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Sample records for adamantyl-substituted retinoid-derived molecule

  1. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH2 groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  2. Crystal and molecular structure of four adamantyl-substituted tetrazoles

    Polyakova, I. N., E-mail: polyakova@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation); Saraev, V. V.; Gavrilov, A. S.; Golod, E. L. [St. Petersburg State Technological Institute (Technical University) (Russian Federation)

    2009-05-15

    Four adamantyltetrazoles-1-(1-adamantyl)tetrazole (I), 2-(1-adamantyl)tetrazole (II), 2-(3-aminoadamantyl-1)tetrazole (III), and 2-(3-aminoadamantyl-1)-5-methyltetrazole (IV)-are synthesized, and their crystal structures are studied. It is found that the tetrazole rings in the 1-substituted molecule I and 2-substituted molecules II-IV have close linear parameters but differ significantly in endocyclic angles. The degree of delocalization of double bonds in I is somewhat smaller than that in II-IV. The identical relative orientation of the tetrazole ring and adamantyl fragment in I-IV is stabilized by intramolecular C-H...N interactions (H...N, 2.57(2)-2.76(2) A). The molecular packings of crystals I-IV are determined by weak intermolecular C-H...N interactions; in III and IV, the packings are in addition affected by N-H...N interactions that involve NH{sub 2} groups. In the series of compounds I-IV, a qualitative dependence of the lengths of intermolecular H...N contacts and antiviral activity on the basicity of nitrogen atoms in the molecules is revealed.

  3. Chemical stability and in vitro and clinical efficacy of a novel hybrid retinoid derivative, bis-retinamido methylpentane.

    Kim, Ki Hyun; Lim, Dae Gon; Lim, Jun Yeul; Kim, Nam Ah; Park, So-Hyun; Cho, Jin Hun; Shin, Beom Soo; Jeong, Seong Hoon

    2015-11-10

    The anti-aging agent, retinol, has fewer side effects and similar biological activity compared to retinoic acid. However, retinol becomes unstable when exposed to light and heat. A novel hybrid retinoid derivative, bis-retinamido methylpentane (RS-2A), was newly developed to overcome the limitations. This study evaluated the chemical stability of RS-2A under thermal and light conditions by examining degradation profiles, and assessed the in vitro biological activity, cytotoxicity, and clinical efficacy. Chemical stability and degradation profiles were investigated with HPLC and LC-MS. Especially, photo-stability of RS-2A was analyzed under various conditions, such as change of physical state and concentration, different solvents, and various excipients. For analyses of cellular activity and cytotoxicity, human dermal fibroblasts were cultured with RS-2A. To evaluate the safety and efficacy of the compound with the cellular results, RS-2A was applied to women who had moderate to severe wrinkles at the periorbital region. All of the experiments were conducted with retinol as a reference. RS-2A was more stable than retinol to thermal conditions, especially in solution. Both RS-2A and retinol were unstable to light, but RS-2A showed enhanced photo-stability with regard to concentration, more polar solvent, and addition of proper excipients. RS-2A exhibited decreased cytotoxicity and enhanced effects on collagen synthesis compared with retinol. In a clinical study, a 4-week treatment with RS-2A significantly improved the appearance of periorbital wrinkles without any side effects. The results indicate that RS-2A might have potential as an anti-aging agent for cosmeceutical preparations because of its enhanced chemical stability, biological activity, safety, and clinical efficacy. PMID:26325317

  4. Combining a BCL2 Inhibitor with the Retinoid Derivative Fenretinide Targets Melanoma Cells Including Melanoma Initiating Cells

    Mukherjee, Nabanita; Reuland, Steven N.; Lu, Yan; Luo, Yuchun; Lambert, Karoline; Fujita, Mayumi; Robinson, William A.; Robinson, Steven E.; David A Norris; Yiqun G Shellman

    2014-01-01

    Investigations from multiple laboratories support the existence of melanoma initiating cells (MICs) that potentially contribute to melanoma's drug resistance. ABT-737, a small molecule BCL-2/BCL-XL/BCL-W inhibitor, is promising in cancer treatments, but not very effective against melanoma, with the anti-apoptotic protein MCL-1 as the main contributor to resistance. The synthetic retinoid fenretinide (4-HPR) has shown promise for treating breast cancers. Here, we tested whether the combination...

  5. Synthesis of Poly(aryl ether ketone) Copolymers Containing Adamantyl-substituted Naphthalene Rings

    ZHU Xiao-liang; ZHANG Shu-ling; REN Dian-fu; GUAN Shao-wei; WANG Gui-bin; JIANG Zhen-hua

    2009-01-01

    @@ 1 Introduction High performance polymers have received considerable attention over the past decade owing to their increased demands as replacements for metals or ceramics in automotive,aerospace,and microelectronic industries.Poly(aryl ether ketone)s(PAEKs) are a class of important high-performance aromatic polymers with excellent mechanical properties,good solvent resistance,size-accuracy,electrical characteristics,and superior thermal stability[1-3].

  6. Photoisomerisable molecules

    Peris Fajarnes, Eduardo Víctor; Mata Martínez, José Antonio; Márquez Linares, Francisco Manuel; Sabater Picot, María José

    2005-01-01

    [EN] The invention relates to a molecule comprising at least one carbon-carbon double bond which is substituted by at least one cyclopentadienyl-metal-cyclopentadienyl complex, having the cis/trans isomerisation property, in a reversible manner in response to the absorption of light. Preferably, the rest of the molecule comprises a dendrimer of any generation, advantageously of the polypropylenimine octaamine type. The inventive molecule can be used as a molecular switch and in various differ...

  7. Enumerating molecules.

    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. CD molecules 2005: human cell differentiation molecules

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

    2005-01-01

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

  9. Formation of Ultracold Molecules

    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.

  10. Trapping molecules on chips

    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.

  11. Electron correlation in molecules

    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

  12. Electron-molecule collisions

    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...

  13. Single molecules and nanotechnology

    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.

  14. Optothermal Molecule Trap

    Duhr, Stefan; Braun, Dieter

    2006-01-01

    Thermophoresis moves molecules along temperature gradients, typically from hot to cold. We superpose fluid flow with thermophoretic molecule flow under well defined microfluidic conditions, imaged by fluorescence microscopy. DNA is trapped and accumulated 16-fold in regions where both flows move in opposite directions. Strong 800-fold accumulation is expected, however with slow trapping kinetics. The experiment is equally described by a three-dimensional and one-dimensional analytical model. ...

  15. Towards single molecule switches.

    Zhang, Jia Lin; Zhong, Jian Qiang; Lin, Jia Dan; Hu, Wen Ping; Wu, Kai; Xu, Guo Qin; Wee, Andrew T S; Chen, Wei

    2015-05-21

    The concept of using single molecules as key building blocks for logic gates, diodes and transistors to perform basic functions of digital electronic devices at the molecular scale has been explored over the past decades. However, in addition to mimicking the basic functions of current silicon devices, molecules often possess unique properties that have no parallel in conventional materials and promise new hybrid devices with novel functions that cannot be achieved with equivalent solid-state devices. The most appealing example is the molecular switch. Over the past decade, molecular switches on surfaces have been intensely investigated. A variety of external stimuli such as light, electric field, temperature, tunneling electrons and even chemical stimulus have been used to activate these molecular switches between bistable or even multiple states by manipulating molecular conformations, dipole orientations, spin states, charge states and even chemical bond formation. The switching event can occur either on surfaces or in break junctions. The aim of this review is to highlight recent advances in molecular switches triggered by various external stimuli, as investigated by low-temperature scanning tunneling microscopy (LT-STM) and the break junction technique. We begin by presenting the molecular switches triggered by various external stimuli that do not provide single molecule selectivity, referred to as non-selective switching. Special focus is then given to selective single molecule switching realized using the LT-STM tip on surfaces. Single molecule switches operated by different mechanisms are reviewed and discussed. Finally, molecular switches embedded in self-assembled monolayers (SAMs) and single molecule junctions are addressed. PMID:25757483

  16. Physical activation of molecules

    A brief review of processes of physical activation of molecules on the basis of phenomena of electronic and vibrational excitation, electron polarization is presented. Consideration is given to activation by electron impact, photo-, magneto- and mechanoactivation, as well as to radiation activation, proceeding under the effect of high-power radiations (102-107 eV). The character of disturbance of molecules, participating in chemical reactions, under the effect of different types of ionizing radiation (α-particles, electrons, γ-quanta etc.) is discussed

  17. Prebiologically Important Interstellar Molecules

    Kuan, Y.-J.; Huang, H.-C.; Charnley, S. B.; Tseng, W.-L.; Snyder, L. E.; Ehrenfreund, P.; Kisiel, Z.; Thorwirth, S.; Bohn, R. K.; Wilson, T. L.

    2004-06-01

    Understanding the organic chemistry of molecular clouds, particularly the formation of biologically important molecules, is fundamental to the study of the processes which lead to the origin, evolution and distribution of life in the Galaxy. Determining the level of molecular complexity attainable in the clouds, and the nature of the complex organic material available to protostellar disks and the planetary systems that form from them, requires an understanding of the possible chemical pathways and is therefore a central question in astrochemistry. We have thus searched for prebiologically important molecules in the hot molecular cloud cores: Sgr B2(N-LMH), W51 e1/e2 and Orion-KL. Among the molecules searched: Pyrimidine is the unsubstituted ring analogue for three of the DNA and RNA bases. 2H-Azirine and Aziridine are azaheterocyclic compounds. And Glycine is the simplest amino acid. Detections of these interstellar organic molecular species will thus have important implications for Astrobiology. Our preliminary results indicate a tentative detection of interstellar glycine. If confirmed, this will be the first detection of an amino acid in interstellar space and will greatly strengthen the thesis that interstellar organic molecules could have played a pivotal role in the prebiotic chemistry of the early Earth.

  18. Atoms, Molecules, and Compounds

    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.

  19. Exotic helium molecules

    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 4He2(23S1-23P0) molecule, or a 4He2(23S1-23S1) 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 4He2(23S1-23S1) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime τ = (1.4 ± 0.3) μs is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  20. OMG: Open Molecule Generator

    Peironcely Julio E

    2012-09-01

    Full Text Available Abstract Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG, which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  1. Bacterial invasion reconstructed molecule by molecule

    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

  2. Molecules without electrons

    Electrons are the glue that holds the atoms in molecules together. Without them the positive charges of nuclei would repel each other, and the world would be a much simpler place. But in the quest to gain control over matter at a fundamental level, physicists in Russia and Canada have come up with a way of binding charged nuclei without any electrons. Instead the researchers use intense laser light. (U.K.)

  3. Atoms, molecules & elements

    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.

  4. Single Molecule Mechanochemistry

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

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

  5. Photonic Molecule Lasers Revisited

    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.

  6. Watching single molecules dance

    Mehta, Amit Dinesh

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

  7. Ultra-cold molecule production.

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

    2005-12-01

    The production of Ultra-cold molecules is a goal of many laboratories through out the world. Here we are pursuing a unique technique that utilizes the kinematics of atomic and molecular collisions to achieve the goal of producing substantial numbers of sub Kelvin molecules confined in a trap. Here a trap is defined as an apparatus that spatially localizes, in a known location in the laboratory, a sample of molecules whose temperature is below one degree absolute Kelvin. Further, the storage time for the molecules must be sufficient to measure and possibly further cool the molecules. We utilize a technique unique to Sandia to form cold molecules from near mass degenerate collisions between atoms and molecules. This report describes the progress we have made using this novel technique and the further progress towards trapping molecules we have cooled.

  8. Magnetic field modification of ultracold molecule-molecule collisions

    Tscherbul, T. V.; Suleimanov, Yu. V.; Aquilanti, V.; Krems, R.V.

    2008-01-01

    We present an accurate quantum mechanical study of molecule-molecule collisions in the presence of a magnetic field. The work focusses on the analysis of elastic scattering and spin relaxation in collisions of O2(3Sigma_g) molecules at cold (~0.1 K) and ultracold (~10^{-6} K) temperatures. Our calculations show that magnetic spin relaxation in molecule-molecule collisions is extremely efficient except at magnetic fields below 1 mT. The rate constant for spin relaxation at T=0.1 K and a magnet...

  9. Passing Current through Touching Molecules

    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...

  10. Efficient single molecule detection and single molecule photochemistry

    Affleck, R.L.; Ambrose, W.P.; Goodwin, P.M. [Los Alamos National Lab., NM (United States)] [and others

    1996-12-31

    Single molecule detection efficiencies greater than 90% in flowing sample streams can be attained by confining the sample to the center of the excitation laser beam and photobleaching the reagent stream immediately before it enters the detection flow cell. Photolysis of single molecules of B-Phycoerythrin dissolved in aqueous solution is observed as an abrupt cessation of the fluorescence from these molecules as they flow through {approximately}40 pl probe volume. An analysis of the survival times of individual molecules in the laser beams yields the photodestruction quantum yield of the molecule. Photon pair correlation measurements of the fluorescence detected from single B-PE molecules demonstrate that the molecule fluoresces from only one bilin chromophore at a time.

  11. Photochemistry of biological molecules

    Earlier studies of the photodamage induced by 254nm irradiation of linear alanine peptides in the solid state have been supplemented by an investigation into the gaseous photoproducts from the cyclic dipeptide, 3,6-dimethyl-2,5-diketopiperazine. The trans and cis isomers have been prepared and the photoproducts compared with those from the DL-mixture. The conformation of the molecule did influence the yield of gaseous products. CO was produced by peptide bond rupture with concomitant release of hydrogen. C02 was also produced. The use of N- and C-deuterated analogues together with relevant crystallographic and EPR data has enabled a detailed study of the mechanism of photodegradation to be made, from which it was concluded that the methyl protons are not inert but rather are the major source of the hydrogen observed on photolysis. (author)

  12. Forces in molecules.

    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? PMID:17328425

  13. Lanthanide single molecule magnets

    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...

  14. Lanthanide single molecule magnets

    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. Reactions of oriented molecules.

    Brooks, P R

    1976-07-01

    Beams of oriented molecules have been used to directly study geometrical requirements in chemical reactions. These studies have shown that reactivity is much greater in some orientations than others and demonstrated the existence of steric effects. For some reactions portions of the orientation results are in good accord with traditional views of steric hindrance, but for others it is clear that our chemical intuition needs recalibrating. Indeed, the information gained from simultaneously orienting the reactants and observing the scattering angle of the products may lead to new insights about the detailed mechanism of certain reactions. Further work must be done to extend the scope and detail of the studies described here. More detailed information is needed on the CH(3)I reaction and the CF(3)I reaction. The effects of alkyl groups of various sizes and alkali metals of various sizes are of interest. In addition, reactions where a long-lived complex is formed should be studied to see if orientation is important. Finally, it would be of interest to apply the technique to the sort of reactions that led to our interest in the first place: the S(N)2 displacements in alkyl halides where the fascinating Walden inversion occurs. PMID:17793988

  16. Molecule-based magnets

    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.

  17. Tunnelling of a molecule

    A quantum-mechanical description of tunnelling is presented for a one-dimensional system with internal oscillator degrees of freedom. The 'charged diatomic molecule' is frustrated on encountering a barrier potential by its centre of charge not being coincident with its centre of mass, resulting in transitions amongst internal states. In an adiabatic limit, the tunnelling of semiclassical coherent-like oscillator states is shown to exhibit the Hartman and Bueuttiker-Landauer times tH and tBL, with the time dependence of the coherent state parameter for the tunnelled state given by α(t) = α e-iω(t+Δt) , Δt = tH - itBL. A perturbation formalism is developed, whereby the exact transfer matrix can be expanded to any desired accuracy in a suitable limit. An 'intrinsic' time, based on the oscillator transition rate during tunnelling, transmission or reflection, is introduced. In simple situations the resulting intrinsic tunnelling time is shown to vanish to lowest order. In the general case a particular (nonzero) parametrisation is inferred, and its properties discussed in comparison with the literature on tunnelling times for both wavepackets and internal clocks. Copyright (1998) CSIRO Australia

  18. Organic Molecules in Meteorites

    Martins, Zita

    2015-08-01

    Carbonaceous meteorites are primitive samples from the asteroid belt, containing 3-5wt% organic carbon. The exogenous delivery of organic matter by carbonaceous meteorites may have contributed to the organic inventory of the early Earth. The majority (>70%) of the meteoritic organic material consist of insoluble organic matter (IOM) [1]. The remaining meteoritic organic material (Haber-Bosch type gas-grain reactions after the meteorite parent body cooled to lower temperatures [13, 14].The analysis of the abundances and distribution of the organic molecules present in meteorites helps to determine the physical and chemical conditions of the early solar system, and the prebiotic organic compounds available on the early Earth.[1] Cody and Alexander (2005) GCA 69, 1085. [2] Cronin and Chang (1993) in: The Chemistry of Life’s Origin. pp. 209-258. [3] Martins and Sephton (2009) in: Amino acids, peptides and proteins in organic chemistry. pp. 1-42. [4] Martins (2011) Elements 7, 35. [5] Botta et al. (2007) MAPS 42, 81. [6] Martins et al. (2015) MAPS, in press. [7] Cooper and Cronin (1995) GCA 59, 1003. [8] Glavin et al. (2006) MAPS. 41, 889. [9] Glavin et al. (2011) MAPS 45, 1948. [10] Elsila et al. (2005) GCA 5, 1349. [11] Glavin and Dworkin (2009) PNAS 106, 5487. [12] Pizzarello et al. (2003) GCA 67, 1589. [13] Chan et al. (2012) MAPS. 47, 1502. [14] Burton et al. (2011) MAPS 46, 1703.

  19. Thread bonds in molecules

    Ivlev, B

    2015-01-01

    Unusual chemical bonds are proposed. Each bond is almost covalent but is characterized by the thread of a small radius $\\sim 0.6\\times 10^{-11}$cm, between two nuclei in a molecule. The main electron density is concentrated outside the thread as in a covalent bond. The thread is formed by the electron wave function which has a tendency to be singular on it. The singularity along the thread is cut off by electron "vibrations" due to the interaction with zero point electromagnetic oscillations. The electron energy has its typical value of (1-10)eV. Due to the small tread radius the uncertainty of the electron momentum inside the thread is large resulting in a large electron kinetic energy $\\sim 1 MeV$. This energy is compensated by formation of a potential well due to the reduction of the energy of electromagnetic zero point oscillations. This is similar to formation of a negative van der Waals potential. Thread bonds are stable and cannot be created or destructed in chemical or optical processes.

  20. Strongly interacting ultracold polar molecules

    Gadway, Bryce; Yan, Bo

    2016-08-01

    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. Strongly interacting ultracold polar molecules

    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.

  2. Molecules Best Paper Award 2012

    Derek J. McPhee

    2012-02-01

    Full Text Available Molecules starts to institute the “Best Paper” award to recognize these outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published in Molecules. We are pleased to announce the first “Molecules Best Paper Award” for 2012. Nominations were selected by the editor-in-chief and selected editorial board members from all the papers published in 2008. [...

  3. Molecules Best Paper Award 2014

    Derek J. McPhee

    2014-01-01

    Full Text Available Molecules instituted some years ago a “Best Paper” award to recognize the most outstanding papers in the area of natural products, medicinal chemistry and molecular diversity published each year in Molecules. We are pleased to announce the third “Molecules Best Paper Award” for 2014. The winners were chosen by the Editor-in-Chief and selected editorial board members from among all the papers published in 2010. Reviews and research papers were evaluated separately.

  4. Molecules Best Paper Award 2013

    Derek J. McPhee

    2013-02-01

    Full Text Available 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. Candidates were chosen by the Editor-in-Chief and selected editorial board members from among all the papers published in 2009.

  5. Recoiling DNA Molecule: Simulation & Experiment

    Neto, Jose Coelho; Dickman, Ronald; Mesquita, O. N.

    2002-01-01

    Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between co...

  6. Labelled molecules, modern research implements

    Details of the synthesis of carbon 14- and tritium-labelled molecules are examined. Although the methods used are those of classical organic chemistry the preparation of carbon 14-labelled molecules differs in some respects, most noticeably in the use of 14CO2 which requires very special handling techniques. For the tritium labelling of organic molecules the methods are somewhat different, very often involving exchange reactions. The following are described in turn: the so-called Wilzbach exchange method; exchange by catalysis in solution; catalytic hydrogenation with tritium; reductions with borotritides. Some applications of labelled molecules in organic chemistry, biochemistry and pharmacology are listed

  7. STM investigation of surfactant molecules

    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.

  8. Molecules Best Paper Award 2015

    Derek J. McPhee

    2015-01-01

    Full Text Available Molecules instituted some years ago a “Best Paper” award to recognize the most outstanding papers in the area of organic synthesis, natural products, medicinal chemistry and molecular diversity published each year in Molecules. We are pleased to announce the third “Molecules Best Paper Award” for 2015. The winners were chosen by the Editor-in-Chief and selected editorial board members from among all the papers published in 2011. Reviews and research papers were evaluated separately. We are pleased to announce that the following eight papers have won the Molecules Best Paper Award for 2015:[...

  9. Aromatic molecules as spintronic devices

    In this paper, we study the spin-dependent electron transport through aromatic molecular chains attached to two semi-infinite leads. We model this system taking into account different geometrical configurations which are all characterized by a tight binding Hamiltonian. Based on the Green's function approach with a Landauer formalism, we find spin-dependent transport in short aromatic molecules by applying external magnetic fields. Additionally, we find that the magnetoresistance of aromatic molecules can reach different values, which are dependent on the variations in the applied magnetic field, length of the molecules, and the interactions between the contacts and the aromatic molecule

  10. Single-molecule magnet engineering

    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...

  11. When water molecules meet air

    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. Quantum transport through aromatic molecules

    In this paper, we study the electronic transport properties through aromatic molecules connected to two semi-infinite leads. The molecules are in different geometrical configurations including arrays. Using a nearest neighbor tight-binding approach, the transport properties are analyzed into a Green's function technique within a real-space renormalization scheme. We calculate the transmission probability and the Current-Voltage characteristics as a function of a molecule-leads coupling parameter. Our results show different transport regimes for these systems, exhibiting metal-semiconductor-insulator transitions and the possibility to employ them in molecular devices

  13. Theoretical Investigations Regarding Single Molecules

    Pedersen, Kim Georg Lind

    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...

  14. Polar molecule dominated electrorheological effect

    Lu Kun-Quan; Shen Rong; Wang Xue-Zhao; Sun Gang; Wen Wei-Jia; Liu Ji-Xing

    2006-01-01

    The yield stress of our newly developed electrorheological (ER) fluids consisting of dielectric nano-particles suspended in silicone oil reaches hundreds of kPa, which is orders of magnitude higher than that of conventional ones. We found that the polar molecules adsorbed on the particles play a decisive role in such new ER fluids. To explain this polar molecule dominated ER (PM-ER) effect a model is proposed based on the interaction of polar molecule-charge between the particles, where the local electric field is significantly enhanced and results in the polar molecules aligning in the direction of the electric field. The model can well explain the giant ER effect and a near-linear dependence of the yield stress on the electric field. The main effective factors for achieving high-performance PM-ER fluids are discussed. The PM-ER fluids with the yield stress higher than one MPa can be expected.

  15. Nuclear molecules with three clusters

    Full text: Recently, in the cold fusion of 252 Cf, indications where found for the existence of nuclear molecules with three clusters. The system identified is 96 Sr + 10 Be + 146 Ba. In the first half of the talk the geometric model for three-cluster molecules is resumed and calculations done are presented. Problems and restrictions of the geometric model will be discussed. In the second half an Ansatz for an algebraic model for nuclear molecules is given. In a first step we restrict to two clusters only, which might have an application to standard two-cluster molecules. A Hamiltonian is proposed. The mapping to a geometric potential is described, which is fitted to the calculation of internuclear potentials using double-folding techniques. (Author)

  16. Single-Molecule DNA Analysis

    Efcavitch, J. William; Thompson, John F.

    2010-07-01

    The ability to detect single molecules of DNA or RNA has led to an extremely rich area of exploration of the single most important biomolecule in nature. In cases in which the nucleic acid molecules are tethered to a solid support, confined to a channel, or simply allowed to diffuse into a detection volume, novel techniques have been developed to manipulate the DNA and to examine properties such as structural dynamics and protein-DNA interactions. Beyond the analysis of the properties of nucleic acids themselves, single-molecule detection has enabled dramatic improvements in the throughput of DNA sequencing and holds promise for continuing progress. Both optical and nonoptical detection methods that use surfaces, nanopores, and zero-mode waveguides have been attempted, and one optically based instrument is already commercially available. The breadth of literature related to single-molecule DNA analysis is vast; this review focuses on a survey of efforts in molecular dynamics and nucleic acid sequencing.

  17. Absorption characteristics of bacteriorhodopsin molecules

    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.

  18. Ultracold molecules and ultracold chemistry

    Softley, Tim; Bell, Martin

    2009-01-01

    Abstract The recent development of a range of new methods for producing samples of gas phase molecules that are translationally cold (T < 1 K) or ultracold (T < 1 mK) is driving efforts to study reactive and inelastic collisional processes in these temperature regimes. In this review article the new methods for cold/ultracold molecule production are reviewed in the context of their potential or current use in collisional studies and progress in the application of these methods i...

