    Dendritic molecules with dodecyl groups as the hyperbranchs were synthesized in methanol by Michael addition withdodecylamine and methyl acrylate as raw materials. This new-type dendritic molecules were called vividly "broom molecules" inthis report. The surface tension of the aqueous solution of broom molecule terminated amino group was measured by using the drop-volume method. The demulsification performance of the broom molecules for the oil/water (O/W) simulated crude oil emulsion wasexamined. The experimental results revealed that, as a new-type of surfactants, the broom molecules terminated amino groupsshowed demulsification for the O/W simulated crude oil emulsion.

  8. Single Molecule Studies on Dynamics in Liquid Crystals

    Directory of Open Access Journals (Sweden)

    Daniela Täuber

    2013-09-01

    Full Text Available 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.

  9. Oligomer Molecules for Efficient Organic Photovoltaics.

    Science.gov (United States)

    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 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, and film-forming properties. Therefore, OMs are a

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

    Science.gov (United States)

    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

  11. Deep learning for single-molecule science.

    Science.gov (United States)

    Albrecht, Tim; Slabaugh, Gregory; Alonso, Eduardo; Al-Arif, Masudur R

    2017-08-01

    Exploring and making predictions based on single-molecule data can be challenging, not only due to the sheer size of the datasets, but also because a priori knowledge about the signal characteristics is typically limited and poor signal-to-noise ratio. For example, hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. Equally, even when the different data categories are known, e.g., the four bases in DNA sequencing, it is often difficult to know how to make best use of the available information content. The latest developments in Machine Learning (ML), so-called Deep Learning (DL) offers an interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional Machine Learning strategies and even human performance. However, to date DL has not been applied much in single-molecule science, presumably in part because relatively little is known about the 'internal workings' of such DL tools within single-molecule science as a field. In this Tutorial, we make an attempt to illustrate in a step-by-step guide how one of those, a Convolutional Neural Network, may be used for base calling in DNA sequencing applications. We compare it with a Support Vector Machine as a more conventional ML method, and and discuss some of the strengths and weaknesses of the approach. In particular, a 'deep' neural network has many features of a 'black box', which has important implications on how we look at and interpret data. © 2017 IOP Publishing Ltd.

  12. What are nuclear molecules?: past and present

    Energy Technology Data Exchange (ETDEWEB)

    Hess, P.O [Universidad Nacional Autonoma de Mexico, Mexico, D.F (Mexico)

    2001-04-01

    A brief history of nuclear molecules, which was discovered for the first time in 1960, is presented. A couple of simple models for their description are discussed, as the Double Resonance Mechanisms and the Two-Center Shell Model. These classical nuclear molecules live only about the order of 10{sup -2}1 seconds, barely sufficient to orbit once around each other. Recently, a new type of nuclear molecules was discovered, with three clusters, which live of the order of 10{sup -1}3 seconds. We discuss shortly the experiment and the conclusions of it. At the end, we present a geometric model and apply it to {sup 9}6Sr + {sup 1}0Be + {sup 1}46Ba observed in the cold fission decay of {sup 2}52 Cf. [Spanish] Se presenta una breve historia de moleculas nucleares, que fueron identificadas por primera vez en 1960. Unos modelos sencillos, para su descripcion, son discutidos, como el Mecanismo de Doble Resonancia y Modelo de Dos Centros. Estas moleculas clasicas solo viven un orden de 10{sup -2}1 segundos, apenas suficiente para dar una vuelta. Recientemente se han descubierto moleculas nucleares de tres cumulos que viven un orden de 10{sup -1}3 segundos. Se discute un poco el experimento y las conclusiones de el. Al final se presenta un modelo geometrico que aplicamos a {sup 9}6Sr + {sup 1}0Be + {sup 1}46Ba, observado en el decaimiento frio de {sup 2}52 Cf.