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

    Jovan Jose, K V; Raghavachari, Krishnan

    2016-02-01

    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. PMID:26760444

  20. Vibrational Circular Dichroism Spectra for Large Molecules through Molecules-in-Molecules Fragment-Based Approach.

    Jose, K V Jovan; Beckett, Daniel; Raghavachari, Krishnan

    2015-09-01

    We present the first implementation of the vibrational circular dichroism (VCD) spectrum of large molecules through the Molecules-in-Molecules (MIM) fragment-based method. An efficient projection of the relevant higher energy derivatives from smaller fragments to the parent molecule enables the extension of the MIM method for the evaluation of VCD spectra (MIM-VCD). The overlapping primary subsystems in this work are constructed from interacting fragments using a number-based scheme and the dangling bonds are saturated with link hydrogen atoms. Independent fragment calculations are performed to evaluate the energies, Hessian matrix, atomic polar tensor (APT), and the atomic axial tensor (AAT). Subsequently, the link atom tensor components are projected back onto the corresponding host and supporting atoms through the Jacobian projection method, as in the ONIOM approach. In the two-layer model, the long-range interactions between fragments are accounted for using a less computationally intensive lower level of theory. The performance of the MIM model is calibrated on the d- and l-enantiomers of 10 carbohydrate benchmark molecules, with strong intramolecular interactions. The vibrational frequencies and VCD intensities are accurately reproduced relative to the full, unfragmented, results for these systems. In addition, the MIM-VCD method is employed to predict the VCD spectra of perhydrotriphenylene and cryptophane-A, yielding spectra in agreement with experiment. The accuracy and performance of the benchmark systems validate the MIM-VCD model for exploring vibrational circular dichroism spectra of large molecules. PMID:26575919

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

    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

  2. Electron Collisions with Large Molecules

    McKoy, Vincent

    2006-10-01

    In recent years, interest in electron-molecule collisions has increasingly shifted to large molecules. Applications within the semiconductor industry, for example, require electron collision data for molecules such as perfluorocyclobutane, while almost all biological applications involve macromolecules such as DNA. A significant development in recent years has been the realization that slow electrons can directly damage DNA. This discovery has spurred studies of low-energy collisions with the constituents of DNA, including the bases, deoxyribose, the phosphate, and larger moieties assembled from them. In semiconductor applications, a key goal is development of electron cross section sets for plasma chemistry modeling, while biological studies are largely focused on understanding the role of localized resonances in inducing DNA strand breaks. Accurate calculations of low-energy electron collisions with polyatomic molecules are computationally demanding because of the low symmetry and inherent many-electron nature of the problem; moreover, the computational requirements scale rapidly with the size of the molecule. To pursue such studies, we have adapted our computational procedure, known as the Schwinger multichannel method, to run efficiently on highly parallel computers. In this talk, we will present some of our recent results for fluorocarbon etchants used in the semiconductor industry and for constituents of DNA and RNA. In collaboration with Carl Winstead, California Institute of Technology.

  3. Laser spectroscopy of cold molecules

    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.

  4. Technetium-aspirin molecule complexes

    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)

  5. Phase structure of soliton molecules

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

  6. Phase structure of soliton molecules

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

    2007-06-01

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

  7. Orbital molecules in electronic materials

    Attfield, J. Paul, E-mail: j.p.attfield@ed.ac.uk [Centre for Science at Extreme Conditions and School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9 3JZ (United Kingdom)

    2015-04-01

    Orbital molecules are made up of coupled orbital states on several metal ions within an orbitally ordered (and sometimes also charge-ordered) solid such as a transition metal oxide. Spin-singlet dimers are known in many materials, but recent discoveries of more exotic species such as 18-electron heptamers in AlV{sub 2}O{sub 4} and magnetic 3-atom trimerons in magnetite (Fe{sub 3}O{sub 4}) have shown that orbital molecules constitute a general new class of quantum electronic states in solids.

  8. Recoiling DNA Molecule Simulation & Experiment

    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.

  9. Teaching lasers to control molecules

    We simulate a method to teach a laser pulse sequences to excite specified molecular states. We use a learning procedure to direct the production of pulses based on ''fitness'' information provided by a laboratory measurement device. Over a series of pulses the algorithm learns an optimal sequence. The experimental apparatus, which consists of a laser, a sample of molecules and a measurement device, acts as an analog computer that solves Schroedinger's equation n/Iexactly, in real time. We simulate an apparatus that learns to excite specified rotational states in a diatomic molecule

  10. Exotic helium molecules; Molecules exotiques d'helium

    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)

  11. Multiphoton dissociation of polyatomic molecules

    The dynamics of infrared multiphoton excitation and dissociation of SF6 was investigated under collision free conditions by a crossed laser-molecular beam method. In order to understand the excitation mechanism and to elucidate the requirements of laser intensity and energy fluence, a series of experiments were carried out to measure the dissociation yield dependences on energy fluence, vibrational temperature of SF6, the pulse duration of the CO2 laser and the frequency in both one and two laser experiments. Translational energy distributions of the SF5 dissociation product measured by time of flight and angular distributions and the dissociation lifetime of excited SF6 as inferred from the observation of secondary dissociation of SF5 into SF4 and F during the laser pulse suggest that the dynamics of dissociation of excited molecules is dominated by complete energy randomization and rapid intramolecular energy transfer on a nanosecond timescale, and can be adequately described by RRKM theory. An improved phenomenological model including the initial intensity dependent excitation, a rate equation describing the absorption and stimulated emission of single photons, and the unimolecular dissociation of excited molecules is constructed based on available experimental results. The model shows that the energy fluence of the laser determines the excitation of molecules in the quasi-continuum and the excess energy with which molecules dissociate after the laser pulse. The role played by the laser intensity in multiphoton dissociation is more significant than just that of overcoming the intensity dependent absorption in the lowest levels. 63 references

  12. Tunneling Ionization of Diatomic Molecules

    Svensmark, Jens Søren Sieg

    2016-01-01

    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...

  13. Monitoring Molecules: Insights and Progress

    Wightman, R Mark

    2014-01-01

    In August, 2014, neuroscientists and physical scientists gathered together on the campus of the University of California, Los Angeles to discuss how to monitor molecules in neuroscience. This field has seen significant growth since its inception in the 1970s. Here, the advances in this field are documented, including its advance into understanding the actions that specific neurotransmitters mediate during behavior.

  14. Azobenzene-functionalized cascade molecules

    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 den...

  15. Engineering crystals of dendritic molecules.

    Lukin, Oleg; Schubert, Dirk; Müller, Claudia M; Schweizer, W Bernd; Gramlich, Volker; Schneider, Julian; Dolgonos, Grygoriy; Shivanyuk, Alexander

    2009-07-01

    A detailed single-crystal X-ray study of conformationally flexible sulfonimide-based dendritic molecules with systematically varied molecular architectures was undertaken. Thirteen crystal structures reported in this work include 9 structures of the second-generation dendritic sulfonimides decorated with different aryl groups, 2 compounds bearing branches of both second and first generation, and 2 representatives of the first generation. Analysis of the packing patterns of 9 compounds bearing second-generation branches shows that despite their lack of strong directive functional groups there is a repeatedly reproduced intermolecular interaction mode consisting in an anchor-type packing of complementary second-generation branches of neighbouring molecules. The observed interaction tolerates a wide range of substituents in meta- and para-positions of the peripheral arylsulfonyl rings. Quantum chemical calculations of the molecule-molecule interaction energies agree at the qualitative level with the packing preferences found in the crystalline state. The calculations can therefore be used as a tool to rationalize and predict molecular structures with commensurate and non-commensurate branches for programming of different packing modes in crystal. PMID:19549870

  16. Nucleic Acids as Information Molecules.

    McInerney, Joseph D.

    1996-01-01

    Presents an activity that aims at enabling students to recognize that DNA and RNA are information molecules whose function is to store, copy, and make available the information in biological systems, without feeling overwhelmed by the specialized vocabulary and the minutia of the central dogma. (JRH)

  17. Quantum interferometry with complex molecules

    Arndt, Markus; Hornberger, Klaus

    2009-01-01

    This chapter reviews recent experiments on matter wave interferometry with large molecules. Starting from an elementary introduction to matter wave physics we discuss far-field diffraction and near-field interferometry with thermally excited many-body systems. We describe the constraints imposed by decoherence and dephasing effects, and present an outlook to the future challenges in macromolecule and cluster interferometry.

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

    Van Dorp, Willem F.; Zhang, Xiaoyan; Feringa, Ben L.; Hansen, Thomas Willum; Wagner, Jakob Birkedal; De Hosson, Jeff Th. M.

    2012-01-01

    The resolution of lithography techniques needs to be extended beyond their current limits to continue the trend of miniaturization and enable new applications. But what is the ultimate spatial resolution? It is known that single atoms can be imaged with a highly focused electron beam. Can single...... atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor on...... graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated...

  19. Ballonet String Model of Molecules

    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.

  20. Electrochemical detection of single molecules.

    Fan, F R; Bard, A J

    1995-02-10

    The electrochemical behavior of a single molecule can be observed by trapping a small volume of a dilute solution of the electroactive species between an ultramicroelectrode tip with a diameter of approximately 15 nanometers and a conductive substrate. A scanning electrochemical microscope was used to adjust the tip-substrate distance ( approximately 10 nanometers), and the oxidation of [(trimethylammonio)methyl] ferrocene (Cp(2)FeTMA(+)) to Cp(2)FeTMA(2+) was carried out. The response was stochastic, and anodic current peaks were observed as the molecule moved into and out of the electrode-substrate gap. Similar experiments were performed with a solution containing two redox species, ferrocene carboxylate (Cp(2)FeCOO(-)) and Os(bpy)(3)(2+) (bpy is 2,2'-bipyridyl). PMID:17813918

  1. Observing electron motion in molecules

    We study analytically the possibility for monitoring electron motion in a molecule using two ultrashort laser pulses. The first prepares a coherent superposition of two electronic molecular states whereas the second (attosecond pulse) photoionizes the molecule. We show that interesting information about electron dynamics can be obtained from measurement of the photoelectron spectra as a function of the time delay between two pulses. In particular, asymmetries in photoelectron angular distribution provide a simple signature of the electron motion within the initial time-dependent coherently coupled two molecular states. Both asymmetries and electron spectra show very strong two-centre interference patterns. We illustrate these effects using as an example a dissociating hydrogen molecular ion probed by the attosecond pulses

  2. Nano trap for polar molecules

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

  3. Laser tunneling from aligned molecules

    Smeenk, C T L; Sokolov, A V; Spanner, M; Lee, K F; Staudte, A; Villeneuve, D M; Corkum, P B

    2013-01-01

    We study multi-photon ionization from N_2, O_2 and benzene using circularly polarized light. By examining molecular frame photo-electron angular distributions, we illustrate how multi-photon ionization acts a momentum-selective probe of the local electron density in the Dyson orbitals for these molecules. We find good agreement with calculations based on a tunneling model and including saturation effects.

  4. Metagenomic small molecule discovery methods

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

    2014-01-01

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

  5. Bioactive molecules from sea hares.

    Kamiya, H; Sakai, R; Jimbo, M

    2006-01-01

    Sea hares, belonging to the order Opisthobranchia, subclass Gastropoda, are mollusks that have attracted many researchers who are interested in the chemical defense mechanisms of these soft and "shell-less" snails. Numbers of small molecules of dietary origin have been isolated from sea hares and some have ecologically relevant activities, such as fish deterrent activity or toxicity. Recently, however, greater attention has been paid to biomedically interesting sea hare isolates such as dolastatins, a series of antitumor peptide/macrolides isolated from Dolabella auricularia. Another series of bioactive peptide/macrolides, as represented by aplyronines, have been isolated from sea hares in Japanese waters. Although earlier studies indicated the potent antitumor activity of aplyronines, their clinical development has never been conducted because of the minute amount of compound available from the natural source. Recent synthetic studies, however, have made it possible to prepare these compounds and analogs for a structure-activity relationship study, and started to uncover their unique action mechanism towards their putative targets, microfilaments. Here, recent findings of small antitumor molecules isolated from Japanese sea hares are reviewed. Sea hares are also known to produce cytotoxic and antimicrobial proteins. In contrast to the small molecules of dietary origin, proteins are the genetic products of sea hares and they are likely to have some primary physiological functions in addition to ecological roles in the sea hare. Based on the biochemical properties and phylogenetic analysis of these proteins, we propose that they belong to one family of molecule, the "Aplysianin A family," although their molecular weights are apparently divided into two groups. Interestingly, the active principles in Aplysia species and Dolabella auricularia were shown to be L-amino acid oxidase (LAAO), a flavin enzyme that oxidizes an alpha-amino group of the substrate with

  6. Simple molecules as complex systems.

    Furtenbacher, Tibor; Arendás, Péter; Mellau, Georg; Császár, Attila G

    2014-01-01

    For individual molecules quantum mechanics (QM) offers a simple, natural and elegant way to build large-scale complex networks: quantized energy levels are the nodes, allowed transitions among the levels are the links, and transition intensities supply the weights. QM networks are intrinsic properties of molecules and they are characterized experimentally via spectroscopy; thus, realizations of QM networks are called spectroscopic networks (SN). As demonstrated for the rovibrational states of H2(16)O, the molecule governing the greenhouse effect on earth through hundreds of millions of its spectroscopic transitions (links), both the measured and first-principles computed one-photon absorption SNs containing experimentally accessible transitions appear to have heavy-tailed degree distributions. The proposed novel view of high-resolution spectroscopy and the observed degree distributions have important implications: appearance of a core of highly interconnected hubs among the nodes, a generally disassortative connection preference, considerable robustness and error tolerance, and an "ultra-small-world" property. The network-theoretical view of spectroscopy offers a data reduction facility via a minimum-weight spanning tree approach, which can assist high-resolution spectroscopists to improve the efficiency of the assignment of their measured spectra. PMID:24722221

  7. Functional molecules in electronic circuits.

    Weibel, Nicolas; Grunder, Sergio; Mayor, Marcel

    2007-08-01

    Molecular electronics is a fascinating field of research contributing to both fundamental science and future technological achievements. A promising starting point for molecular devices is to mimic existing electronic functions to investigate the potential of molecules to enrich and complement existing electronic strategies. Molecules designed and synthesized to be integrated into electronic circuits and to perform an electronic function are presented in this article. The focus is set in particular on rectification and switching based on molecular devices, since the control over these two parameters enables the assembly of memory units, likely the most interesting and economic application of molecular based electronics. Both historical and contemporary solutions to molecular rectification are discussed, although not exhaustively. Several examples of integrated molecular switches that respond to light are presented. Molecular switches responding to an electrochemical signal are also discussed. Finally, supramolecular and molecular systems with intuitive application potential as memory units due to their hysteretic switching are highlighted. Although a particularly attractive feature of molecular electronics is its close cooperation with neighbouring disciplines, this article is written from the point of view of a chemist. Although the focus here is largely on molecular considerations, innovative contributions from physics, electro engineering, nanotechnology and other scientific disciplines are equally important. However, the ability of the chemist to correlate function with structure, to design and to provide tailor-made functional molecules is central to molecular electronics. PMID:17637951

  8. Water molecules orientation in surface layer

    Klingo, V. V.

    2000-08-01

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

  9. The neural cell adhesion molecule

    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...

  10. The molecule-metal interface

    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

  11. Dissociation Energies of Diatomic Molecules

    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.

  12. XUV ionization of aligned molecules

    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.

  13. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    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.

  14. Electric dipole moment of diatomic molecules

    The calculation of the electric dipole moment of diatomic molecules by the Variational Cellular Method is presented, discussed and compared with the semiempirical CNDO/2 method. The molecule HF is taken as example. It is also shown that the value of the electric dipole moment by the VCM improves considerably when the electronegativity of the atoms of the molecule is taken into account. (Author)

  15. Ultrafast electron diffraction from aligned molecules

    Centurion, Martin [Univ. of Nebraska, Lincoln, NE (United States)

    2015-08-17

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

  16. Optoelectronics of Molecules and Polymers

    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...

  17. Photoluminescence of a Plasmonic Molecule.

    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. PMID:26165983

  18. Photonic molecules and spectral engineering

    Boriskina, Svetlana V

    2012-01-01

    This chapter reviews the fundamental optical properties and applications of pho-tonic molecules (PMs) - photonic structures formed by electromagnetic coupling of two or more optical microcavities (photonic atoms). Controllable interaction between light and matter in photonic atoms can be further modified and en-hanced by the manipulation of their mutual coupling. Mechanical and optical tunability of PMs not only adds new functionalities to microcavity-based optical components but also paves the way for their use as testbeds for the exploration of novel physical regimes in atomic physics and quantum optics. Theoretical studies carried on for over a decade yielded novel PM designs that make possible lowering thresholds of semiconductor microlasers, producing directional light emission, achieving optically-induced transparency, and enhancing sensitivity of microcavity-based bio-, stress- and rotation-sensors. Recent advances in material science and nano-fabrication techniques make possible the realization of opt...

  19. Diamond Molecules Found in Petroleum

    Carlson, R. M. K.; Dahl, J. E. P.; Liu, S. G.; Olmstead, M. M.; Buerki, P. R.; Gat, R.

    We recently reported [1,2] the discovery and isolation of new members of the hydrogen-terminated diamond series, ˜1 to ˜2 nm sized higher diamondoids from petroleum. Crystallographic studies [1,2] revealed a wealth of diamond molecules that are nanometer-sized rods, helices, discs, pyramids, etc. Highly rigid, well-defined, readily derivatizable structures make them valuable molecular building blocks for nanotechnology. We now produce certain higher diamondoids in gram quantities. Although more stable than graphite particles of comparable size, higher diamondoids are extraordinarily difficult to synthesize. Attempts to synthesize them were abandoned in the 1980's. We examined extracts of diamond-containing materials synthesized by CO2 laser-induced gas-phase synthesis [3] and commercial CVD in an attempt to detect diamantane to undecamantane. However, high-sensitivity GCMS detected no diamondoids in these materials.

  20. Anti-cancer Lead Molecule

    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

  1. Symmetries in nuclei and molecules

    Recent progress in two different fronts is reported. First, the concept of bisection of a harmonic oscillator or hydrogen atom, used in the past in establishing the connection between U(3) and O(4), is generalized into multisection (trisection, tetra section, etc.). It is then shown that all symmetries of the N-dimensional anisotropic harmonic oscillator with rational ratios of frequencies (RHO), some of which are underlying the structure of superdeformed and hyperdeformed nuclei, can be obtained from the U(N) symmetry of the corresponding isotropic oscillator with the appropriate combination of multisections. Furthermore, it is seen that bisections of the N-dimensional hydrogen atom, which possesses an O(N+1) symmetry, lead to the U(N) symmetry, so that further multisections of the hydrogen atom lead to the symmetries of the N-dim RHO. The opposite is in general not true, i.e. multisections of U(N) do not lead to O(N+1) symmetries, the only exception being the occurrence of O(4) after the bisection of U(3). Second, it is shown that there is evidence that the recently observed in superdeformed nuclear bands δ I=4 bifurcation is also occurring in normal deformed bands of actinides and rare earths, in hyperdeformed nuclear bands, as well as in rotational bands of diatomic molecules. In addition there is evidence that a δ I=8 bifurcation, of the same order of magnitude as the δ I=4 one, is observed in superdeformed nuclear bands and rotational bands of diatomic molecules. (author)

  2. Stability of small exotic molecules

    Complete text of publication follows. Three and four unit-charge particles with different masses may form bound states depending on the mass ratios. The aim of this work is to find out how many particles of unit charges can be put together to form bound states. We explore the possibility of the formation of stable N = 5,6...-particle systems of unit charges. We use a variational approach, in which the trial function is constructed out of generalised Gaussians whose parameters are determined by stochastic sampling. For few-body bound states this method has been shown to produce accurate results. First we made calculations for the five-body system (m+, m-, m+, m-, M+) with 0 ≤ σ ≤ ∞, where σ = m/M. We found that the binding energy of the system is larger than the nearest threshold for 0 ≤ σ ≤ 1.81, so the system in this region of mass ratio is bound. In the case of the system (m+, m-, m-, M+, M+) we cannot find a bound state for σ = 0. For 1 ≤ σ ≤ ∞, however, the system is bound. By decreasing σ from σ = 1, the binding energy is reduced, and around σ = 0.4 the system dissociates into (m-, m-, M+, M+) plus m+. Some six-body systems are under study, and cases have been found both for the existence and non-existence of bound states. From this study we can learn, e.g. that an H2 molecule cannot bind a positron and the positronium molecule can bind a proton, but it cannot bind an electron, unless we make the extra electron non-identical with the others. By comparing systems formed by identical and non-identical particles, we can point out the role of the Pauli principle in reducing the binding energy. (author)

  3. Spin polarization effect of Ni2 molecule

    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.

  4. Spin polarization effect for Cr2 molecule

    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.

  5. Coordination programming of photofunctional molecules.

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

    2013-01-01

    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. PMID:23563859

  6. Coordination Programming of Photofunctional Molecules

    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.

  7. Single Molecule Studies of Chromatin

    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.

  8. Single-molecule stochastic resonance

    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...

  9. NMR of dielectrically oriented molecules

    General information on experimental aspects of EFNMR is given. It is shown that the complete 14N quadrupole tensor (qct) of pyridine and pyrimidine in the liquid state is accessible to EFNMR. Information obtained about 17O qct in liquid nitromethane, is compared with results from other techniques. The 33S qct in liquid sulfolane is investigated. The EFNMR results, combined with those from spin-lattice relaxation time measurements and from Hartree-Fock-Slater MO calculations, allowed the complete assignment of the 33S qct. The quadrupole coupling of both 10B and 11B in a carborane compound is investigated and, together with the results of spin-lattice relaxation time measurements, detailed information about the assignment of the boron qct's could be derived. EFNMR studies of apolar molecules are described. A limitation in EFNMR is the inhomogeneity (delta B) of the magnetic field, which is introduced by the use of non-spinning sample cells. A way out is the detection of zero quantum transitions, their widths being independent of delta B. The results and prospectives of this approach are shown for the simple three spin 1/2 system of acrylonitrile in which the small dipolar proton-proton couplings could be revealed via zero quantum transitions. (Auth.)

  10. NMR studies of oriented molecules

    Sinton, S.W.

    1981-11-01

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

  11. Observation of pendular butterfly Rydberg molecules

    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...

  12. Rotational Cooling of Trapped Polyatomic Molecules.

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

    2015-12-01

    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 (CH_{3}F) 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 (≈30  mK) 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. PMID:26684114

  13. Rotational cooling of trapped polyatomic molecules

    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.

  14. Broadband single-molecule excitation spectroscopy

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

    2016-01-01

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

  15. Laser cooling of a diatomic molecule

    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...

  16. Dynamics of a linear magnetic "microswimmer molecule"

    Babel, Sonja; Löwen, Hartmut; Menzel, Andreas M.

    2015-01-01

    In analogy to nanoscopic molecules that are composed of individual atoms, we consider an active "microswimmer molecule". It is built up from three individual magnetic colloidal microswimmers that are connected by harmonic springs and hydrodynamically interact with each other. In the ground state, they form a linear straight molecule. We analyze the relaxation dynamics for perturbations of this straight configuration. As a central result, with increasing self-propulsion, we observe an oscillat...

  17. Making "Operations" inside a Single Molecule

    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.

  18. Scanning tunneling microscopy of biological molecules

    Scanning Tunnelling Microscopy (STM) has been used to image a number of biological molecules including thrombospondin and glycoprotein 88 (GP88). In this paper, STM images which clearly resolve the morphology of these molecules are presented. Ultimately, it is hoped that STM will provide information about the interaction between these molecules after overcoming problems associated with sample preparation and reproducibility of results which are discussed. 4 refs., 2 figs

  19. Charge correlations in polaron hopping through molecules

    Schmidt, Benjamin B.; Hettler, Matthias H.; Schön, Gerd

    2009-01-01

    In many organic molecules the strong coupling of excess charges to vibrational modes leads to the formation of polarons, i.e., a localized state of a charge carrier and a molecular deformation. Incoherent hopping of polarons along the molecule is the dominant mechanism of transport at room temperature. We study the far-from-equilibrium situation where, due to the applied bias, the induced number of charge carriers on the molecule is high enough such that charge correlations become relevant. W...

  20. RNA Reactions One Molecule at a Time

    Tinoco, Ignacio; Chen, Gang; Qu, Xiaohui

    2010-01-01

    Much of the dynamics information is lost in bulk measurements because of the population averaging. Single-molecule methods measure one molecule at a time; they provide knowledge not obtainable by other means. In this article, we review the application of the two most widely used single-molecule methods—fluorescence resonance energy transfer (FRET) and force versus extension measurements—to several RNA reactions. First, we discuss folding/unfolding studies on a hairpin ribozyme that revealed m...

  1. Single-molecule recognition imaging microscopy

    Stroh, C.; Wang, H.; Bash, R.; B Ashcroft; Nelson, J.; Gruber, H; Lohr, D.; Lindsay, S M; Hinterdorfer, P.

    2004-01-01

    Atomic force microscopy is a powerful and widely used imaging technique that can visualize single molecules and follow processes at the single-molecule level both in air and in solution. For maximum usefulness in biological applications, atomic force microscopy needs to be able to identify specific types of molecules in an image, much as fluorescent tags do for optical microscopy. The results presented here demonstrate that the highly specific antibody–antigen interaction can be used to gener...

  2. Ultracold polar molecules near quantum degeneracy

    Ospelkaus, S.; Ni, K.-K.; de Miranda, M. H. G.; Neyenhuis, B.; Wang, D; Kotochigova, S.; Julienne, P. S.; Jin, D. S.; J. Ye

    2008-01-01

    We report the creation and characterization of a near quantum-degenerate gas of polar $^{40}$K-$^{87}$Rb molecules in their absolute rovibrational ground state. Starting from weakly bound heteronuclear KRb Feshbach molecules, we implement precise control of the molecular electronic, vibrational, and rotational degrees of freedom with phase-coherent laser fields. In particular, we coherently transfer these weakly bound molecules across a 125 THz frequency gap in a single step into the absolute...

  3. Production and Trapping of Ultracold Polar Molecules

    David, DeMille [Yale Univ., New Haven, CT (United States)

    2015-04-21

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

  4. Single-molecule pulling: phenomenology and interpretation

    Franco, Ignacio; Schatz, George C

    2012-01-01

    Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level processes that are familiar from our macroscopic thermodynamic experience. In this Chapter, we summarize the essential phenomenology that is typically observed during single-molecule pulling, provide a general statistical mechanical framework for the interpretation of the equilibrium force spectroscopy and illustrate how to simulate single-molecule pulling experiments using molecular dynamics.

  5. Electron-molecule interactions and their applications

    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

  6. Circularly Polarized Luminescence from Simple Organic Molecules.

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

    2015-09-21

    This article aims to show the identity of "circularly polarized luminescent active simple organic molecules" as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented. PMID:26136234

  7. Reactive scattering of halogen molecules

    A study of the endoergic, bimolecular reactions of F2 with I2, ICl, and HI in a crossed molecular beam experiment is described. The trihalogens IIF, ClIF, and HIF were directly observed as the products of these reactions. At high collision energies a second reactive channel producing IF becomes important. Product angular and velocity distributions show that this IF does not result from a four-center exchange reaction. Measured threshold energies for the formation of IIF, ClIF, and HIF yield lower bounds to the stabilities of these molecules, with respect to the separated atoms, of 69, 81, and 96 kcal/mole, respectively. Analysis of product center-of-mass angular distributions indicates that a slightly nonlinear approach is most effective in bringing about reaction to form the stable triatomic radical. Also described is a crossed molecular beam study of the Cl + Br2 → BrCl + Br reaction at collision energies from 6.8 to 17.7 kcal/mole. The results indicate that this reaction has the characteristics of an exoergic reaction on an attractive potential energy surface with early energy release. Reagent translational energy is very efficiently channeled into product internal energy. At high collision energy the reaction appears to approach the spectator stripping limit. Finally, a series of computer programs which can be used to carry out the requisite data analysis for crossed molecular beam reactive scattering experiments are described. These programs recover the reactive scattering center-of-mass flux distribution from the measured angular and velocity distributions of the products

  8. Submillimeter Spectroscopy of Hydride Molecules

    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.

  9. Spin polarization effect for Fe2 molecule

    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.

  10. Spin polarization effect for Tc2 molecule

    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.

  11. Molecule-oriented programming in Java

    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

  12. Controlled contact to a C-60 molecule

    Neel, N.; Kröger, J.; Limot, L.; Frederiksen, Thomas; Brandbyge, Mads

    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 to...

  13. Infrared emission from electronically excited biacetyl molecules

    Drent, E.; Kommandeur, J.

    1971-01-01

    The infrared emission of electronically excited biacetyl molecules in the gas phase at low pressure was observed. Some experimental details are given, and it is shown that the emission derives from biacetyl molecules in their triplet state. The emission is dependent on the wavelength of excitation.

  14. Single molecule fluorescence detection on functionalized surfaces

    Full text: The immobilization of organic molecules on surfaces is important for various applications in nanolithography and also essential in novel detectors for matter wave interferometry. We use fluorescence imaging up to the single molecule level to study the suppression of long-range surface diffusion of ZnTPP on pyridine functionalized surfaces. (author)

  15. Small azomethine molecules and their use in photovoltaic devices

    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

  16. Spin polarization effect for Co2 molecule

    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.

  17. The symmetry of single-molecule conduction.

    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. PMID:17115774

  18. Chemical principles of single-molecule electronics

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

    2016-03-01

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

  19. Small-molecule-dependent split aptamer ligation.

    Sharma, Ashwani K; Heemstra, Jennifer M

    2011-08-17

    Here we describe the first use of small-molecule binding to direct a chemical reaction between two nucleic acid strands. The reported reaction is a ligation between two fragments of a DNA split aptamer using strain-promoted azide-alkyne cycloaddition. Utilizing the split aptamer for cocaine, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of cocaine concentrations and is compatible with complex biological fluids such as human blood serum. Moreover, studies of split aptamer ligation at varying salt concentrations and using structurally similar analogues of cocaine have revealed new insight into the assembly and small-molecule binding properties of the cocaine split aptamer. The ability to translate the presence of a small-molecule target into the output of DNA ligation is anticipated to enable the development of new, broadly applicable small-molecule detection assays. PMID:21761903

  20. Extracting Models in Single Molecule Experiments

    Presse, Steve

    2013-03-01

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

  1. The Homology Relation between Molecules: a Revival of an Old Way for Classification of Molecules

    Dobrowolski, Jan Cz.

    2009-01-01

    The homology (homolo) relation between molecules was introduced. This relation is a generalization of an old idea of series of homologous compounds. The homolo relation operates on a molecule by removing all the structural fragments that are identical with a certain selected fragment. As a result a multiset of fragments is produced. It was shown that the homolo relation is an equivalence relation in a set of molecules. Thus, by choosing various reference fragments, the molecules can be classi...

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

    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...

  3. High Harmonic Generation from Rotationally Excited Molecules

    Lock, Robynne M.

    2011-12-01

    High harmonic generation (HHG) is understood through a three-step model. A strong laser field ionizes an atom or molecule. The free electron propagates in the laser field and may recombine with the atom or molecule leading to the generation of extreme ultraviolet or soft x-ray light at odd harmonics of the fundamental. Since the wavelength of the recombining electron is on the order of internuclear distances in molecules, HHG acts as a probe of molecular structure and dynamics. Conversely, control of the molecules leads to control of the properties (intensity, phase, and polarization) of the harmonic emission. Rotationally exciting molecules provides field-free molecular alignment at time intervals corresponding to fractions of the rotational period of the molecule. Alignment is necessary for understanding how the harmonic emission depends on molecular structure and alignment. Additionally, HHG acts as a probe of the rotational wavepackets. This thesis reports three experiments on HHG from rotationally excited molecules. Before we can use HHG as a probe of complex molecular dynamics or control harmonic properties through molecules, the harmonic emission from aligned, linear molecules must first be understood. To that end, the first experiment measures the intensity and phase of harmonics generated from N 2O and N2 near times of strong alignment revealing interferences during recombination. The second experiment demonstrates HHG as a sensitive probe of rotational wavepacket dynamics in CO2 and N2O, revealing new revival features not detected by any other probe. The final experiment focuses on understanding and controlling the polarization state of the harmonic emission. Generating elliptically polarized harmonics would be very useful for probing molecular and materials systems. We observe an elliptical dichroism in polarization-resolved measurements of the harmonic emission from aligned N2 and CO2 molecules, revealing evidence for electron-hole dynamics between the

  4. Search for complex organic molecules in space

    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.

  5. Spin polarization effect for Mn2 molecule

    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.

  6. Tuning the Magnetic Anisotropy of Single Molecules.

    Heinrich, Benjamin W; Braun, Lukas; Pascual, Jose I; Franke, Katharina J

    2015-06-10

    The magnetism of single atoms and molecules is governed by the atomic scale environment. In general, the reduced symmetry of the surrounding splits the d states and aligns the magnetic moment along certain favorable directions. Here, we show that we can reversibly modify the magnetocrystalline anisotropy by manipulating the environment of single iron(II) porphyrin molecules adsorbed on Pb(111) with the tip of a scanning tunneling microscope. When we decrease the tip-molecule distance, we first observe a small increase followed by an exponential decrease of the axial anisotropy on the molecules. This is in contrast to the monotonous increase observed earlier for the same molecule with an additional axial Cl ligand ( Nat. Phys. 2013 , 9 , 765 ). We ascribe the changes in the anisotropy of both species to a deformation of the molecules in the presence of the attractive force of the tip, which leads to a change in the d level alignment. These experiments demonstrate the feasibility of a precise tuning of the magnetic anisotropy of an individual molecule by mechanical control. PMID:25942560

  7. Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials.

    Mayhall, Nicholas J; Raghavachari, Krishnan

    2011-05-10

    We present a new extrapolated fragment-based approach, termed molecules-in-molecules (MIM), for accurate energy calculations on large molecules. In this method, we use a multilevel partitioning approach coupled with electronic structure studies at multiple levels of theory to provide a hierarchical strategy for systematically improving the computed results. In particular, we use a generalized hybrid energy expression, similar in spirit to that in the popular ONIOM methodology, that can be combined easily with any fragmentation procedure. In the current work, we explore a MIM scheme which first partitions a molecule into nonoverlapping fragments and then recombines the interacting fragments to form overlapping subsystems. By including all interactions with a cheaper level of theory, the MIM approach is shown to significantly reduce the errors arising from a single level fragmentation procedure. We report the implementation of energies and gradients and the initial assessment of the MIM method using both biological and materials systems as test cases. PMID:26610128

  8. Single molecule microscopy and spectroscopy: concluding remarks.

    van Hulst, Niek F

    2015-01-01

    Chemistry is all about molecules: control, synthesis, interaction and reaction of molecules. All too easily on a blackboard, one draws molecules, their structures and dynamics, to create an insightful picture. The dream is to see these molecules in reality. This is exactly what "Single Molecule Detection" provides: a look at molecules in action at ambient conditions; a breakthrough technology in chemistry, physics and biology. Within the realms of the Royal Society of Chemistry, the Faraday Discussion on "Single Molecule Microscopy and Spectroscopy" was a very appropriate topic for presentation, deliberation and debate. Undoubtedly, the Faraday Discussions have a splendid reputation in stimulating scientific debates along the traditions set by Michael Faraday. Interestingly, back in the 1830's, Faraday himself pursued an experiment that led to the idea that atoms in a compound were joined by an electrical component. He placed two opposite electrodes in a solution of water containing a dissolved compound, and observed that one of the elements of the compound accumulated on one electrode, while the other was deposited on the opposite electrode. Although Faraday was deeply opposed to atomism, he had to recognize that electrical forces were responsible for the joining of atoms. Probably a direct view on the atoms or molecules in his experiment would have convinced him. As such, Michael Faraday might have liked the gathering at Burlington House in September 2015 (). Surely, with the questioning eyes of his bust on the 1st floor corridor, the non-believer Michael Faraday has incited each passer-by to enter into discussion and search for deeper answers at the level of single molecules. In these concluding remarks, highlights of the presented papers and discussions are summarized, complemented by a conclusion on future perspectives. PMID:26606461

  9. Understanding Polymer Properties through Imaging of Molecules.

    Sheiko, Sergei

    2008-03-01

    The unique advantage of Scanning Probe Microscopy (SPM) is that it allows imaging of flexible polymer molecules, whose overall size and local curvature are below the optical resolution limit. The role of molecular visualization has grown to be especially profound with the synthesis of complex macromolecules whose structure is difficult to confirm using conventional techniques such as NMR and light scattering. This is especially true for molecules that are branched, heterogeneous, and polydisperse. Here, SPM images provide unambiguous proof of the molecular architecture along with accurate analysis of size, conformation, and ordering of molecules on surfaces. The unique advantage of SPM is that one obtains molecular dimensions in direct space. This offers more opportunities for statistical analysis including fractionation of molecules by size, branching topology, and chemical composition as well as sorting out the irrelevant species. Unlike molecular characterization of static molecules, it remains challenging to study molecules as they move and react on surfaces. We will discuss pioneering AFM studies of flowing monolayers one molecule at a time. Through use of AFM, the flow process was monitored over a broad range of length scales from the millimeter long precursor film all the way down to the movements of individual molecules within the film. Molecular imaging enabled independent measurements both the driving and frictional forces that control spreading rate. In these studies, one also discovered a new type of flow instability in polymer monolayers caused by flow-induced conformational transitions. Recently, molecular imaging has been successfully used to monitor adsorption-induced degradation of branched molecules. These experiments open an entirely new perspective in chemistry wherein the chemical bonds can be mechanically activated upon the physical contact of a macromolecule with a substrate. This research directly impacts coatings, lubrication, heterogeneous

  10. Imaging Cold Molecules on a Chip

    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. The MHC molecules of nonmammalian vertebrates

    Kaufman, J; Skjoedt, K; Salomonsen, J

    1990-01-01

    encoding polymorphic class I and class II molecules) and evidence for polymorphic class I and class II molecules in reptiles. However, many details differ from the mammals, and it is not clear whether these reflect historical accident or selection for different lifestyles or environment. For example, the...... ontogeny and the consequences for the immune system and survival of the animals. These animals also differ markedly in the level of MHC polymorphism. Another difference from mammals is the presence of previously uncharacterized molecules. In Xenopus and reptiles, there are two populations of class I alpha...

  12. Rotational cooling of trapped polyatomic molecules

    Glöckner, Rosa; Prehn, Alexander; 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 genera...

  13. Aligning molecules with intense nonresonant laser fields

    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....

  14. Tunable optical absorption in silicene molecules

    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.

  15. Handbook of single-molecule electronics

    Moth-Poulsen, Kasper

    2015-01-01

    Single-molecule electronics has evolved as a vibrant research field during the last two decades. The vision is to be able to create electronic components at the highest level of miniaturization-the single molecule. This book compiles and details cutting-edge research with contributions from chemists, physicists, theoreticians, and engineers. It covers all aspects of single-molecule electronics, from the theory through experimental realizations and the chemical synthesis of molecular components to the implementation of molecular components in future integrated circuits. This book describes in d

  16. Single Molecule Biophysics Experiments and Theory

    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

  17. Non-sequential double ionization of molecules

    Prauzner-Bechcicki, J S; Eckhardt, B; Zakrzewski, J; Prauzner-Bechcicki, Jakub S.; Sacha, Krzysztof; Eckhardt, Bruno; Zakrzewski, Jakub

    2004-01-01

    Double ionization of diatomic molecules by short linearly polarized laser pulses is analyzed. We consider the final stage of the ionization process, that is the decay of a highly excited two electron molecule, which is formed after re-scattering. The saddles of the effective adiabatic potential energy close to which simultaneous escape of electrons takes place are identified. Numerical simulations of the ionization of molecules show that the process can be dominated by either sequential or non-sequential events. In order to increase the ratio of non-sequential to sequential ionizations very short laser pulses should be applied.

  18. A Classification Scheme For Toroidal Molecules

    Berger, J; Berger, Jorge; Avron, Joseph E.

    1995-01-01

    We construct a class of periodic tilings of the plane, which corresponds to toroidal arrangements of trivalent atoms, with pentagonal, hexagonal and heptagonal rings. Each tiling is characterized by a set of four integers and determines a toroidal molecule. The tiling rules are motivated by geometric considerations and the tiling patterns are rich enough to describe a wide class of toroidal carbon molecules, with a broad range of shapes and numbers of atoms. The molecular dimensions are simply related to the integers that determine the tiling. The configurational energy and the delocalisation energy of several molecules obtained in this way were computed for Tersoff and H\\"uckel models. The results indicate that many of these molecules are not strained, and may be expected to be stable. We studied the influence of size on the H\\"{u}ckel spectrum: it bears both similarities and differences as compared with the case of tubules.

  19. Molecular junctions: Single-molecule contacts exposed

    Nichols, Richard J.; Higgins, Simon J.

    2015-05-01

    Using a scanning tunnelling microscopy-based method it is now possible to get an atomistic-level description of the most probable binding and contact configuration for single-molecule electrical junctions.

  20. Synaptic Cell Adhesion Molecules in Alzheimer's Disease

    Leshchyns'ka, Iryna

    2016-01-01

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

  1. Models, mysteries, and magic of molecules

    Boeyens, Jan CA

    2007-01-01

    Molecules have for a long time been of central importance in chemistry as the basis on which all new products and materials have been designed, developed and interpreted. Since the discovery and characterization of active biomolecules, biology has also been transformed into a molecular science. With the new developments of molecular devices, single-molecule spectroscopy, time-resolved x-ray diffraction and the study of mass-selected clusters in molecular beams, materials science and electronics may move in the same direction. The understanding of molecules and the dynamics of their transition between isolated and assembled states rests on three pillars: structure, activity and function. Enormous progress has been made in the experimental study of molecules by diffraction and spectroscopic analysis, directed at all three of the basic aspects. In the process molecular scientists have developed efficient working models in terms of which to design and interpret their experiments. A vital feature of such models is...

  2. Stochastic Models of Molecule Formation on Dust

    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

  3. The evolution of polymorphic compatibility molecules

    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

  4. Novel electrostatic trap for cold polar molecules

    Xu Xue-Yan; Ma Hui; Yin Jian-Ping

    2007-01-01

    We propose a novel scheme in which cold polar molecules are trapped by an electrostatic field generated by the combination of a pair of parallel transparent electrodes (i.e., two infinite transparent plates) and a ring electrode (i.e., a ring wire). The spatial distributions of the electrostatic fields from the above charged wire and the charged plates and the corresponding Stark potentials for cold CO molecules are calculated; the dependences of the trap centre position on the geometric parameters of the electrode are analysed. We also discuss the loading process of cold molecules from a cold molecular beam into our trap. This study shows that the proposed scheme is not only simple and convenient to trap, manipulate and control cold polar molecules in weak-field-seeking states, but also provides an opportunity to study cold collisions and collective quantum effects in a variety of cold molecular systems, etc.

  5. Global warming and SF6 molecule

    Gajević Jelena

    2006-01-01

    Full Text Available In this paper the basic SF6 molecule physical characteristics are given concerning its influence on global warming and green house effect. Absorption and relaxation characteristics of this molecule have been investigated within the frame of nonlinear molecule – strong laser field interaction in different gas mixtures. All experiments have been performed on a different gas mixture pressures to analyze and investigate relaxation and energy transfer characteristics of absorbing molecules and non-absorbing collision partners. To show the SF6 absorption and relaxation and energy transfer capability comparison between SF6 and C2H4 was given using the same experimental conditions and argon as a buffer gas. All measurement points and their calculated values presented in this paper have been obtained using the infrared-pulsed photoacoustics technique adopted for atmospheric and subatmospheric pressures.

  6. Sisyphus Cooling of Electrically Trapped Polyatomic Molecules

    Zeppenfeld, M; Glöckner, R; Prehn, A; Mielenz, M; Sommer, C; van Buuren, L D; Motsch, M; Rempe, G

    2012-01-01

    The rich internal structure and long-range dipole-dipole interactions establish polar molecules as unique instruments for quantum-controlled applications and fundamental investigations. Their potential fully unfolds at ultracold temperatures, where a plethora of effects is predicted in many-body physics, quantum information science, ultracold chemistry, and physics beyond the standard model. These objectives have inspired the development of a wide range of methods to produce cold molecular ensembles. However, cooling polyatomic molecules to ultracold temperatures has until now seemed intractable. Here we report on the experimental realization of opto-electrical cooling, a paradigm-changing cooling and accumulation method for polar molecules. Its key attribute is the removal of a large fraction of a molecule's kinetic energy in each step of the cooling cycle via a Sisyphus effect, allowing cooling with only few dissipative decay processes. We demonstrate its potential by reducing the temperature of about 10^6 ...

  7. Single-Molecule Studies in Live Cells

    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.

  8. Electron-impact-induced tryptophan molecule fragmentation

    In our investigation, we have studied the interactions of low-energy (<70 eV) electrons with tryptophan molecule belonging to the essential amino acids in order to probe the intrinsic properties of the molecule and trace its change(s) under the electron impact. The fragmentation of a gas-phase tryptophan molecule by low-energy electrons was studied both experimentally and theoretically. Various positively charged fragments were observed and analyzed. A special attention was paid to the energy characteristics of the ionic fragment yield. The geometrical parameters of the initial molecule rearrangement were also analyzed. The fragmentation observed was due to either a simple bond cleavage or more complex reactions involving molecular rearrangements

  9. Polyatomic molecules under intense femtosecond laser irradiation.

    Konar, Arkaprabha; Shu, Yinan; Lozovoy, Vadim V; Jackson, James E; Levine, Benjamin G; Dantus, Marcos

    2014-12-11

    Interaction of intense laser pulses with atoms and molecules is at the forefront of atomic, molecular, and optical physics. It is the gateway to powerful new tools that include above threshold ionization, high harmonic generation, electron diffraction, molecular tomography, and attosecond pulse generation. Intense laser pulses are ideal for probing and manipulating chemical bonding. Though the behavior of atoms in strong fields has been well studied, molecules under intense fields are not as well understood and current models have failed in certain important aspects. Molecules, as opposed to atoms, present confounding possibilities of nuclear and electronic motion upon excitation. The dynamics and fragmentation patterns in response to the laser field are structure sensitive; therefore, a molecule cannot simply be treated as a "bag of atoms" during field induced ionization. In this article we present a set of experiments and theoretical calculations exploring the behavior of a large collection of aryl alkyl ketones when irradiated with intense femtosecond pulses. Specifically, we consider to what extent molecules retain their molecular identity and properties under strong laser fields. Using time-of-flight mass spectrometry in conjunction with pump-probe techniques we study the dynamical behavior of these molecules, monitoring ion yield modulation caused by intramolecular motions post ionization. The set of molecules studied is further divided into smaller sets, sorted by type and position of functional groups. The pump-probe time-delay scans show that among positional isomers the variations in relative energies, which amount to only a few hundred millielectronvolts, influence the dynamical behavior of the molecules despite their having experienced such high fields (V/Å). High level ab initio quantum chemical calculations were performed to predict molecular dynamics along with single and multiphoton resonances in the neutral and ionic states. We propose the

  10. Spin polarization effect for Os2 molecule

    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.

  11. The coordination chemistry of saturated molecules

    Bercaw, John E.; Labinger, Jay A.

    2007-01-01

    Our understanding of bonding in transition metal complexes, as well as our ability to use that understanding in the synthesis and application of new species, has evolved over the last 100 years; and in some sense this special feature on the coordination chemistry of saturated molecules may be considered to represent its culmination. The nature of complexes between transition metal ions and neutral molecules such as ammonia was first correctly described by Werner around the beginning of the 20...

  12. Single Molecule Applications of Quantum Dots

    Rasmussen, Thomas Elmelund; Jauffred, Liselotte; Brewer, Jonathan R.;

    2013-01-01

    tracking single lipids in lipid bilayers, 4) two-photon fluorescence correlation spectroscopy of QDs and 5) optical trapping and excitation of single QDs. In all of these applications, the focus is on the single particle sensitivity level of QDs. The high applicability of QDs in live cell imaging...... experiments held together with the prospects in localization microscopy and single molecule manipulation experiments gave QDs a promising future in single molecule research....

  13. Dissociation of ultracold molecules with Feshbach resonances

    Dürr, Stephan; Volz, Thomas; Rempe, Gerhard

    2004-01-01

    Ultracold molecules are associated from an atomic Bose-Einstein condensate by ramping a magnetic field across a Feshbach resonance. The reverse ramp dissociates the molecules. The kinetic energy released in the dissociation process is used to measure the widths of 4 Feshbach resonances in 87Rb. This method to determine the width works remarkably well for narrow resonances even in the presence of significant magnetic-field noise. In addition, a quasi-mono-energetic atomic wave is created by ju...

  14. Properties of molecules in tunnel junctions

    Yeriskin, Irene

    2013-01-01

    Molecular tunnel junctions involve studying the behaviour of a single molecule sandwiched between metal leads. When a molecule makes contact with electrodes, it becomes open to the environment which can heavily influence its properties, such as electronegativity and electron transport. While the most common computational approaches remain to be single particle approximations, in this thesis it is shown that a more explicit treatment of electron interactions can be required. By studying an ope...

  15. Small Molecule Subgraph Detector (SMSD) toolkit

    Rahman Syed; Bashton Matthew; Holliday Gemma L; Schrader Rainer; Thornton Janet M

    2009-01-01

    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 S...

  16. Biological mechanisms, one molecule at a time

    Tinoco, Ignacio; Gonzalez, Ruben L.

    2011-01-01

    The last 15 years have witnessed the development of tools that allow the observation and manipulation of single molecules. The rapidly expanding application of these technologies for investigating biological systems of ever-increasing complexity is revolutionizing our ability to probe the mechanisms of biological reactions. Here, we compare the mechanistic information available from single-molecule experiments with the information typically obtained from ensemble studies and show how these tw...

  17. The Escape Rate of a Molecule

    Knauf, Andreas, E-mail: knauf@mi.uni-erlangen.de; Krapf, Markus [Universitaet Erlangen-Nuernberg, Department Mathematik (Germany)

    2010-06-15

    We show existence and give an implicit formula for the escape rate of the n-centre problem of celestial mechanics for high energies. Furthermore we give precise computable estimates of this rate. This exponential decay rate plays an important role especially in semiclassical scattering theory of n-atomic molecules. Our result shows that the diameter of a molecule is measurable in a (classical) high-energy scattering experiment.

  18. Vibrational spectroscopy of polar molecules with superradiance

    Lin, Guin-Dar; Yelin, Susanne F.

    2013-07-01

    We investigate cooperative phenomena and superradiance for vibrational transitions in polar molecule spectroscopy of high optical-depth samples. Such cooperativity comes from the build-up of inter-particle coherence through dipole-dipole interactions and leads to speed-up of decay processes. We compare our calculation to recent work and find very good agreement, suggesting that superradiant effects need to be taken into account in a wide variety of ultracold molecule experiments, including vibrational and rotational states.

  19. Electron affinities of atoms, molecules, and radicals

    We review briefly but comprehensively the theoretical, semiempirical and experimental methods employed to determine electron affinities (EAs) of atoms, molecules and radicals, and summarize the EA data obtained by these methods. The detailed processes underlying the principles of the experimental methods are discussed very briefly. It is, nonetheless, instructive to recapitulate the definition of EA and those of the related quantities, namely, the vertical detachment energy, VDE, and the vertical attachment energy, VAE. The EA of an atom is defined as the difference in total energy between the ground state of the neutral atom (plus the electron at rest at infinity) and its negative ion. The EA of a molecule is defined as the difference in energy between the neutral molecule plus an electron at rest at infinity and the molecular negative ion when both, the neutral molecules and the negative ion, are in their ground electronic, vibrational and rotational states. The VDE is defined as the minimum energy required to eject the electron from the negative ion (in its ground electronic and nuclear state) without changing the internuclear separation; since the vertical transition may leave the neutral molecule in an excited vibrational/rotational state, the VDE, although the same as the EA for atoms is, in general, different (larger than), from the EA for molecules. Similarly, the VAE is defined as the difference in energy between the neutral molecule in its ground electronic, vibrational and rotational states plus an electron at rest at infinity and the molecular negative ion formed by addition of an electron to the neutral molecule without allowing a change in the intermolecular separation of the constituent nuclei; it is a quantity appropriate to those cases where the lowest negative ion state lies above the ground states of the neutral species and is less or equal to EA

  20. Do triatomic molecules echo atomic periodicity?

    Hefferlin, R., E-mail: hefferln@southern.edu; Barrow, J. [Southern Adventist University, PO Box 370, Collegedale, Tennessee 37315 (United States)

    2015-03-30

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

  1. Single-molecule dynamics at variable temperatures

    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 temperatures is demonstrated: Electron transfer has been identified as a crucial step in the photodynamics of organic fluorophores, and long-term memory effects have been discovered in the relaxatio...

  2. Interfacial energies of systems of chiral molecules

    Braides, Andrea; Garroni, Andrea; Palombaro, Mariapia

    2016-01-01

    We consider a simple model for the assembly of chiral molecules in two dimensions driven by maximization of the contact area. We derive a macroscopic model described by a parameter taking nine possible values corresponding to the possible minimal microscopic patterns and modulated phases of the chiral molecules. We describe the overall behaviour by means of an interaction energy of perimeter type between such phases. This energy is a crystalline perimeter energy, highlighting preferred direct...