  13. Raman scattering mediated by neighboring molecules.

    Science.gov (United States)

    Williams, Mathew D; Bradshaw, David S; Andrews, David L

    2016-05-01

    Raman scattering is most commonly associated with a change in vibrational state within individual molecules, the corresponding frequency shift in the scattered light affording a key way of identifying material structures. In theories where both matter and light are treated quantum mechanically, the fundamental scattering process is represented as the concurrent annihilation of a photon from one radiation mode and creation of another in a different mode. Developing this quantum electrodynamical formulation, the focus of the present work is on the spectroscopic consequences of electrodynamic coupling between neighboring molecules or other kinds of optical center. To encompass these nanoscale interactions, through which the molecular states evolve under the dual influence of the input light and local fields, this work identifies and determines two major mechanisms for each of which different selection rules apply. The constituent optical centers are considered to be chemically different and held in a fixed orientation with respect to each other, either as two components of a larger molecule or a molecular assembly that can undergo free rotation in a fluid medium or as parts of a larger, solid material. The two centers are considered to be separated beyond wavefunction overlap but close enough together to fall within an optical near-field limit, which leads to high inverse power dependences on their local separation. In this investigation, individual centers undergo a Stokes transition, whilst each neighbor of a different species remains in its original electronic and vibrational state. Analogous principles are applicable for the anti-Stokes case. The analysis concludes by considering the experimental consequences of applying this spectroscopic interpretation to fluid media; explicitly, the selection rules and the impact of pressure on the radiant intensity of this process.

  14. Deep learning for single-molecule science

    Science.gov (United States)

    Albrecht, Tim; Slabaugh, Gregory; Alonso, Eduardo; Al-Arif, SM Masudur R.

    2017-10-01

    Exploring and making predictions based on single-molecule data can be challenging, not only due to the sheer size of the datasets, but also because a priori knowledge about the signal characteristics is typically limited and poor signal-to-noise ratio. For example, hypothesis-driven data exploration, informed by an expectation of the signal characteristics, can lead to interpretation bias or loss of information. Equally, even when the different data categories are known, e.g., the four bases in DNA sequencing, it is often difficult to know how to make best use of the available information content. The latest developments in machine learning (ML), so-called deep learning (DL) offer interesting, new avenues to address such challenges. In some applications, such as speech and image recognition, DL has been able to outperform conventional ML strategies and even human performance. However, to date DL has not been applied much in single-molecule science, presumably in part because relatively little is known about the ‘internal workings’ of such DL tools within single-molecule science as a field. In this Tutorial, we make an attempt to illustrate in a step-by-step guide how one of those, a convolutional neural network (CNN), may be used for base calling in DNA sequencing applications. We compare it with a SVM as a more conventional ML method, and discuss some of the strengths and weaknesses of the approach. In particular, a ‘deep’ neural network has many features of a ‘black box’, which has important implications on how we look at and interpret data.

  15. Effect of lysosomotropic molecules on cellular homeostasis.

    Science.gov (United States)

    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

  16. Spectral simulations of polar diatomic molecules immersed in He clusters: application to the ICl (X) molecule

    Energy Technology Data Exchange (ETDEWEB)

    Villarreal, P [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lara-Castells, M P de [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Prosmiti, R [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Delgado-Barrio, G [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Lopez-Duran, D [Instituto de Matematicas y Fasica Fundamental (CSIC), Serrano 123, E-28006-Madrid (Spain); Gianturco, F A [Department of Chemistry and INFM, The University of Rome, Citta Universitaria, 00185, Rome (Italy); Jellinek, J [Chemistry Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2007-09-15

    A recently developed quantum-chemistry-like methodology to study molecules solvated in atomic clusters is applied to the ICl (iodine chloride) polar diatomic molecule immersed in clusters of He atoms. The atoms of the solvent clusters are treated as the 'electrons' and the solvated molecule as a structured 'nucleus' of the combined solvent-solute system. The helium-helium and helium-dopant interactions are represented by parametrized two-body and ab initio three-body potentials, respectively. The ground-state wavefunctions are used to compute the infrared (IR) spectra of the solvated molecule. In agreement with the experimental observations, the computed spectra exhibit considerable differences depending on whether the solvent cluster is comprised of bosonic ({sup 4}He) or fermionic ({sup 3}He) atoms. The source of these differences is attributed to the different spin-statistics of the solvent clusters. The bosonic versus fermionic nature of the solvent is reflected in the IR absorption selection rules. Only P and R branches with single state transitions appear in the spectrum when the molecule is solvated in a bosonic cluster. On the other hand, when the solvent represents a fermionic environment, quasi-degenerate multiplets of spin states contribute to each branch and, in addition, the Q-branch becomes also allowed. Combined, these two factors explain the more congested nature of the spectrum in the fermionic case.