  3. Hadronic molecules in the heavy baryon spectrum

    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

  4. Modelling water molecules inside cyclic peptide nanotubes

    Tiangtrong, Prangsai; Thamwattana, Ngamta; Baowan, Duangkamon

    2016-03-01

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

  5. Bipolar Conductance Switching of Single Anthradithiophene Molecules.

    Borca, Bogdana; Schendel, Verena; Pétuya, Rémi; Pentegov, Ivan; Michnowicz, Tomasz; Kraft, Ulrike; Klauk, Hagen; Arnau, Andrés; Wahl, Peter; Schlickum, Uta; Kern, Klaus

    2015-12-22

    Single molecular switches are basic device elements in organic electronics. The pentacene analogue anthradithiophene (ADT) shows a fully reversible binary switching between different adsorption conformations on a metallic surface accompanied by a charge transfer. These transitions are activated locally in single molecules in a low-temperature scanning tunneling microscope . The switching induces changes between bistable orbital structures and energy level alignment at the interface. The most stable geometry, the "off" state, which all molecules adopt upon evaporation, corresponds to a short adsorption distance at which the electronic interactions of the acene rings bend the central part of the molecule toward the surface accompanied by a significant charge transfer from the metallic surface to the ADT molecules. This leads to a shift of the lowest unoccupied molecular orbital down to the Fermi level (EF). In the "on" state the molecule has a flat geometry at a larger distance from the surface; consequently the interaction is weaker, resulting in a negligible charge transfer with an orbital structure resembling the highest occupied molecular orbital when imaged close to EF. The potential barrier between these two states can be overcome reversibly by injecting charge carriers locally into individual molecules. Voltage-controlled current traces show a hysteresis characteristic of a bipolar switching behavior. The interpretation is supported by first-principles calculations. PMID:26580569

  6. Auxin biology revealed by small molecules.

    Ma, Qian; Robert, Stéphanie

    2014-05-01

    The plant hormone auxin regulates virtually every aspect of plant growth and development and unraveling its molecular and cellular modes of action is fundamental for plant biology research. Chemical genomics is the use of small molecules to modify protein functions. This approach currently rises as a powerful technology for basic research. Small compounds with auxin-like activities or affecting auxin-mediated biological processes have been widely used in auxin research. They can serve as a tool complementary to genetic and genomic methods, facilitating the identification of an array of components modulating auxin metabolism, transport and signaling. The employment of high-throughput screening technologies combined with informatics-based chemical design and organic chemical synthesis has since yielded many novel small molecules with more instantaneous, precise and specific functionalities. By applying those small molecules, novel molecular targets can be isolated to further understand and dissect auxin-related pathways and networks that otherwise are too complex to be elucidated only by gene-based methods. Here, we will review examples of recently characterized molecules used in auxin research, highlight the strategies of unraveling the mechanisms of these small molecules and discuss future perspectives of small molecule applications in auxin biology. PMID:24252105

  7. Self-Assemblies of novel molecules, VECAR

    Shrestha, Bijay; Kim, Hye-Young; Lee, Soojin; Novak, Brian; Moldovan, Dorel

    2015-03-01

    VECAR is a newly synthesized molecule, which is an amphiphilic antioxidant molecule that consists of two molecular groups, vitamin-E and Carnosine, linked by a hydrocarbon chain. The hydrocarbon chain is hydrophobic and both vitamin-E and Carnosine ends are hydrophilic. In the synthesis process, the length of the hydrophobic chain of VECAR molecules can vary from the shortest (n =0) to the longest (n =18), where n indicates the number of carbon atoms in the chain. We conducted MD simulation studies of self-assembly of VECAR molecules in water using GROMACS on LONI HPC resources. Our study shows that there is a strong correlation between the shape and atomistic structure of the self-assembled nano-structures (SANs) and the chain-length (n) of VECAR molecules. We will report the results of data analyses including the atomistic structure of each SANs and the dynamic and energetic mechanisms of their formation as function of time. In summary, both VECAR molecules of chain-length n =18 and 9 form worm-like micelles, which may be used as a drug delivery system. This research is supported by the Louisiana Board of Regents-RCS Grant (LEQSF(2012-15)-RD-A-19).

  8. Dissociation and Decay of Ultra-cold Sodium Molecules

    Mukaiyama, T.; Abo-Shaeer, J. R.; Xu, K.; Chin, J. K.; Ketterle, W.

    2003-01-01

    The dissociation of ultracold molecules is studied by ramping an external magnetic field through a Feshbach resonance. The observed dissociation energy shows non-linear dependence on the ramp speed and directly yields the strength of the atom-molecule coupling. In addition, inelastic molecule-molecule and molecule-atom collisions are characterized.

  9. Spin polarization effect for molecule Ta2

    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.

  10. Quantifying molecule-surface interactions using AFM-based single-molecule manipulation

    Tautz, F. S.; Wagner, C.; Temirov, R.; Fournier, N.; Green, M.; Esat, T.; Leinen, P.; Groetsch, A.; Ruiz, V. G.; Tkatchenko, A.; Li, C.; Muellen, K.; Rohlfing, M.

    2015-03-01

    Scanning probe microscopy plays an important role in the investigation of molecular adsorption. Promising, is the possibility to probe the molecule-surface interaction while tuning its strength through AFM tip-induced single-molecule manipulation. Here, we outline a strategy to achieve quantitative understanding of such manipulation experiments. The example of qPlus sensor based PTCDA molecule lifting experiments is used to demonstrate how different aspects of the molecule-surface interaction, namely the short-range adsorption potential, the asymptotic van der Waals potential, local chemical bonds which are the source of the surface corrugation, and molecule-molecule interactions can be measured with SPM and interpreted by the help of force-field simulations.

  11. Image Analysis of Defocused Single-molecule Images for Three-dimensional Molecule Orientation Studies

    Patra, D; Gregor, I.; Enderlein, J.

    2004-01-01

    An efficient algorithm for pattern matching has been developed based on least-squares analysis of fitting a discrete set of master patterns against measured images. This algorithm has been applied to determine three-dimensional molecule orientations in defocused single-molecule images. The developed algorithm exploits the excellent agreement between electrodynamic calculations of single-molecule emission and experimentally measured images. The procedure is found to be reliable and simple and ...

  12. Clusters of mobile molecules in supercooled water

    Giovambattista, Nicolas; Buldyrev, Sergey V.; Stanley, H. Eugene; Starr, Francis W.

    2005-07-01

    We study the spatially heterogeneous dynamics in water via molecular dynamics simulations using the extended simple point charge potential. We identify clusters formed by mobile molecules and study their properties. We find that these clusters grow in size and become more compact as temperature decreases. We analyze the probability density function of cluster size, and we study the cluster correlation length. We find that clusters appear to be characterized by a fractal dimension consistent with that of lattice animals. We relate the cluster size and correlation length to the configurational entropy, Sconf . We find that these quantities depend weakly on 1/Sconf . In particular, the linearity found between the cluster mass n* and 1/Sconf suggests that n* may be interpreted as the mass of the cooperatively rearranging regions that form the basis of the Adam-Gibbs approach to the dynamics of supercooled liquids. We study the motion of molecules within a cluster, and find that each molecule preferentially follows a neighboring molecule in the same cluster. Based on this finding we hypothesize that stringlike cooperative motion may be a general mechanism for molecular rearrangement of complex, as well as simple liquids. By mapping each equilibrium configuration onto its corresponding local potential energy minimum or inherent structure (IS), we are able to compare the mobile molecule clusters in the equilibrium system with the molecules forming the clusters identified in the transitions between IS. We find that (i) mobile molecule clusters obtained by comparing different system configurations and (ii) clusters obtained by comparing the corresponding IS are completely different for short time scales, but are the same on the longer time scales of diffusive motion.

  13. Electromechanical Properties of Single Molecule Devices

    Bruot, Christopher

    Understanding the interplay between the electrical and mechanical properties of single molecules is of fundamental importance for molecular electronics. The sensitivity of charge transport to mechanical fluctuations is a key problem in developing long lasting molecular devices. Furthermore, harnessing this response to mechanical perturbation, molecular devices which can be mechanically gated can be developed. This thesis demonstrates three examples of the unique electromechanical properties of single molecules. First, the electromechanical properties of 1,4-benzenedithiol molecular junctions are investigate. Counterintuitively, the conductance of this molecule is found to increase by more than an order of magnitude when stretched. This conductance increase is found to be reversible when the molecular junction is compressed. The current-voltage, conductance-voltage and inelastic electron tunneling spectroscopy characteristics are used to attribute the conductance increase to a strain-induced shift in the frontier molecular orbital relative to the electrode Fermi level, leading to resonant enhancement in the conductance. Next, the effect of stretching-induced structural changes on charge transport in DNA molecules is studied. The conductance of single DNA molecules with lengths varying from 6 to 26 base pairs is measured and found to follow a hopping transport mechanism. The conductance of DNA molecules is highly sensitive to mechanical stretching, showing an abrupt decrease in conductance at surprisingly short stretching distances, with weak dependence on DNA length. This abrupt conductance decrease is attributed to force-induced breaking of hydrogen bonds in the base pairs at the end of the DNA sequence. Finally, the effect of small mechanical modulation of the base separation on DNA conductance is investigated. The sensitivity of conductance to mechanical modulation is studied for molecules of different sequence and length. Sequences with purine-purine stacking

  14. Mining for Molecules in the Milky Way

    2008-06-01

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

  15. Conduction mechanisms and stability of single molecule nanoparticle/molecule/nanoparticle junctions

    Nanoparticle/molecule/nanoparticle dimer assemblies have been successfully trapped by dielectrophoresis across nanogap electrodes, enabling temperature dependent charge transport measurements through an oligomeric phenylene ethynylene molecule, and transition from direct tunnelling to Fowler-Nordheim tunnelling is observed at ∼1.5 V. Samples formed by dielectrophoresis show better contact stability than those formed by receding meniscus. The junction shows stable operation over several weeks in a vacuum, but current increases with time upon exposure to air, possibly due to the adsorbed water molecules near the molecule/gold nanoparticle contacts

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

    Hou, H [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

    1995-12-01

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

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

    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...

  18. Preparation and manipulation of molecules for fundamental physics tests

    Tarbutt, M. R.; Hudson, J. J.; Sauer, B. E.; Hinds, E. A.

    2008-01-01

    This paper is a chapter from an upcoming book on cold molecule physics. In it we describe techniques for the preparation and manipulation of cold molecules. We further describe techniques for applying said cold molecules to tests of fundamental physics.

  19. Quantum Computer Using Coupled Quantum Dot Molecules

    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...

  20. Ultracold polar molecules near quantum degeneracy.

    Ospelkaus, S; Ni, K K; de Miranda, M H G; Neyenhuis, B; Wang, D; Kotochigova, S; Julienne, P S; Jin, D S; Ye, J

    2009-01-01

    We report the creation and characterization of a near quantum-degenerate gas of polar 40K-87Rb molecules in their absolute rovibrational ground state. Starting from weakly bound heteronuclear KRb Feshbach molecules, we implement precise control of the molecular electronic, vibrational, and rotational degrees of freedom with phase-coherent laser fields. In particular, we coherently transfer these weakly bound molecules across a 125 THz frequency gap in a single step into the absolute rovibrational ground state of the electronic ground potential. Phase coherence between lasers involved in the transfer process is ensured by referencing the lasers to two single components of a phase-stabilized optical frequency comb. Using these methods, we prepare a dense gas of 4 x 10(4) polar molecules at a temperature below 400 nK. This fermionic molecular ensemble is close to quantum degeneracy and can be characterized by a degeneracy parameter of T/T(F) = 3. We have measured the molecular polarizability in an optical dipole trap where the trap lifetime gives clues to interesting decay mechanisms. Given the large measured dipole moment of the KRb molecules of 0.5 Debye, the study of quantum degenerate molecular gases interacting via strong dipolar interactions is now within experimental reach. PACS numbers: 37.10.Mn, 37.10.Pq. PMID:20151553

  1. Difference Raman spectroscopy of DNA molecules

    In this paper the micro-Raman spectra of calf DNA for different points of DNA sample have been recorded. The Raman spectra were made with help of difference Raman spectroscopy technique. Raman spectra were recorded with high spatial resolution from different points of the wet and dry samples in different spectral range (100÷4000cm−1) using two lasers: argon (514.5 nm) and helium -neon (632.8 nm). The significant differences in the Raman spectra for dry and wet DNA and for different points of DNA molecules were observed. The obtained data on difference Raman scattering spectra of DNA molecules may be used for identification of DNA types and for analysis of genetic information associated with the molecular structure of this molecule

  2. Complex Molecule Formation in Grain Mantles

    Hall, P

    2010-01-01

    Context: Complex molecules such as ethanol and dimethyl ether have been observed in a number of hot molecular cores and hot corinos. Attempts to model the molecular formation process using gas phase only models have so far been unsuccessful. Aims : To demonstrate that grain surface processing is a viable mechanism for complex molecule formation in these environments. Methods: A variable environment parameter computer model has been constructed which includes both gas and surface chemistry. This is used to investigate a variety of cloud collapse scenarios. Results: Comparison between model results and observation shows that by combining grain surface processing with gas phase chemistry complex molecules can be produced in observed abundances in a number of core and corino scenarios. Differences in abundances are due to the initial atomic and molecular composition of the core/corino and varying collapse timescales. Conclusions: Grain surface processing, combined with variation of physical conditions, can be reg...

  3. Collision data involving hydro-carbon molecules

    Hydro-carbon molecules are abundantly produced when graphites are used as internal wall materials of hydrogen plasmas and strongly influence properties of low temperature plasmas near the edges as well as those of high temperature plasmas at the center. In this report, following simple description of the production mechanisms of hydro-carbon molecules under the interactions between graphite and hydrogen plasma, the present status of collision data for hydro-carbon molecules by electron impact is discussed and the relevant data are summarized in a series of figures and tables. It should also be noted that, in addition to fusion plasmas, these hydrocarbon data compiled here are quite useful in other applications such as plasma chemistry and material processing. (author)

  4. Watching single protein molecules in action

    Heiðarsson, Pétur Orri

    . This knowledge-gap is partly due to our inability to unveil the details of folding mechanisms that can be buried in the ensemble-averaged output of traditional bulk methods. Single-molecule techniques have provided a perspective beyond the ensemble average and enable studying the folding trajectories...... of protein 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, with...

  5. Sample preparation for single molecule localization microscopy.

    Allen, John R; Ross, Stephen T; Davidson, Michael W

    2013-11-21

    Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations. PMID:24084850

  6. Organization of Lipid Molecules within Biomembranes

    M. Benhamou

    2008-01-01

    Full Text Available In this review, we report on the organization of lipid molecules forming biomembranes. More precisely, the question is how these amphiphiles phase separate under a change of a suitable parameter, like temperature, pressure or membrane environment. The mixture may undergo a lateral or transversal phase separations. This essentially depends on two principal factors, which are the structure (length of hydrocarbon chains of lipid molecules and the curvature asymmetry of membranes. When the former dominates, a lateral separation is then expected. In contrary, for those biomembranes of high curvature asymmetry, a vertical separation is rather observed. We examine the problem from a static (phase diagrams and kinetics (relaxation in time point of view. Finally, the discussion is also extended to the phase separation between lipid molecules and cholesterol in biomembranes (formation of rafts, between phospholipids and grafted polymers on liposomes, or between surfactant and its co-surfactant in bilayer systems.

  7. Photodissociation and excitation of interstellar molecules

    Apart from a rather long introduction containing some elementary astrophysics, quantum chemistry and spectroscopy and an incomplete, historical review of molecular observations, this thesis is divided into three sections. In part A, a rigorous quantum chemical and dynamical study is made of the photodissociation processes in the OH and HCl molecules. In part B, the cross sections obtained in part A are used in various astrophysical problems such as the study of the abundances of the OH and HCl molecules in interstellar clouds, the use of the OH abundance as a measure of the cosmic ray ionization rate, the lifetime of the OH radical in comets and the abundance of OH in the solar photosphere. Part C discusses the excitation of the C2 molecule under interstellar conditions, its use as a diagnostic probe of the temperature, density and strength of the radiation field in interstellar clouds. Quadrupole moments and oscillator strengths are analyzed. (Auth.)

  8. Single-molecule studies using magnetic traps.

    Lionnet, Timothée; Allemand, Jean-François; Revyakin, Andrey; Strick, Terence R; Saleh, Omar A; Bensimon, David; Croquette, Vincent

    2012-01-01

    In recent years, techniques have been developed to study and manipulate single molecules of DNA and other biopolymers. In one such technique, the magnetic trap, a single DNA molecule is bound at one end to a glass surface and at the other to a magnetic microbead. Small magnets, whose position and rotation can be controlled, pull on and rotate the microbead. This provides a simple method to stretch and twist the molecule. The system allows one to apply and measure forces ranging from 10(-3) to >100 pN. In contrast to other techniques, the force measurement is absolute and does not require calibration of the sensor. In this article, we describe the principle of the magnetic trap, as well as its use in the measurement of the elastic properties of DNA and the study of DNA-protein interactions. PMID:22194259

  9. Protein Scaffolding for Small Molecule Catalysts

    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.

  10. Single Molecule Sensitive FRET in Attoliter Droplets

    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...

  11. Multiphoton processes in isolated atoms and molecules

    The theory of coherent excitation of a multilevel quantum mechanical system is developed. Damping of the system is taken into account by the use of a density matrix formalism. General properties of the wave function and/or the density matrix are discussed. The physical implications for the behavior of the system are described, together with possible applications of the formalism, including the infrared multiphoton excitation of molecules, and optical pumping in alkali atoms. Experimental results are presented on the infrared multiphoton dissociation of molecules, followed by a discussion of the general features of this process. The experimental results were obtained using a crossed laser and molecular beam method, and the emphasis is on determining the properties of the dissociating molecule and the dissociation products. The dissociation process is shown to be described very well by the standard statistical theory (RRKM theory) of unimolecular reactions, a brief presentation of which is also included

  12. Observational astrochemistry: The quest for interstellar molecules

    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.

  13. A Nonvolatile Plasmonic Switch Employing Photochromic Molecules

    We demonstrate a surface plasmon-polariton (SPP) waveguide all-optical switch that combines the unique physical properties of small molecules and metallic (plasmonic) nanostructures. The switch consists of a pair of gratings defined in an aluminum film coated with a 65 nm thick layer of photochromic (PC) molecules. The first grating couples a signal beam consisting of free space photons to SPPs that interact effectively with the PC molecules. These molecules can reversibly be switched between transparent and absorbing states using a free space optical pump. In the transparent (signal 'on') state, the SPPs freely propagate through the molecular layer, and in the absorbing (signal 'off') state, the SPPs are strongly attenuated. The second grating serves to decouple the SPPs back into a free space optical beam, enabling measurement of the modulated signal with a far-field detector. In a preliminary study, the switching behavior of the PC molecules themselves was confirmed and quantified by surface plasmon resonance spectroscopy. The excellent (16%) overlap of the SPP mode profile with the thin layer of switching molecules enabled efficient switching with power densities of ∼6.0 mW/cm2 in 1.5 (micro)m x 8 (micro) m devices, resulting in plasmonic switching powers of 0.72 nW per device. Calculations further showed that modulation depths in access of 20 dB can easily be attained in optimized designs. The quantitative experimental and theoretical analysis of the nonvolatile switching behavior in this letter guides the design of future nanoscale optically or electrically pumped optical switches.

  14. Small Molecule Subgraph Detector (SMSD toolkit

    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/

  15. A toy model for a diatomic molecule

    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.

  16. Relativistic Scott correction for atoms and molecules

    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...... 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...

  17. Allosteric small-molecule kinase inhibitors

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

    2015-01-01

    Small-molecule kinase inhibitors are invaluable targeted therapeutics for the treatment of various human diseases, especially cancers. While the majority of approved and developed preclinical small-molecule inhibitors are characterized as type I or type II inhibitors that target the ATP......-binding pocket of kinases, the remarkable sequential and structural similarity among ATP pockets renders the selective inhibition of kinases a daunting challenge. Therefore, targeting allosteric pockets of kinases outside the highly conversed ATP pocket has been proposed as a promising alternative to overcome...

  18. Chemical activation of molecules during coordination

    Activation processes of N2, O2, NO molecules in transition metal complexes and electron reconstructions of coordination sphere of compounds, related with it, were considered on tha basis of single-parameter approximation of vibronic activation theory. A special attention is paid to CO molecule activation in carbonyl complexes of transition metals (V, Nb, Mo, W, Tc, Re, Ru and others) and lanthanides. The effect of metal oxidation degree, the nature of metal and ligand, complex structure on chemical activation processes is analyzed

  19. Organic- and molecule-based magnets

    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.

  20. Collisional Transitions in Interstellar Asymmetric Top Molecules

    Chandra, Suresh

    2012-07-01

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

  1. Single-molecule electrophoresis. Final report

    Castro, A.; Shera, E.B.

    1996-05-22

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

  2. Vibrational spectroscopy of polar molecules with superradiance

    Lin, Guin-Dar

    2013-01-01

    We investigate cooperative phenomena and superradiance for vibrational transitions in polar molecule spectroscopy when a high optical-depth (OD) sample is studied. Such cooperativity comes from the build-up of inter-particle coherence through dipole-dipole interactions and leads to the speed-up of decay process. We compare our calculation to recent work [Deiglmayr et al., Eur. Phys. J. D 65, 99 (2011)] and find very good agreement, suggesting that superradiant effects need to be included in a wide variety of ultracold molecule setups including vibrational and rotational states.

  3. Matter-wave interferometer for large molecules

    Brezger, B; Uttenthaler, S; Petschinka, J; Arndt, M; Zeilinger, Anton

    2002-01-01

    We demonstrate a near-field Talbot-Lau interferometer for C-70 fullerene molecules. Such interferometers are particularly suitable for larger masses. Using three free-standing gold gratings of one micrometer period and a transversally incoherent but velocity-selected molecular beam, we achieve an interference fringe visibility of 40 % with high count rate. Both the high visibility and its velocity dependence are in good agreement with a quantum simulation that takes into account the van der Waals interaction of the molecules with the gratings and are in striking contrast to a classical moire model.

  4. Photoassociative production of ultracold heteronuclear ytterbium molecules

    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.

  5. Extracellular Molecules Involved in Cancer Cell Invasion

    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.

  6. Scanning probe microscopy characterisation of immobilised enzyme molecules on a biosensor surface: visualisation of individual molecules

    JOE G. SHAPTER

    2004-02-01

    Full Text Available Scanning probe microscopy techniques were used to study immobilised enzyme molecules of glucose oxidase (GOD on a biosensor surface. The study was carried out in order to optimise atomic force microscopy (AFM imaging and reveal the molecular resolution of individual GOD molecules. Chemically modified AFM tips and the light tapping mode were found to be the optimal conditions for imaging soft biomolecules such as GOD. The information obtained from the AFM images included spatial distribution and organization of the enzyme molecules on the surface, surface coverage and shape, size and orientation of individual molecules. Two typical shapes of GOD molecules were found, spherical and butterfly, which are in accordance with the shapes obtained from scanning tunnelling microscopy (STM images. Using a model of the orientation of the GOD molecules on the surface, these shapes are assigned to the enzyme standing and lying on the surface. After AFM tip deconvolution, the size of the spherical shaped GOD molecules was found to be 12 ± 2.1 nm in diameter, whereas the butterfly shapes were 16.5 ± 3.3 nm ´10.2 ± 2.5 nm. Corresponding STM images showed smaller lateral dimensions of 10 ± 1 nm ´ 6 ± 1 nm and 6.5 ± 1 nm ´ 5 ± 1 nm. The disagreement between these two techniques is attributed to the deformation of the GOD molecules caused by the tapping process.

  7. Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

    Max Greenfeld

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

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

    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.

  9. Long-lived dipolar molecules and Feshbach molecules in a 3D optical lattice

    Chotia, Amodsen; Moses, Steven A; Yan, Bo; Covey, Jacob P; Foss-Feig, Michael; Rey, Ana Maria; Jin, Deborah S; Ye, Jun

    2011-01-01

    We have realized long-lived ground-state polar molecules in a 3D optical lattice, with a lifetime of up to 25 s, which is limited only by off-resonant scattering of the trapping light. Starting from a 2D optical lattice, we observe that the lifetime increases dramatically as a small lattice potential is added along the tube-shaped lattice traps. The 3D optical lattice also dramatically increases the lifetime for weakly bound Feshbach molecules. For a pure gas of Feshbach molecules, we observe a lifetime of >20 s in a 3D optical lattice; this represents a 100-fold improvement over previous results. This lifetime is also limited by off-resonant scattering, the rate of which is related to the size of the Feshbach molecule. Individually trapped Feshbach molecules in the 3D lattice can be converted to pairs of K and Rb atoms and back with nearly 100% efficiency.

  10. Self and directed assembly: people and molecules.

    James, Tony D

    2016-01-01

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

  11. Progress in Computational Electron-Molecule Collisions

    Rescigno, Tn

    1997-10-01

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

  12. Uranium-mediated activation of small molecules.

    Arnold, Polly L

    2011-08-28

    Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power. PMID:21614341

  13. Photoelectron spectroscopy of heavy atoms and molecules

    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

  14. Comprehensive Map of Molecules Implicated in Obesity.

    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.

  15. Comprehensive Map of Molecules Implicated in Obesity.

    Jagannadham, Jaisri; Jaiswal, Hitesh Kumar; Agrawal, Stuti; Rawal, Kamal

    2016-01-01

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

  16. Orbits in the H2O molecule

    Efstathiou, K; Contopoulos, G

    2001-01-01

    We study the forms of the orbits in a symmetric configuration of a realistic model of the H2O molecule with particular emphasis on the periodic orbits. We use an appropriate Poincare surface of section (PSS) and study the distribution of the orbits on this PSS for various energies. We find both orde

  17. Chiral Sensitivity in Electron-Molecule Interactions

    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.

  18. Electron attachment to the SF6 molecule

    Smirnov, B. M.; Kosarim, A. V.

    2015-09-01

    Various models for transition between electron and nuclear subsystems are compared in the case of electron attachment to the SF6 molecule. Experimental data, including the cross section of electron attachment to this molecule as a function of the electron energy and vibrational temperature, the rate constants of this process in swarm experiments, and the rates of the chemionization process involving Rydberg atoms and the SF6 molecule, are collected and treated. Based on the data and on the resonant character of electron capture into an autodetachment ion state in accordance with the Breit-Wigner formula, we find that intersection of the molecule and negative ion electron terms proceeds above the potential well bottom of the molecule with the barrier height 0.05-0.1 eV, and the transition between these electron terms has both the tunnel and abovebarrier character. The limit of small electron energies e for the electron attachment cross section at room vibrational temperature takes place at ɛ ≪ 2 meV, while in the range 2 meV ≪ ɛ ≪ 80 meV, the cross section is inversely proportional to ɛ. In considering the attachment process as a result of the interaction between the electron and vibrational degrees of freedom, we find the coupling factor f between them to be f = aT at low vibrational temperatures T with a ≈ 3 × 10-4 K-1. The coupling factor is independent of the temperature at T > 400 K.

  19. Molecules for Fluorescence Detection of Specific Chemicals

    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

  20. Prebiotic molecules and interstellar grain clumps

    It is stated that interstellar molecules detected by radioastronomical techniques in galactic clouds cover a wide range of types and complexities. Amongst the heaviest recently discovered is cyanodiacetylene. There have also been earlier detections of precursors to the simplest amino-acid, glycine and probably detections of polyoxymethylene polymers and co-polymers. A possible identification of organic molecules of even greater complexity is here discussed, together with implications for the commencement of biological activity. The large departures from thermodynamic equilibrium in the interstellar medium and the co-existence of solid grains, molecules, radicals, ions, and uv photons provide conditions that are ideal for production of 'exotic' molecular species. The effect of clumping of dust grains is discussed. The possible spectral identification of highly complex organic species in the interstellar medium is also discussed and reference is made to a property common to a wide class of such molecules, that is, an absorption band centered at 2,200 A. It is tempting to identify this feature with the well-known 2,200 A band of the interstellar extinction curve. It is thought that it may be tentatively concluded that the data so far obtained could be interpreted as independent new chemical evidence of the existence of composite grain clumps in the interstellar medium and in carbonaceous chondrites, and that these grain clumps probably include a significant mass fraction of highly complex organic pre-biotic molecules that could have led to the start and dispersal of biological activity on the Earth and elsewhere in the Galaxy. Processes of natural selection probably also played an important part, particularly in the production of self-replicable peptide chains. The problem of protection of pre-biotic material against external disruptive agencies, such as u/v light, is also discussed. (U.K.)

  1. Handbook of Single-Molecule Biophysics

    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...

  2. Is the focus on "molecules" obsolete?

    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. PMID:23772657

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

    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.

  4. Exploring $X(5568)$ as a meson molecule

    Agaev, S S; Sundu, H

    2016-01-01

    The parameters, i.e. the mass and decay constant of the exotic $X_b(5568)$ state newly observed by D0 Collaboration, as well as the decay width of the process $X_b \\to B_s^{0}\\pi^{+}$ are explored using $B\\overline{K}$ molecule assumption on its structure. Computational methods employed here encompass QCD two-point and light-cone sum rules, latter being considered in the soft-meson approximation. The obtained results are compared with the data of the D0 Collaboration, as well as with the predictions of the diquark-antidiquark model. This comparison strengthens the diquark-antidiquark picture for the $X_b(5568)$ state rather than a meson molecule structure.

  5. Imaging Genetic Molecules At Atomic Resolution

    Coles, L. Stephen

    1993-01-01

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

  6. Photochemical dynamics of surface oriented molecules

    The period 8/01/91-7/31/92 is the first year of a new project titled ''Photochemical Dynamics of Surface Oriented Molecules'', initiated with DOE Support. The main objective of this project is to understand the dynamics of elementary chemical reactions by studying photochemical dynamics of surface-oriented molecules. In addition, the mechanisms of photon-surface interactions need to be elucidated. The strategy is to carry out experiments to measure the translational energy distribution, as a function of the angle from the surface normal, of the photoproducts by time-of-flight (TOF) technique by varying the photon wavelength, intensity, polarization, and pulse duration. By choosing adsorbates with different bonding configuration, the effects of adsorbate orientation on surface photochemical dynamics can be studied

  7. - Fourier Transform Infrared Spectroscopy of Small - Molecules

    Li, G.; Bernath, P. F.

    2011-06-01

    A series of small boron-containing molecules were synthesized in the gas phase using a tube furnace. High-resolution spectra of these species were recorded in either emission or absorption in the mid-infrared region using a Bruker IFS-125HR spectrometer. Our observations contain vibration-rotation bands of BO, the V1 and V3 bands of HBO, the V1 and V3 bands of HBS, the V1 band of FBO, and the V1 band of HBF2. The vibrational bands of HOBO, BF2OH and other boron-containing molecules may also be present. Ab initio calculations were performed at the MRCI level to assist in the vibrational assignments. Preliminary assignments of the spectra for these species will be reported.

  8. Interstellar molecules - Formation in solar nebulae

    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.

  9. Chirally-sensitive electron-molecule interactions

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

    2015-09-01

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

  10. Photoassociative Excitation Spectroscopy of Excimer Molecules

    Jones, Ronald Blake

    Laser excitation spectroscopy of transitions having dissociative ground states was explored as a tool for the study of excimer molecules. Since the repulsive nature of the ground state constrains collision pairs to large internuclear transitions, bound >=ts free excitation spectra contain more structure than the bound to free fluorescence spectra for the same molecules, therefore containing more information about the potential surfaces. Unique properties of the photoassociative excitation spectroscopy technique are described which allow the dependence of the dipole transition moment on the internuclear separation (mu (R)) to be extracted in a very direct manner. Excitation spectra are presented for the B >=ts X transitions of KrF and XeI for the wavelength (lambda) interval 206 nm KrI are given. This work required the development of a tunable VUV source, which is described.

  11. Modelling proton transfer in water molecule chains

    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...

  12. Photoluminescence of a quantum-dot molecule

    The coherent coupling of quantum dots is a sensitive indicator of the energy and phase relaxation processes taking place in the nanostructure components. We formulate a theory of low-temperature, stationary photoluminescence from a quantum-dot molecule composed of two spherical quantum dots whose electronic subsystems are resonantly coupled via the Coulomb interaction. We show that the coupling leads to the hybridization of the first excited states of the quantum dots, manifesting itself as a pair of photoluminescence peaks with intensities and spectral positions strongly dependent on the geometric, material, and relaxation parameters of the quantum-dot molecule. These parameters are explicitly contained in the analytical expression for the photoluminescence differential cross section derived in the paper. The developed theory and expression obtained are essential in interpreting and analyzing spectroscopic data on the secondary emission of coherently coupled quantum systems

  13. Atomic Rydberg Reservoirs for Polar Molecules

    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.

  14. Artifacts in single-molecule localization microscopy.

    Burgert, Anne; Letschert, Sebastian; Doose, Sören; Sauer, Markus

    2015-08-01

    Single-molecule localization microscopy provides subdiffraction resolution images with virtually molecular resolution. Through the availability of commercial instruments and open-source reconstruction software, achieving super resolution is now public domain. However, despite its conceptual simplicity, localization microscopy remains prone to user errors. Using direct stochastic optical reconstruction microscopy, we investigate the impact of irradiation intensity, label density and photoswitching behavior on the distribution of membrane proteins in reconstructed super-resolution images. We demonstrate that high emitter densities in combination with inappropriate photoswitching rates give rise to the appearance of artificial membrane clusters. Especially, two-dimensional imaging of intrinsically three-dimensional membrane structures like microvilli, filopodia, overlapping membranes and vesicles with high local emitter densities is prone to generate artifacts. To judge the quality and reliability of super-resolution images, the single-molecule movies recorded to reconstruct the images have to be carefully investigated especially when investigating membrane organization and cluster analysis. PMID:26138928

  15. Vibrational and coherence dynamics of molecules

    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.

  16. Multichannel quantum defect theory for ro-vibrational transitions in ultracold molecule-molecule collisions

    Hazra, Jisha; Ruzic, Brandon P.; Balakrishnan, N.; Bohn, John L.

    2014-01-01

    Multichannel quantum defect theory (MQDT) has been widely applied to resonant and non-resonant scattering in a variety of atomic collision processes. In recent years, the method has been applied to cold collisions with considerable success, and it has proven to be a computationally viable alternative to full-close coupling (CC) calculations when spin, hyperfine and external field effects are included. In this paper, we describe a hybrid approach for molecule-molecule scattering that includes ...

  17. Femtosecond dynamics of molecules and clusters

    Baumert, Thomas,; Thalweiser, Rainer; Weiss, V.; Wiedenmann, Ernst; Gerber, Gustav

    1994-01-01

    The real-time dynamics of multiphoton ionization and fragmentation of molecules - Na_2 , Na_3 - and clusters - Na_n, Hg_n - has been studied in molecular beam experiments employing ion and electron spectroscopy together with femtosecond pump-probe techniques. Experiments with Na_2 and Na_3 reveal unexpected features of the dynamics of the absorption of several photons as seen in the one- and three dimensional vibrational wave packet motion in different potential surfaces and...

  18. Excitonic molecules in type-II superlattices

    Tsuchiya, T.; Katayama, S.; Ando, T.

    1998-01-01

    Excitonic molecules in GaAs/AlAs type-II superlattices are numerically investigated. In spite of large difference of electronic structures between type-II and type-I superlattices, variational calculations show that the configuration of particles is similar to that in type-I superlattices. This is because the layer width is smaller than the extent of excitonic wavefunctions in the direction parallel to the layers in the present superlattices.

  19. Isatin, a versatile molecule: studies in Brazil

    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)

  20. Field-free orientation of molecules

    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...... be generated after the turn-off of a state-of-the-art electromagnetic half-cycle pulse....

  1. Rotations and Vibrations of trinuclear molecules

    A model describing the rotations and vibrations of trinuclear molecules is presented. The treatment is made in the spirit of Bohr-Mottelson collective model of nucleus. The two-body interactions between the composing clusters are calculated assuming the density independent M3Y forces, supplemented by a phenomenological repulsive component. Under simplifying assumptions, such as linear chain quasi-equilibrium configuration and freezing of the contact point between the light cluster and the heavy clusters, analytical solutions are available. (authors)

  2. Development of proneurogenic, neuroprotective small molecules

    MacMillan, Karen S.; Naidoo, Jacinth; Liang, Jue; Melito, Lisa; Williams, Noelle S.; Morlock, Lorraine; Huntington, Paula J.; Estill, Sandi Jo; Longgood, Jamie; Becker, Ginger L.; McKnight, Steven L.; Pieper, Andrew A.; De Brabander, Jef K.; Ready, Joseph M.

    2011-01-01

    Degeneration of the hippocampus is associated with Alzheimer’s disease, and occurs very early in the progression of the disease. Current options for treating the cognitive symptoms associated with Alzheimer’s are inadequate, giving urgency to the search for novel therapeutic strategies. Pharmacologic agents that safely enhance hippocampal neurogenesis may provide new therapeutic approaches. We discovered the first synthetic molecule, named P7C3, which protects newborn neurons from apopotic ce...

  3. Small Molecule Library Synthesis Using Segmented Flow

    Thompson, Christina M.; Djuric, Stevan W.; Cross, Jeffrey L.; Irini Akritopoulou-Zanze; Poole, Jennifer L.

    2011-01-01

    Flow chemistry has gained considerable recognition as a simple, efficient, and safe technology for the synthesis of many types of organic and inorganic molecules ranging in scope from large complex natural products to silicon nanoparticles. In this paper we describe a method that adapts flow chemistry to the synthesis of libraries of compounds using a fluorous immiscible solvent as a spacer between reactions. The methodology was validated in the synthesis of two small heterocycle containing l...

  4. Femtosecond Photodissociation of Molecules Facilitated by Noise

    Singh, Kamal P.; Kenfack, Anatole; Rost, Jan M

    2007-01-01

    We investigate the dynamics of diatomic molecules subjected to both a femtosecond mid-infrared laser pulse and Gaussian white noise. The stochastic Schr\\"odinger equation with a Morse potential is used to describe the molecular vibrations under noise and the laser pulse. For weak laser intensity, well below the dissociation threshold, it is shown that one can find an optimum amount of noise that leads to a dramatic enhancement of the dissociation probability. The enhancement landscape which i...

  5. Colloquium: Quantum interference of clusters and molecules

    Hornberger, Klaus; Gerlich, Stefan; Haslinger, Philipp; Nimmrichter, Stefan; Arndt, Markus

    2011-01-01

    We review recent progress and future prospects of matter wave interferometry with complex organic molecules and inorganic clusters. Three variants of a near-field interference effect, based on diffraction by material nanostructures, at optical phase gratings, and at ionizing laser fields are considered. We discuss the theoretical concepts underlying these experiments and the experimental challenges. This includes optimizing interferometer designs as well as understanding the role of decoheren...

  6. Stepwise oscillatory circuits of a DNA molecule

    Xu, Kunming

    2009-01-01

    A DNA molecule is characterized by a stepwise oscillatory circuit where every base pair is a capacitor, every phosphate bridge is an inductance, and every deoxyribose is a charge router. The circuitry accounts for DNA conductivity through both short and long distances in good agreement with experimental evidence that has led to the identification of the so-called super-exchange and multiple-step hopping mechanisms. However, in contrast to the haphazard hopping and super-exchanging events, the...

  7. Single molecules as whispering galleries for electrons

    Reecht, G.; Bulou, H.; Schull, G.; Scheurer, F.

    2016-04-01

    Whispering gallery modes, well-known for acoustic and optical waves, have been shown recently for electrons in molecules on surfaces. The existence of such waves opens new possibilities for nanoelectronic devices. Here we propose a simple analytical textbook model which allows the main characteristic features of such electronic waves to be understood. The model is illustrated by two- and three-dimensional experimental situations.

  8. Imaging Cold Molecules on a Chip

    Marx, S.; Adu Smith, D.; Abel, M.; Zehentbauer, T.; Meijer, G.J.M.; Santambrogio, G.

    2013-01-01

    We present the integrated imaging of cold molecules in a microchip environment. The on-chip detection is based on resonance-enhanced multiphoton ionization, which is quantum state selective and generally applicable. We demonstrate 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 molecular ensemble with a view to future high-resolution spectroscopic studies. Th...

  9. Bringing Molecules Back into Molecular Evolution

    Wilke, Claus O.

    2012-01-01

    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 a...

  10. TBD Resistence mechanisms and small molecules

    Corneila Zumbrunn

    2015-01-01

    The bacterial topoisomerases Gyrase and Topoisomerase IV are well validated targets in antibiotic research and discovery. Fluoroquinolones (eg. Ciprofloxacin) are potent inhibitors of these targets and are an important weapon in the battle against infections. Unfortunately their utility has lately been limited due to emerging resistance. Over the last years several companies have discovered molecules that inhibit topoisomerases by a novel mode of action and are therefore devoid of cross-resis...

  11. Sisyphus Cooling of Electrically Trapped Polyatomic Molecules

    Zeppenfeld, M.; Englert, B. G. U.; Glöckner, R.; Prehn, A; Mielenz, M; Sommer, C.; van Buuren, L. D.; Motsch, M.; Rempe, G.

    2012-01-01

    The rich internal structure and long-range dipole-dipole interactions establish polar molecules as unique instruments for quantum-controlled applications and fundamental investigations. Their potential fully unfolds at ultracold temperatures, where a plethora of effects is predicted in many-body physics, quantum information science, ultracold chemistry, and physics beyond the standard model. These objectives have inspired the development of a wide range of methods to produce cold molecular en...

  12. Vibrational spectroscopy of polar molecules with superradiance

    Lin, Guin-Dar; Yelin, Susanne F.

    2013-01-01

    We investigate cooperative phenomena and superradiance for vibrational transitions in polar molecule spectroscopy when a high optical-depth (OD) sample is studied. Such cooperativity comes from the build-up of inter-particle coherence through dipole-dipole interactions and leads to the speed-up of decay process. We compare our calculation to recent work [Deiglmayr et al., Eur. Phys. J. D 65, 99 (2011)] and find very good agreement, suggesting that superradiant effects need to be included in a...

  13. Caspr2 : possible synaptogenic cell adhesion molecule

    Do, Trinh Thuy

    2011-01-01

    Synapses are crucial for communication among neurons in the central nervous system. Contactin-associated protein- like 2 (Caspr2) is a neuronal protein that is a member of the neurexin superfamily and is found in the juxtaparanodal regions of myelinated axons. Caspr2 has also been found in synapses and therefore is also thought to function as a cell adhesion molecule. As such, it should also induce synaptogenesis in vitro similar to the interaction between neurexins (located presynaptically) ...

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

    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.

  15. Circular Intensity Differential Scattering of chiral molecules

    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.

  16. Matter-wave interferometer for large molecules

    Brezger, B.; Hackermüller, L.; Uttenthaler, S.; Petschinka, J.; Arndt, M.; Zeilinger, A.

    2002-01-01

    We demonstrate a near-field Talbot-Lau interferometer for C-70 fullerene molecules. Such interferometers are particularly suitable for larger masses. Using three free-standing gold gratings of one micrometer period and a transversally incoherent but velocity-selected molecular beam, we achieve an interference fringe visibility of 40 % with high count rate. Both the high visibility and its velocity dependence are in good agreement with a quantum simulation that takes into account the van der W...

  17. Dipole-Dipole coupled double Rydberg molecules

    Kiffner, Martin; Park, Hyunwook; Li, Wenhui; Gallagher, Tom F.

    2012-01-01

    We show that the dipole-dipole interaction between two Rydberg atoms can give rise to long range molecules. The binding potential arises from two states that converge to different separated atom asymptotes. These states interact weakly at large distances, but start to repel each other strongly as the van der Waals interaction turns into a resonant dipole-dipole interaction with decreasing separation between the atoms. This mechanism leads to the formation of an attractive well for one of the ...

  18. Electron correlation in molecules and condensed phases

    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

  19. Single Molecule Data Analysis: An Introduction

    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.

  20. Electrical transport through individual DNA molecules

    Li, Xin-Qi; Yan, YiJing

    2001-01-01

    A theoretical study is presented to quantitatively analyze the transport experiment through individual DNA molecules reported recently by Porath {\\it et al.} [Nature {\\bf 403}, 635 (2000)]. A variety of valuable quantities are identified by contacting the theoretical model with the measured data. The partially decoherent nature on the GC pairs of DNA is elaborated in contrast to the completely incoherent hopping mechanism discussed in the context of charge transfer experiments.

  1. Electron attachment to the phthalide molecule

    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.

  2. Quantum Optics of Ultra-Cold Molecules

    Meiser, D.; Miyakawa, T.; Uys, H.; Meystre, P.

    Quantum optics has been a major driving force behind the rapid experimental developments that have led from the first laser cooling schemes to the Bose-Einstein condensation (BEC) of dilute atomic and molecular gases. Not only has it provided experimentalists with the necessary tools to create ultra-cold atomic systems, but it has also provided theorists with a formalism and framework to describe them: many effects now being studied in quantum-degenerate atomic and molecular systems find a very natural explanation in a quantum optics picture. This article briefly reviews three such examples that find their direct inspiration in the trailblazing work carried out over the years by Herbert Walther, one of the true giants of that field. Specifically, we use an analogy with the micromaser to analyze ultra-cold molecules in a double-well potential; study the formation and dissociation dynamics of molecules using the passage time statistics familiar from superradiance and superfluorescence studies; and show how molecules can be used to probe higher-order correlations in ultra-cold atomic gases, in particular bunching and antibunching.

  3. Small molecule-guided thermoresponsive supramolecular assemblies

    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.

  4. J-factors of short DNA molecules.

    Zoli, Marco

    2016-06-01

    The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain end boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length (N) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales. PMID:27276942

  5. Single-Molecule Imaging of Cellular Signaling

    De Keijzer, Sandra; Snaar-Jagalska, B. Ewa; Spaink, Herman P.; Schmidt, Thomas

    Single-molecule microscopy is an emerging technique to understand the function of a protein in the context of its natural environment. In our laboratory this technique has been used to study the dynamics of signal transduction in vivo. A multitude of signal transduction cascades are initiated by interactions between proteins in the plasma membrane. These cascades start by binding a ligand to its receptor, thereby activating downstream signaling pathways which finally result in complex cellular responses. To fully understand these processes it is important to study the initial steps of the signaling cascades. Standard biological assays mostly call for overexpression of the proteins and high concentrations of ligand. This sets severe limits to the interpretation of, for instance, the time-course of the observations, given the large temporal spread caused by the diffusion-limited binding processes. Methods and limitations of single-molecule microscopy for the study of cell signaling are discussed on the example of the chemotactic signaling of the slime-mold Dictyostelium discoideum. Single-molecule studies, as reviewed in this chapter, appear to be one of the essential methodologies for the full spatiotemporal clarification of cellular signaling, one of the ultimate goals in cell biology.

  6. Driving Organic Molecule Crystalliztion with Surface Reconstructions

    Bickel, Jessica; Trovato, Gianfranco

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

  7. Stark quantum beat spectroscopy of polyatomic molecules

    We derive analytical expressions for Stark quantum beat signals of polyatomic molecules and discuss them with regard to molecular and geometrical parameters. The general treatment is specified for near prolate asymmetric rotor molecules and a method for determining rotational constants and all components of the dipole moment of electronically excited polyatomic molecules is presented. The method is tested and illustrated for the vibrationless S1 state of deuterated propynal (HCtriple bondCCDO, Cs symmetry) and its lowest frequency non-totally symmetric state 121. The results of the vibrationless state are compared with structural data reported in the literature. For the 121 state we obtain A=1.5004(43) cm-1, B=0.16131(34) cm-1, C=0.14623(34) cm-1, and the components of the electric dipole moment in the molecular plane μa=-0.88(2) D, μb=1.03(2) D. Furthermore, it is shown that the modulation depth of Stark quantum beat signals can be utilized to quantify the contribution of the individual components of the transition moment to the total emission. (orig.)

  8. Rescattering photoelectron spectroscopy of small molecules

    Highlights: • We extracted DCSs of electron scattering from ions using electron spectroscopy. • Detail of the extraction procedure of DCS from the experiment is presented. • Experimentally extracted DCSs are compared with ab initio calculations. • Factorization model of rescattering is confirmed for molecules experimentally. - Abstract: We have measured angle-resolved rescattering photoelectron spectra of three small molecules (O2, CO2, and C2H4) using intense near-infrared laser pulses at several laser intensities. Based on the factorization formula for rescattering processes, we have extracted, from the electron spectra, the field-free differential cross sections of elastic electron scattering by the molecular ions. The detail of the extraction procedure is described. The experimentally extracted differential cross sections are compared with theoretical calculations of the field-free differential cross sections. Fairly good agreement between the experimentally extracted and theoretically calculated DCSs for wide range of the collision momentum indicates the validity of the present extraction procedure for the molecules

  9. Single- and multiphoton ionization processes in molecules

    This dissertation is theoretical in nature and can be separated into two main areas: (1) single- and multiphoton ionization studies of a novel photoelectron effect, and (2) single-photon ionization studies of simple clusters as models for adsorbate photoemission. The first area centers on the phenomenon of circular dichroism in photoelectron angular distributions (CDAD). CDAD is shown to exist from oriented linear molecules, adsorbed atoms, and aligned atoms and molecules in the gas phase. The calculations presented here are the first to demonstrate the experimental feasability of CDAD studies. CDAD is shown to be a measureable effect which exists because the photoelectron collection direction can break the symmetry of these otherwise highly symmetric systems. As a direct results of the work presented here, CDAD has now been observed experimentally. Coupled with resonantly enhanced multiphoton ionization (REMPI), CDAD is shown to be a powerful probe of unknown alignment in gas phase atomic and molecular samples. The second area of research focuses on the simple oriented molecules NiCO and NiN2 as models for the corresponding adsorbate systems. These simple models provide insight into features observed in the experimental angle-resolved photoemission spectra

  10. Designing a small molecule erythropoietin mimetic.

    Guarnieri, Frank

    2015-01-01

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

  11. Heavy Exotic Molecules with Charm and Bottom

    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.

  12. [Aerodynamic focusing of particles and heavy molecules

    By accelerating a gas containing suspended particles or large molecules through a converging nozzle, the suspended species may be focused and therefore used to write fine lines on a surface. Our objective was to study the limits on how narrow this focal region could be as a function of particle size. We find that, for monodisperse particles with masses mp some 3.6 x 105 times larger than the molecular mass m of the carrier gas (diameters above some 100 angstrom), there is no fundamental obstacle to directly write submicron features. However, this conclusion has been verified experimentally only with particles larger than 0.1 μm. Experimental, theoretical and numerical studies on the defocusing role of Brownian motion for very small particles or heavy molecules have shown that high resolution (purely aerodynamic) focusing is impossible with volatile molecules whose masses are typically smaller than 1000 Dalton. For these, the minimal focal diameter after optimization appears to be 5√(m/mp) times the nozzle diameter dn. But combinations of focused lasers and aerodynamic focusing appear as promising for direct writing with molecular precursors. Theoretical and numerical schemes capable of predicting the evolution of the focusing beam, including Brownian motion effects, have been developed, although further numerical work would be desirable. 11 refs

  13. Biomedical applications of single molecule detection

    Kelso, D. M.

    1997-05-01

    The search for increased sensitivity of bio-analytical techniques has recently shifted from signal generation to detection. While enzyme amplifiers and chemiluminescent reporters developed by chemists over the last two decades gradually moved detection limits to the attomol level, it has taken engineers only a few years to reach single- molecule sensitivity with the development of new instrumentation. A number of different approaches have successfully achieved single-molecule fluorescence detection including confocal and near-field scanning optical microscopy, photon-counting cameras, fluorescence- correlation and time-gated spectroscopy. They detect labels immobilized on substrates, diffusing in solution and flowing in electro-osmotic and hydrodynamically focused streams. Biotechnology has created numerous application s for single- molecule detection. In research labs, it can dramatically increase the rate of DNA sequencing, screen libraries for products of directed evolution, and characterize compounds in drug discovery programs. In medical diagnostics, ultra- sensitive detection technologies can be used for genetic screening, detection of infectious diseases, or multi- analyte profiles. It can be applied to immunoassays as well as DNA or RNA hybridization assays.

  14. Electron attachment to the phthalide molecule

    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

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

    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...

  16. Single Molecule Studies on Dynamics in Liquid Crystals

    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.

  17. Oligomer Molecules for Efficient Organic Photovoltaics.

    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

  18. Energy distribution in dissociations of polyatomic molecules

    In this thesis studies are reported of fragmentation processes in polyatomic molecules. In order to find out which dessocaciation reactions take place, how they are brought about by the internal energy of the reactant, and to investigate the structure of the dissociating 'transition state', the fragment mass and the corresponding kinetic energy release (KER) are determined by differential translational spectroscopy using a position and time sensitive two-particle coincidence detector. The results are interpreted using the statistical theory of unimolecular dissociation. It turns out that the standard assumptions of the theory, especially in calculating KER-distributions, are not realistic in all molecules considered. Dissociation is induced by the neutralization with alkali metal vapour. In ch. 2 the experimental method and the analysis of the data (dissociation pathways, branching ratios and ε-d-distributions) are introduced and exemplified by measurements of cyclohexane, which represents the upper limit in precursor and fragment mass accessible in the apparatus. In ch. 3 a study is reported of the molecules methylchloride (CH3Cl) and the acetylradical (CH3CO). In spite of their similar geometric structures, completely different dissociation mechanisms have been found. Methylchloride dissociates via a repulsive state; acetyl radicals show energy scrambling. The energy distribution from dissociating acetyl exemplifies dynamical effects in the dissociation. In ch. 4 an investigation of a number of prototype hydrocarbons is presented. The dissociation pathways of several small linear alkanes indicate that neutralization takes place to unknown repulsive potentials, of which the position and steepness are determined from the kinetic energy release. (author). 118 refs.; 40 figs.; 5 tabs

  19. Raman scattering mediated by neighboring molecules

    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.