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

    Science.gov (United States)

    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.

  18. Molecular-beam spectroscopy of interhalogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    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.

  19. Photonic molecules formed by coupled hybrid resonators

    CERN Document Server

    Peng, Bo; Zhu, Jiangang; Yang, Lan; 10.1364/OL.37.003435

    2013-01-01

    We describe a method that enables free-standing whispering-gallery-mode microresonators, and report spectral tuning of photonic molecules formed by coupled free and on-chip resonators with different geometries and materials. We study direct coupling via evanescent fields of free silica microtoroids and microspheres with on-chip polymer coated silica microtoroids. We demonstrate thermal tuning of resonance modes to achieve maximal spectral overlap, mode splitting induced by direct coupling, and the effects of distance between the resonators on the splitting spectra.

  20. Gaseous Electronics Tables, Atoms, and Molecules

    CERN Document Server

    Raju, Gorur Govinda

    2011-01-01

    With the constant emergence of new research and application possibilities, gaseous electronics is more important than ever in disciplines including engineering (electrical, power, mechanical, electronics, and environmental), physics, and electronics. The first resource of its kind, Gaseous Electronics: Tables, Atoms, and Molecules fulfills the author's vision of a stand-alone reference to condense 100 years of research on electron-neutral collision data into one easily searchable volume. It presents most--if not all--of the properly classified experimental results that scientists, researchers,

  1. Plasmonic molecules via glass annealing in hydrogen

    Science.gov (United States)

    Redkov, Alexey; Chervinskii, Semen; Baklanov, Alexander; Reduto, Igor; Zhurikhina, Valentina; Lipovskii, Andrey

    2014-11-01

    Growth of self-assembled metal nanoislands on the surface of silver ion-exchanged glasses via their thermal processing in hydrogen followed by out-diffusion of neutral silver is studied. The combination of thermal poling of the ion-exchanged glass with structured electrode and silver out-diffusion was used for simple formation of separated groups of several metal nanoislands presenting plasmonic molecules. The kinetics of nanoisland formation and temporal evolution of their size distribution on the surface of poled and unpoled glass are modeled.

  2. Bringing molecules back into molecular evolution.

    Directory of Open Access Journals (Sweden)

    Claus O Wilke

    Full Text Available Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

  3. Faddeev Random Phase Approximation for Molecules

    CERN Document Server

    Degroote, Matthias; Barbieri, Carlo

    2010-01-01

    The Faddeev Random Phase Approximation is a Green's function technique that makes use of Faddeev-equations to couple the motion of a single electron to the two-particle--one-hole and two-hole--one-particle excitations. This method goes beyond the frequently used third-order Algebraic Diagrammatic Construction method: all diagrams involving the exchange of phonons in the particle-hole and particle-particle channel are retained, but the phonons are described at the level of the Random Phase Approximation. This paper presents the first results for diatomic molecules at equilibrium geometry. The behavior of the method in the dissociation limit is also investigated.

  4. Structure of molecules and internal rotation

    CERN Document Server

    Mizushima, San-Ichiro

    1954-01-01

    Structure of Molecules and Internal Rotation reviews early studies on dihalogenoethanes. This book is organized into two parts encompassing 8 chapters that evaluate the Raman effect in ethane derivatives, the energy difference between rotational isomers, and the infrared absorption of ethane derivatives. Some of the topics covered in the book are the potential barrier to internal rotation; nature of the hindering potential; entropy difference between the rotational isomers; internal rotation in butane, pentane, and hexane; and internal rotation in long chain n-paraffins. Other chapters deal wi

  5. Electron impact excitations of S2 molecules

    CERN Document Server

    Tashiro, Motomichi

    2007-01-01

    Low-energy electron impact excitations of S_2 molecules are studied using the fixed-bond R-matrix method based on state-averaged complete active space SCF orbitals. Integral cross sections are calculated for elastic electron collision as well as impact excitation of the 7 lowest excited electronic states. Also, differential cross sections are obtained for elastic collision and excitation of the a^1 Delta_g, b^1 Sigma_g^+ and B^3 Sigma_u^- states. The integrated cross section of optically allowed excitation of the B^3 Sigma_u^- state agrees reasonably well with the available theoretical result.

  6. Kondo tunneling through real and artificial molecules.

    Science.gov (United States)

    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.

  7. Inorganic Nanoparticles Conjugated with Biofunctional Molecules

    Institute of Scientific and Technical Information of China (English)

    J.H.Choy

    2007-01-01

    1 Results We have attempted to conjugate inorganic nanoparticles with biofunctional molecules.Recently we were quite successful in demonstrating that a two-dimensional inorganic compound like layered double hydroxide (LDH),and natural and synthetic clays can be used as gene or drug delivery carriers1-4.To the best of our knowledge,such inorganic vectors are completely new and different from conventionally developed ones such as viruses and cationic liposomes,those which are limited in certain cases of ap...

  8. Humidity Effects on Conductivity of DNA Molecules

    Institute of Scientific and Technical Information of China (English)

    YAN Xun-Ling; DONG Rui-Xin; LIN Qing-De

    2006-01-01

    We present a model related to the humidity to describe the conductivity of homogeneous DNA molecule,where the hydration of phosphate group and bases are taken into account. The calculated results show the oscillation feature of dⅠ/dⅤ-Ⅴ curves and the semiconductor behavior of DNA. With the relative humidity increasing, the voltage gap becomes narrow and the maximum of conductance increases nonlinearly. The conductivity of DNA approaches to stabilization when the relative humidity reaches a certain value. These results are in agreement with experimental measurements.

  9. Spectra of Linear Polyene Molecule-canthaxanthin

    Institute of Scientific and Technical Information of China (English)

    OUYANG Shun-li; LI Zuo-wei; CHEN Yuan-zheng; MEN Zhi-wei; WU Nan-nan; SUN Cheng-lin

    2011-01-01

    Raman spectra and ultraviolet-visible(UV-Vis) absorption spectra of linear polyene molecule-canthaxanthin in n-hexane are measured and analyzed.In addition,the optimized structure of canthaxanthin was calculated via density functional theory(DFT) functional B3LYP.With decreasing the concentration,Raman scattering cross section (RSCS) of fundamental frequency is extremely high,and the UV-Vis absorption bands become narrower.The results of coherent weakly damped electron-Lattice vibration model were analyzed.

  10. Alignment of D-state Rydberg molecules

    CERN Document Server

    Krupp, Alexander T; Balewski, Jonathan B; Ilzhöfer, Philipp; Hofferberth, Sebastian; Löw, Robert; Pfau, Tilman; Kurz, Markus; Schmelcher, Peter

    2014-01-01

    We report on the formation of ultralong-range Rydberg D-state molecules via photoassociation in an ultracold cloud of rubidium atoms. By applying a magnetic offset field on the order of 10 G and high resolution spectroscopy, we are able to resolve individual rovibrational molecular states. A full theory, using the Born-Oppenheimer approximation including s- and p-wave scattering, reproduces the measured binding energies. The calculated molecular wavefunctions show that in the experiment we can selectively excite stationary molecular states with an extraordinary degree of alignment or anti-alignment with respect to the magnetic field axis.

  11. Control of dephasing in rotationally hot molecules

    Science.gov (United States)

    Bartram, David; Ivanov, Misha

    2010-04-01

    We consider a rotationally hot diatomic molecule as an example of an open quantum system, where molecular vibrational wave packets are subject to dephasing due to rovibrational coupling. We report analytical and numerical results addressing whether the dephasing rate can be controlled by adjustment of the initial wave packet phases. It appears that over long time scales, phase-only control is not possible, but for earlier time scales the possibility of phase-only control of dephasing remains. In addition, we point out that the time dependence of the dephasing process depends significantly upon the degeneracy of the rotational environment states.

  12. Nonrelativistic Lamb shift for muonic molecules

    Science.gov (United States)

    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.

  13. Assembling molecular electronic junctions one molecule at a time.

    Science.gov (United States)