  20. A New Interstellar Cyclic Molecule, Ethylene Oxide

    Dickens, J. E.; Irvine, W. M.; Ohishi, M.; Ikeda, M.; Ishikawa, S.; Nummelin, A.; Hjalmarson, A.

    1997-12-01

    Ethylene oxide (c-C2H4O) is only the fourth known ring molecule identified in the interstellar medium, detected in the Galactic Center cloud SgrB2(N) by Dickens et al. (1997). It is the higher energy isomer of both the more familiar interstellar species acetaldehyde (CH3CHO) and the as yet undetected molecule vinyl alcohol (CH2CHOH). Dickens et al. (1997) reported a c-C2H4O molecular column density about an order of magnitude less than that reported for CH3CHO in SgrB2(N). This is a factor of 200 larger than the predictions of the new standard gas phase chemistry model of Lee, Bettens, and Herbst (1996), suggesting that the formation of c-C2H4O may be related to molecular formation on interstellar grains. We present observations of the c-C2H4O to CH3CHO abundance ratio in 5 additional molecular clouds. The data were taken in October 1997 with the Swedish-European Submillimeter Telescope in Chile. The confirmation of ethylene oxide in molecular clouds provides an appealing scenario for the first link in the chain of reactions leading to the origin of life, since it has been suggested as a possible pathway to the formation of the related cyclic molecule oxiranecarbonitrile (c-C3H3NO; cf., Dickens et al. 1996), a precursor to the synthesis of sugar phosphates which comprise the backbone of our molecular genetic structure. References: Dickens, J.E., Irvine, W.M., Ohishi, M., Ikeda, M., Ishikawa, S., Nummelin, A., and Hjalmarson, A. 1997, Astrophys. J., 489 (in press). Dickens, J.E. et al. 1996, Orig. Life Evol. Biosphere, 26, 97. Lee, H.-H., Bettens, R.P.A., and Herbst, E. 1996, Astron. Astrophys. Supp., 119, 111.

  1. Transport properties of individual C60-molecules

    Géranton, G.; Seiler, C.; Bagrets, A.; Venkataraman, L.; Evers, F.

    2012-01-01

    Electrical and thermal transport properties of C60 molecules are investigated with density-functional-theory based calculations. These calculations suggest that the optimum contact geometry for an electrode terminated with a single-Au atom is through binding to one or two C-atoms of C60 with a tendency to promote the sp2-hybridization into an sp3-type one. Transport in these junctions is primarily through an unoccupied molecular orbital that is partly hybridized with the Au, which results in ...

  2. Humidity Effects on Conductivity of DNA Molecules

    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.

  3. Tunnel magnetoresistance of an organic molecule junction

    Coherent spin-dependent electronic transport is investigated in a molecular junction based on oligophenylene attached to two the semi-infinite ferromagnetic (FM) electrodes with finite cross sections. The work is based on the tight-binding Hamiltonian model and within the framework of a non-equilibrium Green's function (NEGF) technique. It is shown that tunnel magnetoresistance (TMR) of molecular junction can be large (over 60 %) by adjusting the related parameters, and depends on: (i) the applied voltages and (ii) the length of oligophenylele molecule.

  4. Molecular-beam spectroscopy of interhalogen molecules

    A molecular-beam electric-resonance spectrometer employing a supersonic nozzle source has been used to obtain hyperfine spectra of 79Br35Cl. 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

  5. Chiral control of electron transmission through molecules.

    Skourtis, Spiros S; Beratan, David N; Naaman, Ron; Nitzan, Abraham; Waldeck, David H

    2008-12-01

    Electron transmission through chiral molecules induced by circularly polarized light can be very different for mirror-image structures, a peculiar fact given that the electronic energy spectra of the systems are identical. We propose that this asymmetry--as large as 10% for resonant transport--arises from different dynamical responses of the mirrored structures to coherent excitation. This behavior is described in the context of a general novel phenomenon of current transfer (transfer of charge with its momentum information) and accounts for the observed asymmetry and its dependence on structure. PMID:19113598

  6. Inorganic Nanoparticles Conjugated with Biofunctional Molecules

    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...

  7. Heavy Meson Molecules in Effective Field Theory

    AlFiky, Mohammad T.; Gabbiani, Fabrizio; Petrov, Alexey A.

    2006-01-01

    We consider the implications from the possibility that the recently observed state X(3872) is a meson-antimeson molecule. We write an effective Lagrangian consistent with the heavy-quark and chiral symmetries needed to describe X(3872). We explore the consequences of the assumption that X(3872) is a molecular bound state of D^{*0} and anti-D^0 mesons for the existence of bound states in the D^0-anti-D^0 and D^{*0}-anti-D^{*0}.

  8. Optical spectroscopy of ultra cold molecules

    Supersonic free jets of helium expanded from 100 atm into a vacuum of 10-2 torr permit the cooling of molecules seeded into the flow. There are a relatively large number of two-body collisions and a relatively small number of three body collisions in these expansions. Those processes which are easily accomplished by two body collisions such as translational and rotational energy exchange substantially equilibrate with the carrier gas temperature. Those processes that are not easily accomplished by two body collisions or require three body collisions such as vibrational-translational energy exchange or condensation will not equilibrate with the carrier gas temperature. (Auth.)

  9. Collective effects in Single Molecule Magnets

    Subedi, Pradeep

    Single molecule magnets (SMMs), such as Mn12-acetate, are composed of transition metal ions and consists of identical molecules with large ground-state spin (S = 10) and a strong uniaxial anisotropy (65 K). Below about 3 K, Mn12-acetate exhibits magnetic hysteresis with steps at specific values of longitudinal magnetic field due to resonant quantum tunneling between spin up and down projections along the easy axis. The intermolecular exchange interactions between spins on molecules are quite small and spins are considered to be independent and non-interacting. However, the molecules do interact with each other both through magnetic dipolar interactions and through the lattice (e.g. phonons). I have investigated collective effects in SMMs due to these intermolecular interactions. In the thesis I will present experiments that explored magnetic ordering due to magnetic dipole interactions in Mn12-acetate and Mn12-acetate-MeOH. I will also present exper- iments on the onset of magnetic de agration in Mn12-acetate due to a thermal instability. The magnetic ordering studies involved investigating the effect of transverse fields on the susceptibility of single crystals of Mn12-acetate and Mn12-acetate- MeOH. Transverse fields increase quantum spin uctuations that suppress long- range order. However, the suppression of the Curie temperature by transverse fields in Mn12-acetate is far more rapid than predicted by the Transverse-Field Ising Ferromagnetic Model (TFIFM) and instead agrees with the predictions of the Random-Field Ising Ferromagnet Model. It appears that solvent disorder in Mn12-acetate gives rise to a distribution of random-fields that further suppress long-range order. Subsequent studies on Mn12-acetate-MeOH, with the same spin and similar lattice constants but without solvent disorder as Mn12-acetate, agrees with the TFIFM. The magnetic de agration studies involved studying the instability that leads to the ignition of magnetic deflagration in a thermally

  10. Small-Molecule Target Engagement in Cells.

    Schürmann, Marc; Janning, Petra; Ziegler, Slava; Waldmann, Herbert

    2016-04-21

    Monitoring how, when, and where small molecules engage their targets inside living cells is a critical step in chemical biology and pharmacological research, because it enables compound efficacy and confirmation of mode of action to be assessed. In this mini-review we summarize the currently available methodologies to detect and prove direct target engagement in cells and offer a critical view of their key advantages and disadvantages. As the interest of the field shifts toward discovery and validation of high-quality agents, we expect that efforts to develop and refine these types of methodologies will also intensify in the near future. PMID:27049669

  11. Bringing molecules back into molecular evolution.

    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.

  12. Photonic molecules formed by coupled hybrid resonators

    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.

  13. Gaseous Electronics Tables, Atoms, and Molecules

    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,

  14. The (e,2e) reaction in molecules

    The aplication of the (e,2e) technique is discussed in the framework of (e,2e) on molecular hydrogen. It is shown that the technique is sufficiently sensitive to distinguish between simple wavefunctions and those containing configuration interactions. By comparing the data on H2 and D2 is shown that the Born-Oppenheimer approximation is confirmed to an accuracy of about 3 per cent. The data is also used to contrast other methods of determining electron momentum distributions in molecules. Data on methane, carbon monoxide and molecular nitrogen is also presented. (author)

  15. Single cell analysis of signaling molecules

    Klepárník, Karel; Luksch, Jaroslav; Adamová, Eva; Potáčová, Anna; Matalová, E.; Foret, František

    Grupo VLS Print Solution, 2014 - (Guzman, N.; Taveres, M.). s. 49-49 [International Symposium on Electro- and Liquid Phase-Separation Techniques /21./ and Latin-American Symposium on Biotechnology, Biomedical, Biopharmaceutical, and Industrial Applications of Capillary Electrophoresis and Microchip Technology /21./. 04.10.2014-08.10.2014, Natal] R&D Projects: GA ČR(CZ) GA14-28254S Institutional support: RVO:68081715 ; RVO:67985904 Keywords : single cell analysis * signaling molecules * caspase Subject RIV: CB - Analytical Chemistry, Separation

  16. Aging-From molecules to populations

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

    2008-01-01

    The mean age of the human population is steadily increasing in many areas around the globe, a phenomenon with large social, political, economic and biological/medical implications. Inevitably, this phenomenon is stimulating great interest in understanding and potentially modulating the process of......-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...

  17. Inelastic Collisions and Chemical Reactions of Molecules at Ultracold Temperatures

    Quéméner, Goulven; Balakrishnan, Naduvalath; Dalgarno, Alexander

    2010-01-01

    This paper summarizes the recent theoretical works on inelastic collisions and chemical reactions at cold and ultracold temperatures involving neutral or ionic systems of atoms and molecules. Tables of zero-temperature rate constants of various molecules are provided.

  18. Formation of Ultracold NaRb Feshbach Molecules

    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.

  19. Recent advances in developing small molecules targeting RNA.

    Guan, Lirui; Disney, Matthew D

    2012-01-20

    RNAs are underexploited targets for small molecule drugs or chemical probes of function. This may be due, in part, to a fundamental lack of understanding of the types of small molecules that bind RNA specifically and the types of RNA motifs that specifically bind small molecules. In this review, we describe recent advances in the development and design of small molecules that bind to RNA and modulate function that aim to fill this void. PMID:22185671

  20. Controlling single-molecule junction conductance by molecular interactions

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

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact ...

  1. Can STM be used to image molecules on surfaces?

    Ramos, Marta M. D.

    1993-01-01

    The STM's ability to image adsorbates depends on the probability that the electronic states localized on the adsorbed molecule contribute to the tunnelling current. When the STM images are dominated by the substrate, any interpretation in terms of the actual positions of the atoms within the molecule is controversial. A criterion is presented for deciding whether an STM observation is of the adsorbed molecule directly or of the indirect effect of the molecule on the current from the substrate...

  2. Medical diagnostics using designed molecules with sense and logic

    Cardona, Mario; Farrugia, Kristina; David C. Magri

    2013-01-01

    Luminescent molecules responsive to cations, anions and even small molecules can be designed with the appropriate selectivity and sensitivity for monitoring physiological and pathological levels of analytes. We highlight some recent examples of designed molecules that can sense for a specific analyte or a combination of analytes in blood and in living cells. Furthermore, we demonstrate how molecules can be designed with built-in algorithms according to principles of Boolean logic to perform i...

  3. Quantum Effects at Low Energy Atom-Molecule Interface

    Deb, B.; Rakshit, A.; Hazra, J.; Chakraborty, D.

    2013-01-01

    Quantum interference effects in inter-conversion between cold atoms and diatomic molecules are analysed. Within the framework of Fano's theory, continuum-bound anisotropic dressed state formalism of atom-molecule quantum dynamics is presented. This formalism is applicable in photo- and magneto-associative strong-coupling regimes. The significance of Fano effect in ultracold atom-molecule transitions is discussed. Quantum effects at low energy atom-molecule interface are important for explorin...

  4. Axion Dark Matter Detection with Cold Molecules

    Graham, Peter W

    2011-01-01

    Current techniques cannot detect axion dark matter over much of its parameter space, particularly in the theoretically well-motivated region where the axion decay constant f_a lies near the GUT and Planck scales. We suggest a novel experimental method to search for QCD axion dark matter in this region. The axion field oscillates at a frequency equal to its mass when it is a component of dark matter. These oscillations induce time varying CP-odd nuclear moments, such as electric dipole and Schiff moments. The coupling between internal atomic fields and these nuclear moments gives rise to time varying shifts to atomic energy levels. These effects can be enhanced by using elements with large Schiff moments such as the light Actinides, and states with large spontaneous parity violation, such as molecules in a background electric field. The energy level shift in such a molecule can be ~ 10^-24 eV or larger. While challenging, this energy shift may be observable in a molecular clock configuration with technology pr...

  5. Sisyphus Laser Cooling of a Polyatomic Molecule

    Kozyryev, Ivan; Matsuda, Kyle; Augenbraun, Benjamin L; Anderegg, Loic; Sedlack, Alexander P; Doyle, John M

    2016-01-01

    We perform magnetically-assisted Sisyphus laser cooling of the triatomic free radical strontium monohydroxide (SrOH). This is achieved with principal optical cycling in the rotationally closed $P\\left(N"=1\\right)$ branch of either the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{A}^{2}\\Pi_{1/2}\\left(000\\right)$ or the $\\tilde{X}^{2}\\Sigma^{+}\\left(000\\right)\\leftrightarrow\\tilde{B}^{2}\\Sigma^{+}\\left(000\\right)$ vibronic transitions. Molecules lost into the excited vibrational states during the cooling process are repumped back through the $\\tilde{B}\\left(000\\right)$ state for both the $\\left(100\\right)$ level of the Sr-O stretching mode and the $\\left(02^{0}0\\right)$ level of the bending mode. The transverse temperature of a SrOH molecular beam is reduced in one dimension by two orders of magnitude to $\\sim700\\ {\\rm \\mu K}$. This approach opens a path towards creating a variety of ultracold polyatomic molecules, including much larger ones, by means of direct laser cooling.

  6. Toroidal nanotraps for cold polar molecules

    Salhi, Marouane; Passian, Ali; Siopsis, George

    2015-09-01

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

  7. Spin-crossover molecule based thermoelectric junction

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

  8. Quantum optics of ultra-cold molecules

    Meiser, D; Uys, H; Meystre, P

    2005-01-01

    Quantum optics has been a major driving force behind the rapid experimental developments that have led from the first laser cooling schemes to the Bose-Einstein condensation (BEC) of dilute atomic and molecular gases. Not only has it provided experimentalists with the necessary tools to create ultra-cold atomic systems, but it has also provided theorists with a formalism and framework to describe them: many effects now being studied in quantum-degenerate atomic and molecular systems find a very natural explanation in a quantum optics picture. This article briefly reviews three such examples that find their direct inspiration in the trailblazing work carried out over the years by Herbert Walther, one of the true giants of that field. Specifically, we use an analogy with the micromaser to analyze ultra-cold molecules in a double-well potential; study the formation and dissociation dynamics of molecules using the passage time statistics familiar from superradiance and superfluorescence studies; and show how mole...

  9. Complex molecules in W51 North region

    Rong, Jialei; Zapata, Luis A; Wu, Yuefang; Liu, Tie; Zhang, Chengpeng; Peng, Yaping; Zhang, Li; Liu, Ying

    2015-01-01

    We present Submillimeter Array (SMA) molecular line observations in two 2 GHz-wide bands centered at 217.5 and 227.5 GHz, toward the massive star forming region W51 North. We identified 84 molecular line transitions from 17 species and their isotopologues. The molecular gas distribution of these lines mainly peaks in the continuum position of W51 North, and has a small tail extending to the west, probably associated with W51 d2. In addition to the commonly detected nitrogen and oxygen-bearing species, we detected a large amount of transitions of the Acetone (CH$_3$COCH$_3$) and Methyl Formate (CH$_3$OCHO), which may suggest that these molecules are present in an early evolutionary stage of the massive stars. We also found that W51 North is an ethanol-rich source. There is no obvious difference in the molecular gas distributions between the oxygen-bearing and nitrogen-bearing molecules. Under the assumption of Local Thermodynamic Equilibrium (LTE), with the XCLASS tool, the molecular column densities, and rota...

  10. Small Molecule Docking from Theoretical Structural Models

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

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

  11. Interstellar grain chemistry and organic molecules

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

    1990-01-01

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

  12. Size selective hydrophobic adsorbent for organic molecules

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

    1997-01-01

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

  13. Quantum Monte Carlo for vibrating molecules

    Quantum Monte Carlo (QMC) has successfully computed the total electronic energies of atoms and molecules. The main goal of this work is to use correlation function quantum Monte Carlo (CFQMC) to compute the vibrational state energies of molecules given a potential energy surface (PES). In CFQMC, an ensemble of random walkers simulate the diffusion and branching processes of the imaginary-time time dependent Schroedinger equation in order to evaluate the matrix elements. The program QMCVIB was written to perform multi-state VMC and CFQMC calculations and employed for several calculations of the H2O and C3 vibrational states, using 7 PES's, 3 trial wavefunction forms, two methods of non-linear basis function parameter optimization, and on both serial and parallel computers. In order to construct accurate trial wavefunctions different wavefunctions forms were required for H2O and C3. In order to construct accurate trial wavefunctions for C3, the non-linear parameters were optimized with respect to the sum of the energies of several low-lying vibrational states. In order to stabilize the statistical error estimates for C3 the Monte Carlo data was collected into blocks. Accurate vibrational state energies were computed using both serial and parallel QMCVIB programs. Comparison of vibrational state energies computed from the three C3 PES's suggested that a non-linear equilibrium geometry PES is the most accurate and that discrete potential representations may be used to conveniently determine vibrational state energies

  14. Spin-crossover molecule based thermoelectric junction

    Ghosh, Dibyajyoti [Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India); Parida, Prakash [Institute for Theoretical Physics, University of Regensburg, D-93040 Regensburg (Germany); Pati, Swapan K. [Theoretical Sciences Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064 (India)

    2015-05-11

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

  15. Electric field breakdown in single molecule junctions.

    Li, Haixing; Su, Timothy A; Zhang, Vivian; Steigerwald, Michael L; Nuckolls, Colin; Venkataraman, Latha

    2015-04-22

    Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S-Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor-acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si-Si and Ge-Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si-Si, Si-C, and Si-O bonds and find that Si-C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level. PMID:25675085

  16. Organic- and molecule-based magnets

    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.

  17. Diversification of self-replicating molecules

    Sadownik, Jan W.; Mattia, Elio; Nowak, Piotr; Otto, Sijbren

    2016-03-01

    How new species emerge in nature is still incompletely understood and difficult to study directly. Self-replicating molecules provide a simple model that allows us to capture the fundamental processes that occur in species formation. We have been able to monitor in real time and at a molecular level the diversification of self-replicating molecules into two distinct sets that compete for two different building blocks (‘food’) and so capture an important aspect of the process by which species may arise. The results show that the second replicator set is a descendant of the first and that both sets are kinetic products that oppose the thermodynamic preference of the system. The sets occupy related but complementary food niches. As diversification into sets takes place on the timescale of weeks and can be investigated at the molecular level, this work opens up new opportunities for experimentally investigating the process through which species arise both in real time and with enhanced detail.

  18. Radical inactivation of a biological sulphydryl molecule

    Reactive species produced from the free radical-induced chain oxidation of low molecular weight sulphydryl-containing molecules in aerated solutions deactivate the sulphydryl-containing enzyme papain, forming both reparable mixed disulphides and non-reparable products. This inactivation is highly efficient for penicillamine and glutathione, but almost negligible with cysteine, which is a protector of papain for [cysteine] / [papain] >= 5 under all conditions used. In the case of glutathione, superoxide dismutase caused only a small reduction in the inactivation and peroxide yields were small, implying that the deactivating species are not .O2- but RSOO. radicals or products from them. For penicillamine, however, dimutase was highly effective and the peroxide yields were relatively large, demonstrating that .O2- or a radical with similar capabilities for forming H2O2 and being deactivated by dismutase was involved. Although in the presence of dismutase penicillamine is a better protector of non-reparable papain inactivation than glutathione, it suffers from a deficiency in that the papain-penicillamine mixed disulphide, which is always formed, cannot be repaired by spontaneous reaction with RSH molecules. (author)

  19. In Search of the Molecules of Life

    Crawford, Ronald L.; Paszczynski, Andrzej; Lang, Qingyong; Cheng, I. Francis; Barnes, Bruce; Anderson, Tony J.; Wells, Richard; Wai, Chien; Corti, Giancarlo; Allenbach, Lisa; Erwin, Daniel P.; Park, Joohye; Assefi, Touraj; Mojarradi, Mohammad

    2001-12-01

    The remote detection of a chemical signature of extraterrestrial life ideally requires a broad and nonEarth-centric definition of life. Thus, our proposed approach to detection is based on fundamental thermodynamic assumptions, and some assumptions of how life might obtain energy from its environment. Life, defined as the ability to self-perpetuate, requires a continual input of energy and information. The energy must be tapped in controlled oxidation-reduction reactions between electron donors and acceptors along an electron transport chain. Therefore, the core chemical components of such electron transport chains should be detectable as a signature of life. On Earth, such core structures are principally molecules resembling the porphyrins, quinones, flavins, and nicotinamides (e.g., photosynthetic or respiratory pigments, redox enzymes, and cytochromes). Similar redox-active molecules, perhaps with different structures, might be associated with extraterrestrial life. To validate an approach based on redox signature, signature chemicals were extracted from soil and analyzed by different methods and equipment that may eventually form an integrated "laboratory on a chip" to be used on other planets or their moons. Its components are a supercritical fluid or solvent extraction module, a separation module, and a detection module with an electrochemical detector and electrospray tandem mass-spectrometer.

  20. Conformational elasticity theory of chain molecules

    YANG; Xiaozhen

    2001-01-01

    This paper develops a conformational elasticity theory of chain molecules, which is based on three key points: (ⅰ) the molecular model is the rotational isomeric state (RIS) model; (ⅱ) the conformational distribution function of a chain molecule is described by a function of two variables, the end-to-end distance of a chain conformation and the energy of the conformation; (ⅲ) the rule of changes in the chain conformational states during deformation is that a number of chain conformations would vanish. The ideal deformation behavior calculated by the theory shows that the change in chain conformations is physically able to make the upward curvature of the stress-strain curve at the large-scale deformation of natural rubber. With the theory, different deformation behaviors between polymers with different chemical structures can be described, the energy term of the stress in the deformations can be predicted, and for natural rubber the fraction of the energy term is around 13%, coinciding with the experimental results.

  1. Chemokines: Small Molecules Participate in Diabetes

    S. Mostafa Hosseini-Zijoud

    2013-04-01

    Full Text Available Background: Chemokines are small protein molecules involved in cell signaling processes. They play a crucial role in many physiological and pathological processes. Chemokines are functionally classified into two categories; inflammatory/inducible and constitutive. Their biologic functional differences are the result of their receptors structural differences. Recently some studies were performed about the chemokines changes in diabetes. Inflammatory mechanisms have an important role in diabetes.Materials and Methods: In this review article we searched the keywords chemokines, diabetes, diabetes pathogenesis, and type 1 and 2 diabetes in Persian resources, PubMed and famous English-language websites through advanced search engines and found the newest studies about the role of chemokines in the pathogenesis of diabetes.Results: The results of the studies showed that diabetes and its disorders enhance the activation of immune cells and the expression of cytokines such as IL-1, IL-6, IL-8, IL-10, SDF-1, INF-γ, TGF-β, MCP-1, IP-10, TNF-α, and RANTES; most of them have impact on the pathogenesis of diabetes.Conclusion: Comparison and analysis of the results obtained from our research and the results of performed studies in the world and Iran shows that chemokines, like other protein molecules involved in the pathogenesis and etiology of diabetes, play a role in this process.

  2. Small molecule phagocytosis inhibitors for immune cytopenias.

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

    2016-08-01

    Immune cytopenias are conditions characterized by low blood cell counts, such as platelets in immune thrombocytopenia (ITP) and red blood cells in autoimmune hemolytic anemia (AIHA). Chronic ITP affects approximately 4 in 100,000 adults annually while AIHA is much less common. Extravascular phagocytosis and massive destruction of autoantibody-opsonized blood cells by macrophages in the spleen and liver are the hallmark of these conditions. Current treatment modalities for ITP and AIHA include the first-line use of corticosteroids; whereas, IVIg shows efficacy in ITP but not AIHA. One main mechanism of action by which IVIg treatment leads to the reduction in platelet destruction rates in ITP is thought to involve Fcγ receptor (FcγR) blockade, ultimately leading to the inhibition of extravascular platelet phagocytosis. IVIg, which is manufactured from the human plasma of thousands of donors, is a limited resource, and alternative treatments, particularly those based on bioavailable small molecules, are needed. In this review, we overview the pathophysiology of ITP, the role of Fcγ receptors, and the mechanisms of action of IVIg in treating ITP, and outline the efforts and progress towards developing novel, first-in-class inhibitors of phagocytosis as synthetic, small molecule substitutes for IVIg in ITP and other conditions where the pathobiology of the disease involves phagocytosis. PMID:27296447

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

    Centelles, Josep J.; Imperial, Santiago

    2005-01-01

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

  4. Single-Molecule Electronic Measurements with Metal Electrodes

    Lindsay, Stuart

    2005-01-01

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

  5. Atomic-Scale Control of Electron Transport through Single Molecules

    Wang, Y. F.; Kroger, J.; Berndt, R.;

    2010-01-01

    Tin-phthalocyanine molecules adsorbed on Ag(111) were contacted with the tip of a cryogenic scanning tunneling microscope. Orders-of-magnitude variations of the single-molecule junction conductance were achieved by controllably dehydrogenating the molecule and by modifying the atomic structure of...

  6. Filming the Birth of Molecules and Accompanying Solvent Rearrangement

    Lee, Jae Hyuk; Wulff, Michael; Bratos, Savo;

    2013-01-01

    Molecules are often born with high energy and large-amplitude vibrations. In solution, a newly formed molecule cools down by transferring energy to the surrounding solvent molecules. The progression of the molecular and solute−solvent cage structure during this fundamental process has been elusiv...