    Bonifas, Andrew P; McCreery, Richard L

    2011-11-01

    Diffusion of metal atoms onto a molecular monolayer attached to a conducting surface permits electronic contact to the molecules with minimal heat transfer or structural disturbance. Surface-mediated metal deposition (SDMD) involves contact between "cold" diffusing metal atoms and molecules, due to shielding of the molecules from direct exposure to metal vapor. Measurement of the current through the molecular layer during metal diffusion permits observation of molecular conductance for junctions containing as few as one molecule. Discrete conductance steps were observed for 1-10 molecules within a monolayer during a single deposition run, corresponding to "recruitment" of additional molecules as the contact area between the diffusing Au layer and molecules increases. For alkane monolayers, the molecular conductance measured with SDMD exhibited an exponential dependence on molecular length with a decay constant (β) of 0.90 per CH(2) group, comparable to that observed by other techniques. Molecular conductance values were determined for three azobenzene molecules, and correlated with the offset between the molecular HOMO and the contact Fermi level, as expected for hole-mediated tunneling. Current-voltage curves were obtained during metal deposition showed no change in shape for junctions containing 1, 2, and 10 molecules, implying minimal intermolecular interactions as single molecule devices transitioned into several molecules devices. SDMD represents a "soft" metal deposition method capable of providing single molecule conductance values, then providing quantitative comparisons to molecular junctions containing 10(6) to 10(10) molecules.

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

    Science.gov (United States)

    Carr, Lincoln D.; Ye, Jun

    2009-05-01

    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

  15. Nanodevices for generating power from molecules and batteryless sensing

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-01-03

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

  16. Formation of Ultracold NaRb Feshbach Molecules

    CERN Document Server

    Wang, Fudong; Li, Xiaoke; Zhu, Bing; Chen, Jun; Wang, Dajun

    2015-01-01

    We report the creation of ultracold bosonic $^{23}$Na$^{87}$Rb Feshbach molecules via magneto-association. By ramping the magnetic field across an interspecies Feshbach resonance, at least 4000 molecules can be produced out of the near degenerate ultracold mixture. Fast loss due to inelastic atom-molecule collisions is observed, which limits the pure molecule number, after residual atoms removal, to 1700. The pure molecule sample can live for 21.8(8) ms in the optical trap, long enough for future molecular spectroscopy studies toward coherently transferring to the singlet ro-vibrational ground state, where these molecules are stable against chemical reaction and have a permanent electric dipole moment of 3.3 Debye. We have also measured the Feshbach molecule's binding energy near the Feshbach resonance by the oscillating magnetic field method and found these molecules have a large closed-channel fraction.

  17. Nanodevices for generating power from molecules and batteryless sensing

    Science.gov (United States)

    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. Nonlinear optical absorption of photosynthetic pigment molecules in leaves.

    Science.gov (United States)

    Ye, Zi-Piao

    2012-04-01

    A mathematical formulation of the relationship between optical absorption coefficient of photosynthetic pigment molecules and light intensity was developed. It showed that physical parameters of photosynthetic pigment molecule (i.e., light absorption cross-section of photosynthetic pigment molecule, its average lifetime in the excited state, total photosynthetic pigment molecules, the statistical weight, or degeneracy of energy level of photosynthetic pigment molecules in the ground state and in the excited state) influenced on both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules. Moreover, it also showed that both the light absorption coefficient and effective light absorption cross-section of photosynthetic pigment molecules were not constant, they decreased nonlinearly with light intensity increasing. The occupation numbers of photosynthetic pigment molecules in the excited states increased nonlinearly with light intensity increasing.

  19. Grafting single molecule magnets on gold nanoparticles.

    Science.gov (United States)

    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. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Organic- and molecule-based magnets

    Directory of Open Access Journals (Sweden)

    Joel S. Miller

    2014-06-01

    Full Text Available Magnets have been known for millennia and are strongly associated with metals (e.g. Fe, Co, Ni, Gd, intermetallics (e.g. Co17Sm2, Nd2Fe14B, or their oxides (e.g. CrO2, Fe3O4. The development of new magnetic materials has led to ubiquitous uses for electricity generation, memory storage media, and devices such as electric motors, microphones, telephones and computers. These magnets are fabricated via energy demanding metallurgical methods and are frequently brittle, chemically reactive, and possess elements in limited supply. The end of the last millennium has seen a surge in using organic, molecular, and polymeric materials as substitutes for metal and ceramic materials in many applications. Also, in the past few decades organic and molecule-based materials have been shown to magnetically order with examples having ordering temperatures exceeding room temperature, higher-than-iron saturation magnetizations, large coercive fields, etc. An overview of organic-based, and more generally molecule-based magnetic materials that exhibit unusual magnetic properties ranging from ferromagnets to synthetic antiferromagnets with emphasis on magnetic ordering using examples possessing organic nitriles (—CN or inorganic cyanide (CN− is described.