  7. Small Molecule Agonists of Cell Adhesion Molecule L1 Mimic L1 Functions In Vivo.

    Kataria, Hardeep; Lutz, David; Chaudhary, Harshita; Schachner, Melitta; Loers, Gabriele

    2016-09-01

    Lack of permissive mechanisms and abundance of inhibitory molecules in the lesioned central nervous system of adult mammals contribute to the failure of functional recovery after injury, leading to severe disabilities in motor functions and pain. Peripheral nerve injury impairs motor, sensory, and autonomic functions, particularly in cases where nerve gaps are large and chronic nerve injury ensues. Previous studies have indicated that the neural cell adhesion molecule L1 constitutes a viable target to promote regeneration after acute injury. We screened libraries of known drugs for small molecule agonists of L1 and evaluated the effect of hit compounds in cell-based assays in vitro and in mice after femoral nerve and spinal cord injuries in vivo. We identified eight small molecule L1 agonists and showed in cell-based assays that they stimulate neuronal survival, neuronal migration, and neurite outgrowth and enhance Schwann cell proliferation and migration and myelination of neurons in an L1-dependent manner. In a femoral nerve injury mouse model, enhanced functional regeneration and remyelination after application of the L1 agonists were observed. In a spinal cord injury mouse model, L1 agonists improved recovery of motor functions, being paralleled by enhanced remyelination, neuronal survival, and monoaminergic innervation, reduced astrogliosis, and activation of microglia. Together, these findings suggest that application of small organic compounds that bind to L1 and stimulate the beneficial homophilic L1 functions may prove to be a valuable addition to treatments of nervous system injuries. PMID:26253722

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

    Yoo, Hyejin

    2012-10-25

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

  9. Engineering and control of cold molecules. Making manipulating and exploiting ultra-cold polar molecules

    In the last 12 months several groups have demonstrated the use of photo association to create cold heteronuclear (polar) molecules. We report on the formation of translationally cold NaCs molecules starting from a laser-cooled atomic vapor of Na and Cs atoms. Colliding atoms are transferred into bound molecular states in a two-step photoactivated process. We find a translational temperature of T ≅ 260 mK. To increase the density and number of trapped atoms, dark-spot techniques are used on the MOT and a Zeeman slowed sodium beam is used to load the sodium atoms into the trap. Spectroscopy of these molecules is underway using time-of-flight ion detection and trap-loss. Initial REMPI measurements indicate that both singlet and triplet states are being populated by the spontaneous-decay driven process. We measure a rate constant for molecule formation of KNaCs = 7.43 · 1015 cm3 s-1. (author)

  10. Deflection of Neutral Molecules using the Nonresonant Dipole Force

    The ac Stark shift produced by nonresonant radiation creates a potential minimum for a ground state molecule at the position where the laser intensity is maximum. The gradient of this potential exerts a force on the molecule. We experimentally observe this force when a beam of CS2 molecules is redirected by sending it through the intensity gradient near the focus of a laser beam. We trace the direction of the molecules in the molecular beam, showing that the molecules that pass near the center of the high intensity laser beam will focus. copyright 1997 The American Physical Society

  11. Simulation Studies of Protein and Small Molecule Interactions and Reaction.

    Yang, L; Zhang, J; Che, X; Gao, Y Q

    2016-01-01

    Computational studies of protein and small molecule (protein-ligand/enzyme-substrate) interactions become more and more important in biological science and drug discovery. Computer modeling can provide molecular details of the processes such as conformational change, binding, and transportation of small molecules/proteins, which are not easily to be captured in experiments. In this chapter, we discussed simulation studies of both protein and small molecules from three aspects: conformation sampling, transportations of small molecules in enzymes, and enzymatic reactions involving small molecules. Both methodology developments and examples of simulation studies in this field were presented. PMID:27497167

  12. Spin Hall separation of ultracold atom-molecule mixed gases

    Ye, Chong; Fu, Li-Bin; Liu, Jie

    2016-05-01

    We propose a theoretical scheme to separate a molecular cloud from atoms in analogy to the spin Hall effect and to completely transfer Feshbach molecules to the ground state by applying a spatially modulated laser field to an atom-molecule mixed gas. In particular, the laser-molecule interaction induces a synthetic U(1) gauge potential for the dressed molecular dark state. Through numerical simulation, we demonstrate that such a gauge field leads to a spin Hall separation of atoms and molecules. In such a process, molecules can be transformed into the ground state completely.

  13. Dipole-Dipole coupled double Rydberg molecules

    Kiffner, Martin; Li, Wenhui; Gallagher, Tom F

    2012-01-01

    We show that the dipole-dipole interaction between two Rydberg atoms can give rise to long range molecules. The binding potential arises from two states that converge to different separated atom asymptotes. These states interact weakly at large distances, but start to repel each other strongly as the van der Waals interaction turns into a resonant dipole-dipole interaction with decreasing separation between the atoms. This mechanism leads to the formation of an attractive well for one of the potentials. If the two separated atom asymptotes come from the small Stark splitting of an atomic Rydberg level, which lifts the Zeeman degeneracy, the depth of the well and the location of its minimum are controlled by the external electric field. We discuss two different geometries that result in a localized and a donut shaped potential, respectively.

  14. Colloquium: Quantum interference of clusters and molecules

    Hornberger, Klaus; Haslinger, Philipp; Nimmrichter, Stefan; Arndt, Markus

    2011-01-01

    We review recent progress and future prospects of matter wave interferometry with complex organic molecules and inorganic clusters. Three variants of a near-field interference effect, based on diffraction by material nanostructures, at optical phase gratings, and at ionizing laser fields are considered. We discuss the theoretical concepts underlying these experiments and the experimental challenges. This includes optimizing interferometer designs as well as understanding the role of decoherence. The high sensitivity of matter wave interference experiments to external perturbations is demonstrated to be useful for accurately measuring internal properties of delocalized nanoparticles. We conclude by investigating the prospects for probing the quantum superposition principle in the limit of high particle mass and complexity.

  15. Slow neutron scattering by water molecules

    In this work some new, preliminary formulae for slow neutron scattering cross section calculation by heavy and light water molecules have been done. The idea was to find, from the sum which exists in well known Nelkin model, other cross sections in a more simple analytical form, so that next approximations may be possible. In order to sum a series it was starting from Euler-Mclaurin formula. Some new summation formulae have been derived there, and defined in two theorems. Extensive calculations, especially during the evaluation of residues, have been made at the CDC 3600 computer. validation of derived formulae was done by comparison with the BNL-325 results. Good agreement is shown. (author)

  16. Small Molecule Library Synthesis Using Segmented Flow

    Christina M. Thompson

    2011-11-01

    Full Text Available Flow chemistry has gained considerable recognition as a simple, efficient, and safe technology for the synthesis of many types of organic and inorganic molecules ranging in scope from large complex natural products to silicon nanoparticles. In this paper we describe a method that adapts flow chemistry to the synthesis of libraries of compounds using a fluorous immiscible solvent as a spacer between reactions. The methodology was validated in the synthesis of two small heterocycle containing libraries. The reactions were performed on a 0.2 mmol scale, enabling tens of milligrams of material to be generated in a single 200 mL reaction plug. The methodology allowed library synthesis in half the time of conventional microwave synthesis while maintaining similar yields. The ability to perform multiple, potentially unrelated reactions in a single run is ideal for making small quantities of many different compounds quickly and efficiently.

  17. Entanglement of electrons in interacting molecules

    Maiolo, T A C; Sala, F D; Soliani, G; Maiolo, Tina A.C.; Martina, Luigi; Sala, Fabio Della; Soliani, Giulio

    2006-01-01

    Quantum entanglement is a concept commonly used with reference to the existence of certain correlations in quantum systems that have no classical interpretation. It is a useful resource to enhance the mutual information of memory channels or to accelerate some quantum processes as, for example, the factorization in Shor's Algorithm. Moreover, entanglement is a physical observable directly measured by the von Neumann entropy of the system. We have used this concept in order to give a physical meaning to the electron correlation energy in systems of interacting electrons. The electronic correlation is not directly observable, since it is defined as the difference between the exact ground state energy of the many--electrons Schroedinger equation and the Hartree--Fock energy. We have calculated the correlation energy and compared with the entanglement, as functions of the nucleus--nucleus separation using, for the hydrogen molecule, the Configuration Interaction method. Then, in the same spirit, we have analyzed ...

  18. Infrared spectroscopy of small-molecule endofullerenes

    Rõõm, T; Ge, Min; Hüvonen, D; Nagel, U; Mamone, S; Levitt, M H; Carravetta, M; Chen, J Y -C; Lei, Xuegong; Turro, N J; Murata, Y; Komatsu, K

    2013-01-01

    Hydrogen is one of the few molecules which has been incarcerated in the molecular cage of C$_{60}$ and forms endohedral supramolecular complex H$_2$@C$_{60}$. In this confinement hydrogen acquires new properties. Its translational motion becomes quantized and is correlated with its rotations. We applied infrared spectroscopy to study the dynamics of hydrogen isotopologs H$_2$, D$_2$ and HD incarcerated in C$_{60}$. The translational and rotational modes appear as side bands to the hydrogen vibrational mode in the mid infrared part of the absorption spectrum. Because of the large mass difference of hydrogen and C$_{60}$ and the high symmetry of C$_{60}$ the problem is identical to a problem of a vibrating rotor moving in a three-dimensional spherical potential. The translational motion within the C$_{60}$ cavity breaks the inversion symmetry and induces optical activity of H$_2$. We derive potential, rotational, vibrational and dipole moment parameters from the analysis of the infrared absorption spectra. Our ...

  19. Microemulsions as carriers for therapeutic molecules.

    Mehta, Surinder K; Kaur, Gurpreet

    2010-01-01

    The thrust for finding newer drug delivery systems for exiting therapeutic molecules has opened a wide window for colloidal systems. Due to the presence of different domains of variable polarity in the microemulsion systems, they show a huge potential to be used as drug delivery vehicles for a variety of drugs. The use of microemulsion as drug delivery vehicles through a number of routes has engaged a large number of research groups in this area. Microemulsion media finds several applications ranging from drug delivery to drug nanoparticle templating due to its ability to enhance solubility, stability and bioavailability. This review on patent articles recounts the patent literature dealing with different kind of microemulsion carriers used via different routes, solubility and permeability enhancement and its use as a template for nanoparticle synthesis. PMID:19807681

  20. Transport properties of individual C60-molecules

    Electrical and thermal transport properties of C60 molecules are investigated with density-functional-theory based calculations. These calculations suggest that the optimum contact geometry for an electrode terminated with a single-Au atom is through binding to one or two C-atoms of C60 with a tendency to promote the  sp2-hybridization into an  sp3-type one. Transport in these junctions is primarily through an unoccupied molecular orbital that is partly hybridized with the Au, which results in splitting the degeneracy of the lowest unoccupied molecular orbital triplet. The transmission through these junctions, however, cannot be modeled by a single Lorentzian resonance, as our results show evidence of quantum interference between an occupied and an unoccupied orbital. The interference results in a suppression of conductance around the Fermi energy. Our numerical findings are readily analyzed analytically within a simple two-level model

  1. Adiabatic theory for anisotropic cold molecule collisions

    We developed an adiabatic theory for cold anisotropic collisions between slow atoms and cold molecules. It enables us to investigate the importance of the couplings between the projection states of the rotational motion of the atom about the molecular axis of the diatom. We tested our theory using the recent results from the Penning ionization reaction experiment 4He(1s2s 3S) + HD(1s2) → 4He(1s2) + HD+(1s) + e− [Lavert-Ofir et al., Nat. Chem. 6, 332 (2014)] and demonstrated that the couplings have strong effect on positions of shape resonances. The theory we derived provides cross sections which are in a very good agreement with the experimental findings

  2. Adiabatic theory for anisotropic cold molecule collisions.

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

    2015-08-21

    We developed an adiabatic theory for cold anisotropic collisions between slow atoms and cold molecules. It enables us to investigate the importance of the couplings between the projection states of the rotational motion of the atom about the molecular axis of the diatom. We tested our theory using the recent results from the Penning ionization reaction experiment (4)He(1s2s (3)S) + HD(1s(2)) → (4)He(1s(2)) + HD(+)(1s) + e(-) [Lavert-Ofir et al., Nat. Chem. 6, 332 (2014)] and demonstrated that the couplings have strong effect on positions of shape resonances. The theory we derived provides cross sections which are in a very good agreement with the experimental findings. PMID:26298122

  3. Adiabatic theory for anisotropic cold molecule collisions

    Pawlak, Mariusz [Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000 (Israel); Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Gagarina 7, 87-100 Toruń (Poland); Shagam, Yuval; Narevicius, Edvardas [Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100 (Israel); Moiseyev, Nimrod [Schulich Faculty of Chemistry, Technion–Israel Institute of Technology, Haifa 32000 (Israel); Faculty of Physics, Technion–Israel Institute of Technology, Haifa 32000 (Israel)

    2015-08-21

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

  4. Rotational transitions in compound muonic molecules

    Padial, N.T.; Cohen, J.S.; Walker, R.B.

    1988-01-15

    Cross sections and rate constants are calculated for collision-induced rotational transitions of compound muonic molecules, which determine relaxation rates important to muon-catalyzed fusion processes. The interaction potential is derived from the H/sub 2/-H/sub 2/ potential, and the R-matrix propagation method is used to solve the set of coupled collisional equations for the systems D/sub 2/+((dt..mu..)dee), D/sub 2/+((dd..mu..)dee), T/sub 2/+((dt..mu..)dee), D/sub 2/+((dt..mu..)tee), and H/sub 2/+((dd..mu..)pee). Calculations are also done on H/sub 2/+HD and D/sub 2/+HD for comparison with previous work.

  5. Small polaron hopping transport along DNA molecules

    Triberis, G P [University of Athens, Physics Department, Solid State Section, Panepistimiopolis, GR-15784 Zografos, Athens (Greece); Simserides, C [University of Athens, Physics Department, Solid State Section, Panepistimiopolis, GR-15784 Zografos, Athens (Greece); Leibniz Institute for Neurobiology, Special Laboratory for Non-Invasive Brain Imaging, Brenneckestrasse 6, D-39118 Magdeburg (Germany); Karavolas, V C [University of Athens, Physics Department, Solid State Section, Panepistimiopolis, GR-15784 Zografos, Athens (Greece)

    2005-05-04

    We present a small polaron hopping model for interpreting the strong temperature (T) dependence of the electrical conductivity, {sigma}, observed at high (h) temperatures along DNA molecules. The model takes into account the one-dimensional character of the system and the presence of disorder in the DNA double helix. Percolation-theoretical considerations lead to analytical expressions for the high temperature multiphonon-assisted small polaron hopping conductivity, the hopping distance and their temperature dependence. The experimental data for lambda phage DNA ({lambda}-DNA) and poly(dA)-poly(dT) DNA follow nicely the theoretically predicted behaviour (ln{sigma}{sup h}{proportional_to}T{sup -2/3}). Moreover, our model leads to realistic values of the maximum hopping distances, supporting the idea of multiphonon-assisted hopping of small polarons between next nearest neighbours of the DNA molecular 'wire'. The low temperature case is also investigated.

  6. Small polaron hopping transport along DNA molecules

    Triberis, G. P.; Simserides, C.; Karavolas, V. C.

    2005-05-01

    We present a small polaron hopping model for interpreting the strong temperature (T) dependence of the electrical conductivity, σ, observed at high (h) temperatures along DNA molecules. The model takes into account the one-dimensional character of the system and the presence of disorder in the DNA double helix. Percolation-theoretical considerations lead to analytical expressions for the high temperature multiphonon-assisted small polaron hopping conductivity, the hopping distance and their temperature dependence. The experimental data for lambda phage DNA (λ-DNA) and poly(dA)-poly(dT) DNA follow nicely the theoretically predicted behaviour (lnσh~T-2/3). Moreover, our model leads to realistic values of the maximum hopping distances, supporting the idea of multiphonon-assisted hopping of small polarons between next nearest neighbours of the DNA molecular 'wire'. The low temperature case is also investigated.

  7. Combinatorial analysis of interacting RNA molecules

    Li, Thomas J X

    2010-01-01

    Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.

  8. Simulated single molecule microscopy with SMeagol

    Lindén, Martin; Boucharin, Alexis; Fange, David; Elf, Johan

    2015-01-01

    Recent advances in single particle tracking (SPT) microscopy 1 make it possible to obtain tens of thousands macromolecular trajectories from within a living cell in just a few minutes. Since molecules typically change their movement properties upon interactions, these trajectories contain information about both locations and rates of intracellular reactions. This information is unfortunately obscured by physical limitations of the optical microscope and noise in detection systems, making statistical methods development for SPT analysis a very active research field. Unbiased testing and comparison of such methods are however difficult given the absence of in vivo data of intracellular dynamics where the true states of interaction are known, a.k.a. the ground truth. A common resort is to instead use simulated, synthetic, data. However, tests using such data give unrealistically optimistic results if the simplifying assumptions underlying the analysis method are satisfied in the synthetic data, a practice known ...

  9. Extracellular Matrix Molecules Facilitating Vascular Biointegration

    Martin K.C. Ng

    2012-08-01

    Full Text Available All vascular implants, including stents, heart valves and graft materials exhibit suboptimal biocompatibility that significantly reduces their clinical efficacy. A range of biomolecules in the subendothelial space have been shown to play critical roles in local regulation of thrombosis, endothelial growth and smooth muscle cell proliferation, making these attractive candidates for modulation of vascular device biointegration. However, classically used biomaterial coatings, such as fibronectin and laminin, modulate only one of these components; enhancing endothelial cell attachment, but also activating platelets and triggering thrombosis. This review examines a subset of extracellular matrix molecules that have demonstrated multi-faceted vascular compatibility and accordingly are promising candidates to improve the biointegration of vascular biomaterials.

  10. Positron Interactions with Biologically Relevant Molecules

    Palihawadana, P.; Machacek, J. R.; Anderson, E.; Makochekanwa, C.; Sullivan, J. P.; Garcia, G.; Brunger, M. J.; Buckman, S. J.

    2011-05-01

    A series of measurements of positron interactions with biologically relevant molecules have been undertaken. We present both total scattering and differential scattering cross sections for Uracil (C4H4N2O2) , Tetrahydrofuran or THF (C4H8O), 3-hydroxy-THF(C4H8O2) and Pyrimidine (C4H4N2) . These measurements are absolute and include the positronium formation cross section which is important to investigations of positron transport in biological systems. The energy of the magnetically confined positron beam can be tuned between 1 and 200 eV, and the energy resolution of the beam is between 60 and 100 meV. We will discuss the experimental techniques, the sources of systematic errors which limit the current results, and prospects for the future. This work is supported by the Australian Research Council and the Australian Government's ISL Program.

  11. Low energy ion-molecule reactions

    Farrar, J.M. [Univ. of Rochester, NY (United States)

    1993-12-01

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

  12. hermal decomposition of irradiated casein molecules

    NON-Isothermal studies were carried out using the derivatograph where thermogravimetry (TG) and differential thermogravimetry (DTG) measurements were used to obtain the activation energies of the first and second reactions for casein (glyco-phospho-protein) decomposition before and after exposure to 1 Gy γ-rays and up to 40 x 104 μg Gy fast neutrons. 25Cf was used as a source of fast neutrons, associated with γ-rays. 137Cs source was used as pure γ-source. The activation energies for the first and second reactions for casein decomposition were found to be smaller at 400 μGy than that at lower and higher fast neutron doses. However, no change in activation energies was observed after γ-irradiation. it is concluded from the present study that destruction of casein molecules by low level fast neutron doses may lead to changes of shelf storage period of milk

  13. Aggregation of Benzene Molecules with Molecules of Methanol and Formic Acid

    Calculations and experimental studies of Raman scattering spectra show that there is a dimeric aggregation of benzene molecules with the molecule of methyl alcohol with the use of π-electrons of the benzene ring. In this process, the H-active hydrogen atom of O-H group is oriented to the edge of the benzene ring (a distance along the normal to the plane of the benzene ring is 2.850 A). The unusual position of the H-active hydrogen atom is conditioned by the interaction of two hydrogen atoms of the alcohols methyl group with π-electrons of the benzene ring. In Raman scattering spectra, the aggregation of molecules in the liquid state of the substance leads to a broadening of the band of full-symmetric vibrations with the maximum at 992 cm-1, as well as to a shift of this band toward lower frequencies by ∼ 1 cm-1. The band at 992 cm-1 is narrowed more than twice at the strong dilution of the benzene-methyl alcohol mixture by a large amount of heptane. The aggregation of benzene molecules takes place also with the molecules of formic acid with the use of π-electrons of the benzene ring. As in the case of the benzene-methyl alcohol mixture, the H-active hydrogen atom of O-H group of the acid is shifted toward the edge of the benzene ring. The energy of the benzene-formic acid dimerization is 9.2 kJ/mole.

  14. Quantum Monte Carlo for vibrating molecules

    Brown, W.R. [Univ. of California, Berkeley, CA (United States). Chemistry Dept.]|[Lawrence Berkeley National Lab., CA (United States). Chemical Sciences Div.

    1996-08-01

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

  15. Small Organic Molecules for Direct Aldol Reaction

    TANG Zhuo; GONG Liu-Zhu; MI Ai-Qiao; JIANG Yao-Zhong

    2004-01-01

    Since the pioneering finding by List and Barbas Ⅲ and their coworkers that L-proline could work as a catalyst in the intermolecular direct aldol reaction, the concept of small organic molecules as catalysts has received great attention. However, new organic molecule which have better catalysis ability are reported scarcely.Our groups1 found L-Prolinamides 1 to be active catalysts for the direct aldol reaction of 4-nitrobenaldehyde with neat acetone at room temperature. The enantioselectivity increases as the amide N-H becomes more acidic and thus a better hydrogen bond donor. Introducing another proton donor, hydroxyl, in the catalyst lead to a further improvement in the catalytic enantioselectivity.The calculations reveal that the amide N-H and the terminal hydroxyl groups form hydrogen bonds with the benzaldehyde substrate. These hydrogen bonds reduce the activation energy and cause high enantioselectivity.Catalyst 2, prepared from L-proline and (1S, 2S)-diphenyl-2-aminoethanol, exhibits high enantioselectivities of up to 93% ee for aromatic aldehydes and up to >99% ee for aliphatic aldehydes. It is noteworthy that our results refuted the conventional wisdom that the carboxylic acid group of proline is a reqirement for high enatioselectivity and provide a powerful strategy in the molecular design of new organic catalyst because plentiful chiral resource containing multi-hydrogen bonding donor, for example, peptides.Very recently, we found that L-proline-based peptides 3-7 can catalyze the aldol reactions of hydroxyacetone with aldehydes 8 in aqueous media, to give 1,4-diols 9, the disfavored products with either aldolase or L-proline. Both peptides 5 and 6 give good results.The abilities of peptides 5 and 6 to catalyze the direct aldol reactions of hydroxyacetone with avariety of aldehydes were examined under optimal conditions. The results are shown in table. Highyields and entioselectivities of up to 96% ee were observed for aromatic aldehydes

  16. From single molecule to single tubules

    Guo, Chin-Lin

    2012-02-01

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

  17. The Beryllium tetramer: profiling an elusive molecule.

    Ascik, Peter N; Wilke, Jeremiah J; Simmonett, Andrew C; Yamaguchi, Yukio; Schaefer, Henry F

    2011-02-21

    The structure and energetics of Be(4) are investigated using state-of-the-art coupled-cluster methods. We compute the optimized bond length, dissociation energy, and anharmonic vibrational frequencies. A composite approach is employed, starting from coupled-cluster theory with single, double, and perturbative triple excitations extrapolated to the complete basis set (CBS) limit using Dunning's correlation consistent cc-pCVQZ and cc-pCV5Z basis sets. A correction for full triple and connected quadruple excitations in the smaller cc-pCVDZ basis set is then added, yielding an approximation to CCSDT(Q)/CBS denoted c∼CCSDT(Q). Corrections are included for relativistic and non-Born-Oppenheimer effects. We obtain D(e) = 89.7 kcal mol(-1), D(0) = 84.9 kcal mol(-1), and r(e) = 2.043 Å. Second-order vibrational perturbation theory (VPT2) is applied to a full quartic force field computed at the c∼CCSDT(Q) level of theory, yielding B(e) = 0.448 cm(-1) and fundamental frequencies of 666 (a(1)), 468 (e), and 571 (t(2)) cm(-1). Computations on the spectroscopically characterized Be(2) molecule are reported for the purpose of benchmarking our methods. Perturbative estimates of the effect of quadruple excitations are found to be essential to computing accurate parameters for Be(2); however, they seem to exert a much smaller influence on the structure and energetics of Be(4). Our extensive characterization of the Be(4) bonding potential energy surface should aid in the experimental identification of this thermodynamically viable but elusive molecule. PMID:21341831

  18. High-resolution scanning tunneling microscopy for molecules

    Scanning tunneling microscopy (STM) can detect individual molecular configuration with its high spatial resolution ability, but some intrinsical and extrinsic factors result in the complexities of STM imaging of single molecules. By combining STM experimental work and theoretical simulation with the local density approximation based on Bardeen perturbation method, we have explored the atomic-scale configuration of the following molecular systems: C60 molecules adsorbed on Si(1 1 1)-(7x7); alkanethiol self-assembly monolayers on Au(1 1 1); C60 molecule imaged by STM tip adsorbed with another C60 molecule; O2 molecule adsorbed on Ag(1 1 0) and CO molecule adsorbed on Cu(1 1 1) imaged by CO chemically modified STM tip. Some related problems including: molecule-substrate interactions, STM imaging mechanism, chemically modified STM tip, etc., are discussed

  19. Atoms and Molecules Interacting with Light

    van der Straten, Peter; Metcalf, Harold

    2016-02-01

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

  20. Metal-Molecule Contacts: From Adsorption to Charge Transport

    Full text: Highly ordered monolayers and thin films of electrically active molecules on single crystal metal surfaces are excellent model systems for metal-molecule contacts. They can be used to study fundamental properties of metal-molecule contacts, employing a wide range of surface analytical techniques. In this talk I will give examples of our recent work regarding structure and bonding at the organic-metal interface, interface energetics, and precision measurements of current transport through metal-adsorbed molecules using an STM tip. The adsorption of large organic molecules on metal surfaces is often affected by a sizeable contribution of van der Waals attraction to the interaction energy. This makes theoretical simulations challenging. Precise measurements of structural parameters of adsorbed molecules are therefore important as benchmarks for novel simulation approaches. On the other hand, with a universal theoretical description still missing, empirical rules, such as the scaling of the adsorption height with the substrate work function that was observed for PTCDA on noble metal surfaces, provide important guidelines for our understanding. Apart from the molecule-substrate interaction, intermolecular interactions play an important role. For example, networks of hydrogen bonds can influence the internal geometry of adsorbed molecules and their adsorption height, whereas intermolecular polarization screening can influence their electronic structure. Adsorbed molecules on single-crystal surfaces are also an excellent starting point for precise and well-controlled charge transport experiments through individual molecules, because with an STM they can be contacted at a defined position within the molecule. In this way, the influence of electron correlation on quantum transport can be studied. Finally, we show that if an STM is equipped with a single D2 molecule that is confined in the STM junction, Pauli repulsion is probed and can be used to record images of

  1. An in vitro selection for small molecule induced switching RNA molecules.

    Martini, Laura; Ellington, Andrew D; Mansy, Sheref S

    2016-08-15

    The selection of RNA and DNA aptamers now has a long history. However, the ability to directly select for conformational changes upon ligand binding has remained elusive. These difficulties have stymied attempts at making small molecule responsive strand displacement circuitry as well as synthetic riboswitches. Herein we present a detailed strand displacement based selection protocol to directly select for RNA molecules with switching activity. The library was based on a previously selected thiamine pyrophosphate riboswitch. The fully in vitro methodology gave sequences that showed strong strand displacement activity in the presence of thiamine pyrophosphate. Further, the selected sequences possessed riboswitch activity similar to that of natural riboswitches. The presented methodology should aid in the design of more complex, environmentally responsive strand displacement circuitry and in the selection of riboswitches responsive to toxic ligands. PMID:26899430

  2. Molecules in strong laser fields. In depth study of H2 molecule

    A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H2, fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H2 molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H2 molecule. By selecting a very small value of the internuclear distance close to zero for the H2 molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including above

  3. Molecules in strong laser fields. In depth study of H{sub 2} molecule

    Awasthi, Manohar

    2009-10-29

    A method for solving the time-dependent Schroedinger equation (TDSE) describing the electronic motion of the molecules exposed to very short intense laser pulses has been developed. The time-dependent electronic wavefunction is expanded in terms of a superposition of field-free eigenstates. The field-free eigenstates are calculated in two ways. In the first approach, which is applicable to two electron systems like H{sub 2}, fully correlated field-free eigenstates are obtained in complete dimensionality using configuration-interaction calculation where the one-electron basis functions are built from B splines. In the second approach, which is even applicable to larger molecules, the field-free eigenstates are calculated within the single-active-electron (SAE) approximation using density functional theory. In general, the method can be divided into two parts, in the first part the field-free eigenstates are calculated and then in the second part a time propagation for the laser pulse parameters is performed. The H{sub 2} molecule is the testing ground for the implementation of both the methods. The reliability of the configuration interaction (CI) based method for the solution of TDSE (CI-TDSE) is tested by comparing results in the low-intensity regime to the prediction of lowest-order perturbation theory. Another test for the CI-TDSE method is in the united atom limit for the H{sub 2} molecule. By selecting a very small value of the internuclear distance close to zero for the H{sub 2} molecule, Helium atom is obtained. Once the functionality and the reliability of the method is established, it is used for obtaining accurate results for molecular hydrogen exposed to intense laser fields. The results for the standard 800 nm Titanium-Sapphire laser and its harmonics at 400 nm and 266 nm are shown. The results for a scan over a wide range of incident photon energies as well as dependence on the internuclear distance are presented. The photoelectron spectra including

  4. Killer bee molecules: antimicrobial peptides as effector molecules to target sporogonic stages of Plasmodium.

    Victoria Carter

    Full Text Available A new generation of strategies is evolving that aim to block malaria transmission by employing genetically modified vectors or mosquito pathogens or symbionts that express anti-parasite molecules. Whilst transgenic technologies have advanced rapidly, there is still a paucity of effector molecules with potent anti-malaria activity whose expression does not cause detrimental effects on mosquito fitness. Our objective was to examine a wide range of antimicrobial peptides (AMPs for their toxic effects on Plasmodium and anopheline mosquitoes. Specifically targeting early sporogonic stages, we initially screened AMPs for toxicity against a mosquito cell line and P. berghei ookinetes. Promising candidate AMPs were fed to mosquitoes to monitor adverse fitness effects, and their efficacy in blocking rodent malaria infection in Anopheles stephensi was assessed. This was followed by tests to determine their activity against P. falciparum in An. gambiae, initially using laboratory cultures to infect mosquitoes, then culminating in preliminary assays in the field using gametocytes and mosquitoes collected from the same area in Mali, West Africa. From a range of 33 molecules, six AMPs able to block Plasmodium development were identified: Anoplin, Duramycin, Mastoparan X, Melittin, TP10 and Vida3. With the exception of Anoplin and Mastoparan X, these AMPs were also toxic to an An. gambiae cell line at a concentration of 25 µM. However, when tested in mosquito blood feeds, they did not reduce mosquito longevity or egg production at concentrations of 50 µM. Peptides effective against cultured ookinetes were less effective when tested in vivo and differences in efficacy against P. berghei and P. falciparum were seen. From the range of molecules tested, the majority of effective AMPs were derived from bee/wasp venoms.

  5. Ultracold molecules from ultracold atoms: a case study with the KRb molecule

    Julienne, Paul S.

    2008-01-01

    Ultracold collisions of cold atoms or molecules make the bound states of the collision complex formed from the two colliding species accessible for control and manipulation of the cold species or the complex. Such resonances are best treated by a resonant scattering theory, which in the ultracold domain can take advantage of the properties of the long-range potential and the methods of multichannel quantum defect theory. Coupled channels calculations on the threshold scattering states and bou...

  6. Single-Molecule Conductance in a Series of Extended Viologen Molecules

    Kolivoška, Viliam; Valášek, Michal; Gál, Miroslav; Sokolová, Romana; Kocábová, Jana; Pospíšil, Lubomír; Mészáros, G.; Hromadová, Magdaléna

    2013-01-01

    Roč. 4, č. 4 (2013), s. 589-595. ISSN 1948-7185 R&D Projects: GA ČR GA203/09/0705; GA AV ČR IAA400400802; GA MŠk(CZ) MEB041006 Institutional support: RVO:61388955 ; RVO:61388963 Keywords : single molecule conductance * extended viologens * electron transfer Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.687, year: 2013

  7. Dynamics of Hadronic Molecule in One-Boson Exchange Approach and Possible Heavy Flavor Molecules

    Ding, Gui-Jun; Yan, Mu-Lin

    2009-01-01

    We extend the one pion exchange model at quark level to include the short distance contributions coming from $\\eta$, $\\sigma$, $\\rho$ and $\\omega$ exchange. This formalism is applied to discuss the possible molecular states of $D\\bar{D}^{*}/\\bar{D}D^{*}$, $B\\bar{B}^{*}/\\bar{B}B^{*}$, $DD^{*}$, $BB^{*}$, the pseudoscalar-vector systems with $C=B=1$ and $C=-B=1$ respectively. The "$\\delta$ function" term contribution and the S-D mixing effects have been taken into account. We find the conclusions reached after including the heavier mesons exchange are qualitatively the same as those in the one pion exchange model. The previous suggestion that $1^{++}$ $B\\bar{B}^{*}/\\bar{B}B^{*}$ molecule should exist, is confirmed in the one boson exchange model, whereas $DD^{*}$ bound state should not exist. The $D\\bar{D}^{*}/\\bar{D}D^{*}$ system can accomodate a $1^{++}$ molecule close to the threshold, the mixing between the molecule and the conventional charmonium has to be considered to identify this state with X(3872). Fo...

  8. Molecule-optimized Basis Sets and Hamiltonians for Accelerated Electronic Structure Calculations of Atoms and Molecules

    Gidofalvi, Gergely

    2014-01-01

    Molecule-optimized basis sets, based on approximate natural orbitals, are developed for accelerating the convergence of quantum calculations with strongly correlated (multi-referenced) electrons. We use a low-cost approximate solution of the anti-Hermitian contracted Schr{\\"o}dinger equation (ACSE) for the one- and two-electron reduced density matrices (RDMs) to generate an approximate set of natural orbitals for strongly correlated quantum systems. The natural-orbital basis set is truncated to generate a molecule-optimized basis set whose rank matches that of a standard correlation-consistent basis set optimized for the atoms. We show that basis-set truncation by approximate natural orbitals can be viewed as a one-electron unitary transformation of the Hamiltonian operator and suggest an extension of approximate natural-orbital truncations through two-electron unitary transformations of the Hamiltonian operator, such as those employed in the solution of the ACSE. The molecule-optimized basis set from the ACS...

  9. PREFACE: Processes in Isotopes and Molecules

    Bogdan, Diana; Tosa, Valer

    2009-07-01

    These Proceedings present some of the Invited Lectures and Contributed Papers of the International Conference 'Processes in Isotopes and Molecules' (PIM), held in Cluj-Napoca, Romania, 24-26 September 2009. The PIM conference, started in 1999 as a local event, is now an international conference organized every two years by the National Institute for R&D of Isotopic and Molecular Technologies in Cluj-Napoca, the capital city of Transylvania, Romania. The meetings are attended by researchers in the field of atomic and molecular physics as well as those developing new materials and technologies. The scientific subjects are at the cross-roads of three fundamental research areas: physics, chemistry, and biology. The papers here are grouped according to the five conference topics: T1 - Molecular and biomolecular systems T2 - Modern techniques and technologies T3 - Environmental molecular processes T4 - Hydrogen and renewable sources of energy T5 - Nanostructured materials and nanocomposites We gratefully acknowledge the contribution of our colleagues from the Scientific Committee and Program Committee who contributed their time, energy and expertise to the refereeing process. Finally, we would like to thank people from IOP Publishing for their friendly advice and prompt help during the editing process, as well as for their efforts making the Journal of Physics: Conference Series available to the scientific community. Diana Bogdan and Valer Tosa National Institute for R&D Isotopic and Molecular Technologies, Cluj-Napoca

  10. Electron transport through a diatomic molecule

    Electron transport through a diatomic molecular tunnel junction shows wave like interference phenomenon. By using Keldysh non-equilibrium Green's function (NEGF) theory, we have explicitly presented current and differential conductance calculation for a diatomic molecular and two isolated atoms (two atoms having zero hybridization between their energy orbitals) tunnel junctions. In case of a diatomic molecular tunnel junction, Green's function propagators entering into current and differential conductance formula interfere constructively for a molecular anti-bonding state and destructively for bonding state. Consequently, conductance through a molecular bonding state is suppressed, and to conserve current, conductance through anti-bonding state is enhanced. Therefore, current steps and differential conductance peaks amplitude show asymmetric correspondence between molecular bonding and anti-bonding states. Interestingly, for a diatomic molecule, comprising of two atoms of same energy level, these propagators interfere completely destructively for molecular bonding state and constructively for molecular anti-bonding state. Hence under such condition, a single step or a single peak is shown up in current versus voltage or differential conductance versus voltage studies.

  11. Electron transport through a diatomic molecule

    Imran, Muhammad, E-mail: imran1gee@gmail.com

    2014-08-01

    Electron transport through a diatomic molecular tunnel junction shows wave like interference phenomenon. By using Keldysh non-equilibrium Green's function (NEGF) theory, we have explicitly presented current and differential conductance calculation for a diatomic molecular and two isolated atoms (two atoms having zero hybridization between their energy orbitals) tunnel junctions. In case of a diatomic molecular tunnel junction, Green's function propagators entering into current and differential conductance formula interfere constructively for a molecular anti-bonding state and destructively for bonding state. Consequently, conductance through a molecular bonding state is suppressed, and to conserve current, conductance through anti-bonding state is enhanced. Therefore, current steps and differential conductance peaks amplitude show asymmetric correspondence between molecular bonding and anti-bonding states. Interestingly, for a diatomic molecule, comprising of two atoms of same energy level, these propagators interfere completely destructively for molecular bonding state and constructively for molecular anti-bonding state. Hence under such condition, a single step or a single peak is shown up in current versus voltage or differential conductance versus voltage studies.

  12. Low Energy Ion-Molecule Reactions

    James M. Farrar

    2004-05-01

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

  13. Database of Small Molecule Thermochemistry for Combustion

    Goldsmith, C. Franklin

    2012-09-13

    High-accuracy ab initio thermochemistry is presented for 219 small molecules relevant in combustion chemistry, including many radical, biradical, and triplet species. These values are critical for accurate kinetic modeling. The RQCISD(T)/cc-PV∞QZ//B3LYP/6-311++G(d,p) method was used to compute the electronic energies. A bond additivity correction for this method has been developed to remove systematic errors in the enthalpy calculations, using the Active Thermochemical Tables as reference values. On the basis of comparison with the benchmark data, the 3σ uncertainty in the standard-state heat of formation is 0.9 kcal/mol, or within chemical accuracy. An uncertainty analysis is presented for the entropy and heat capacity. In many cases, the present values are the most accurate and comprehensive numbers available. The present work is compared to several published databases. In some cases, there are large discrepancies and errors in published databases; the present work helps to resolve these problems. © 2012 American Chemical Society.

  14. Quantum Monte Carlo for atoms and molecules

    The diffusion quantum Monte Carlo with fixed nodes (QMC) approach has been employed in studying energy-eigenstates for 1--4 electron systems. Previous work employing the diffusion QMC technique yielded energies of high quality for H2, LiH, Li2, and H2O. Here, the range of calculations with this new approach has been extended to include additional first-row atoms and molecules. In addition, improvements in the previously computed fixed-node energies of LiH, Li2, and H2O have been obtained using more accurate trial functions. All computations were performed within, but are not limited to, the Born-Oppenheimer approximation. In our computations, the effects of variation of Monte Carlo parameters on the QMC solution of the Schroedinger equation were studied extensively. These parameters include the time step, renormalization time and nodal structure. These studies have been very useful in determining which choices of such parameters will yield accurate QMC energies most efficiently. Generally, very accurate energies (90--100% of the correlation energy is obtained) have been computed with single-determinant trail functions multiplied by simple correlation functions. Improvements in accuracy should be readily obtained using more complex trial functions

  15. Visualizing ligand molecules in twilight electron density

    A software script is presented for facilitating the analysis and visual inspection of ligand molecules in the context of the electron-density maps calculated from experimental data associated with protein structures determined by X-ray crystallography. Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight//

  16. Perspective: Mechanochemistry of biological and synthetic molecules

    Makarov, Dmitrii E.

    2016-01-01

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

  17. Perspective: Mechanochemistry of biological and synthetic molecules

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

  18. Accurate adiabatic correction in the hydrogen molecule

    Pachucki, Krzysztof, E-mail: krp@fuw.edu.pl [Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw (Poland); Komasa, Jacek, E-mail: komasa@man.poznan.pl [Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań (Poland)

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  19. Molecules to migration: pressures of life.

    Vosloo, André

    2010-01-01

    The highly successful Fourth International Conference in Africa for Comparative Physiology and Biochemistry (ICA-CPB) was held in the Maasai Mara National Reserve in July 2008. The theme of the meeting was "Molecules to Migration: Pressures of Life." To enhance the theme, the venue and timing of the meeting were chosen to coincide with the arrival of approximately 1.4 million wildebeest on their annual migration from the Serengeti National Park in Tanzania. Like the three previous ICA-CPB meetings, the discussion topics and the resulting collection of synthesia presented here were very diverse. The articles in this special collection reflect the authors' interest in broadening our understanding of the field of comparative physiology and biochemistry and their commitment to engaging in global research with international colleagues. These articles are brief, synthetic reviews integrating information presented at and inspired by the meeting. From seasonal migration and reproduction in birds, to cardiovascular system development in vertebrates, to strategies for hypoxia survival, papers range from specific to broad interactions. What they all have in common: they increase our understanding of how animals are affected by and respond to the pressures of life. PMID:20653447

  20. Perspective: Mechanochemistry of biological and synthetic molecules

    Makarov, Dmitrii E., E-mail: makarov@cm.utexas.edu [Department of Chemistry and Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712 (United States)

    2016-01-21

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

  1. Polycyclic aromatic hydrocarbon molecules in astrophysics

    Rastogi, Shantanu; Pathak, Amit; Maurya, Anju

    2013-06-01

    Polycyclic aromatic hydrocarbon (PAH) molecules are responsible for the mid-infrared emission features. Their ubiquitous presence in almost all types of astrophysical environments and related variations in their spectral profilesmake them an important tool to understand the physics and chemistry of the interstellar medium. The observed spectrum is generally a composite superposition of all different types of PAHs possible in the region. In the era of space telescopes the spectral richness of the emission features has enhanced their importance as probe and also the need to understand the variations with respect to PAH size, type and ionic state. Quantum computational studies of PAHs have proved useful in elucidating the profile variations and put constraints on the possible types of PAHs in different environments. The study of PAHs has also significantly contributed to the problems of diffuse interstellar bands (DIBs), UV extinction and understanding the chemistry of the formation of complex organics in space. The review highlights the results of various computational models for the understanding of infrared emission features, the PAH-DIB relation, formation of prebiotics and possible impact in the understanding of far-infrared features.

  2. X(3872) is not a true molecule

    Coito, Susana; van Beveren, Eef

    2012-01-01

    The wave function of the charmonium-like meson X(3872) is expected to have a very significant $D^0\\bar{D}^{*0}$ component, as the latter threshold lies only 0.16 MeV above the meson's mass. Some conclude from this mass coincidence that X(3872) is a meson-meson molecule, whatever the dynamics giving rise to the state. This would imply that the $D^0\\bar{D}^{*0}$ component of the X(3872) wave function is the only relevant one. In the present paper we study this issue by employing a soluble model for a $^3P_1$ $c\\bar{c}$ state coupled to an S-wave $D^0\\bar{D}^{*0}$ decay channel, communicating via the $^3P_0$ mechanism. The model is a simplified, coordinate-space version of the resonance-spectrum expansion previously employed in a detailed investigation of X(3872)'s nature. The resulting two-component wave function is calculated for different values of the binding energy (BE) and the transition radius $a$. Thus, a significant $c\\bar{c}$ component is found in all situations. However, the long tail of the $D^0\\bar{...

  3. Indexing molecules with chemical graph identifiers.

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

    2011-09-01

    Fast and robust algorithms for indexing molecules have been historically considered strategic tools for the management and storage of large chemical libraries. This work introduces a modified and further extended version of the molecular equivalence number naming adaptation of the Morgan algorithm (J Chem Inf Comput Sci 2001, 41, 181-185) for the generation of a chemical graph identifier (CGI). This new version corrects for the collisions recognized in the original adaptation and includes the ability to deal with graph canonicalization, ensembles (salts), and isomerism (tautomerism, regioisomerism, optical isomerism, and geometrical isomerism) in a flexible manner. Validation of the current CGI implementation was performed on the open NCI database and the drug-like subset of the ZINC database containing 260,071 and 5,348,089 structures, respectively. The results were compared with those obtained with some of the most widely used indexing codes, such as the CACTVS hash code and the new InChIKey. The analyses emphasize the fact that compound management activities, like duplicate analysis of chemical libraries, are sensitive to the exact definition of compound uniqueness and thus still depend, to a minor extent, on the type and flexibility of the molecular index being used. PMID:21647928

  4. Evidence for genistein as a mitochondriotropic molecule.

    de Oliveira, Marcos Roberto

    2016-07-01

    Genistein (4',5,7-trihydroxyisoflavone; C15H10O5), an isoflavone, has been investigated as an anti-cancer agent due to its ability to trigger cell death (both intrinsic and extrinsic apoptotic pathways) in different cancer cells in vitro and in vivo. Furthermore, genistein has been viewed as a mitochondriotropic molecule due to the direct effects this isoflavone induces in mitochondria, such as modulation of enzymatic activity of components of the oxidative phosphorylation system. Apoptosis triggering may also be mediated by genistein through activation of the mitochondria-dependent pathway by a mechanism associated with mitochondrial dysfunction (i.e., disruption of the mitochondrial membrane potential - MMP, release of cytochrome c, activation of the apoptosome, among others). Efforts have been made in order to elucidate how genistein coordinate these biochemical phenomena. Nonetheless, some areas of the mitochondria-associated research (mitochondrial biogenesis, redox biology of mitochondria, and mitochondria-associated bioenergetic parameters) need to be explored regarding the role of genistein as a mitochondria-targeted agent. This is a pharmacologically relevant issue due to the possibility of using genistein as a mitochondria-targeted drug in cases of cancer, neurodegeneration, cardiovascular, and endocrine disease, for example. The present review aims to describe, compare, and discuss relevant data about the effects of genistein upon mitochondria. PMID:27223841

  5. Complex organic molecules in protoplanetary disks

    Walsh, Catherine; Nomura, Hideko; Herbst, Eric; Weaver, Susanna L Widicus; Aikawa, Yuri; Laas, Jake C; Vasyunin, Anton I

    2014-01-01

    (Abridged) Protoplanetary disks are vital objects in star and planet formation, possessing all the material which may form a planetary system orbiting the new star. We investigate the synthesis of complex organic molecules (COMs) in disks to constrain the achievable chemical complexity and predict species and transitions which may be observable with ALMA. We have coupled a 2D model of a protoplanetary disk around a T Tauri star with a gas-grain chemical network including COMs. We compare compare synthesised line intensities and calculated column densities with observations and determine those COMs which may be observable in future. COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances 1e-6 - 1e-4 that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, 1e-12 - 1e-...

  6. Thermal decomposition of irradiated casein molecules

    Non-isothermal studies were carried out using the derivatograph where thermogravimetry (TG), and differential thermogravimetry (DTG) measurements were used to obtain the activation energies of the first and second reactions for casein decomposition before and after exposure to gamma rays and fast neutrons. Cf- 252 was used as a source of fast neutrons associated with gamma rays. TG and DTG patterns were also recorded for casein samples before and after irradiation with 1 Gy gamma-rays of 0.662 MeV from Cs - 137. However, no change in a activation energies were observed after exposure to gamma-irradiation. On the other hand, the activation energies for first and second reactions were found to be smaller at 0.4 m Gy than that at lower and higher neutron doses. However, no change in activation energies was observed after γ irradiation. It is concluded from the present study that destruction of casein molecules by low level fast neutron doses may lead to changes of shelf storage period milk. 3 figs., 1 tab

  7. Theoretically predicted Fox-7 based new high energy density molecules

    Ghanta, Susanta

    2016-08-01

    Computational investigation of CHNO based high energy density molecules (HEDM) are designed with FOX-7 (1, 1-dinitro 2, 2-diamino ethylene) skeleton. We report structures, stability and detonation properties of these new molecules. A systematic analysis is presented for the crystal density, activation energy for nitro to nitrite isomerisation and the C-NO2 bond dissociation energy of these molecules. The Atoms in molecules (AIM) calculations have been performed to interpret the intra-molecular weak H-bonding interactions and the stability of C-NO2 bonds. The structure optimization, frequency and bond dissociation energy calculations have been performed at B3LYP level of theory by using G03 quantum chemistry package. Some of the designed molecules are found to be more promising HEDM than FOX-7 molecule, and are proposed to be candidate for synthetic purpose.

  8. Controlling single-molecule junction conductance by molecular interactions.

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

    2015-01-01

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

  9. Theory of electron transport through single molecules of polyaniline

    Lee, Myeong H [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States); Speyer, Gil [Fulton High Performance Computing Center, Arizona State University, Tempe, AZ 85287-1504 (United States); Sankey, Otto F [Department of Physics, Arizona State University, Tempe, AZ 85287-1504 (United States)

    2007-05-30

    We present theoretical results for the electron transport properties of the organic molecule polyaniline, especially leucoemeraldine (LEB), the fully reduced form. The electron tunnelling characteristics of these chain-like molecules are described by their complex band-structure. We explore how the bandgap and tunnelling decay parameter {beta} depend on the oxidation state of the molecule and on the torsion angle between rings. It is found that the metal Fermi level lies near the HOMO for gold contacts with a single leucoemeraldine molecule, which results in non-linear I-V characteristics. The conductance of a hepta-aniline (LEB) oligomer is obtained from a first-principles I-V curve and compared with the recent experimental results. We examine the effect of stretching of the molecule on its conductance to explain the discrepancy between the theoretical simulations and single-molecule conductance measurement experiment.

  10. Imaging and manipulation of a polar molecule on Ag(111)

    Lin, R.; Braun, K.F.; Tang, H.;

    2001-01-01

    A scanning tunneling microscope (STM) was applied to image and laterally manipulate isolated phosphangulene molecules on Ag(111) at 6 K. Atomic-resolution images clearly revealed three characteristic types of appearances (three-lobed, fish and bump shape) for the adsorbed molecules, which could...... correspond to three distinct binding configurations. From a detailed analysis of the relative distance between neighboring three-lobed molecules we determine the adsorption site. Applying the lateral manipulation technique ws demonstrate that the molecule can be pulled, slid or pushed by the tip on the...... surface. Accompanying with the reposition, molecular rotation and/or changing of binding configurations can also be induced. It is found that the dipole moment of the molecule has minor effects on its lateral movement. The results demonstrate that due to many degrees of freedom for large molecules! their...

  11. Imaging and manipulation of a polar molecule oil Ag(111)

    Lin, Rong; Braun, K.F.; Tang, H.;

    2001-01-01

    A scanning tunneling microscope (STM) was applied to image and laterally manipulate isolated phosphangulene molecules on Ag(111) at 6 K. Atomic-resolution images clearly revealed three characteristic types of appearances (three-lobed, fish and bump shape) for the adsorbed molecules, which could...... correspond to three distinct binding configurations. From a detailed analysis of the relative distance between neighboring three-lobed molecules we determine the adsorption site. Applying the lateral manipulation technique ws demonstrate that the molecule can be pulled, slid or pushed by the tip on the...... surface. Accompanying with the reposition, molecular rotation and/or changing of binding configurations can also be induced. It is found that the dipole moment of the molecule has minor effects on its lateral movement. The results demonstrate that due to many degrees of freedom for large molecules! their...

  12. Human thymic epithelial cells express functional HLA-DP molecules

    Jørgensen, A; Röpke, C; Nielsen, M;

    1996-01-01

    HLA-DP molecules function as restriction elements in the presentation of foreign antigens to T cells by antigen presenting cells and certain HLA-DP molecules confer susceptibility to autoimmune disease. Because HLA molecules play an essential role in thymic selection and elimination of autoreactive...... T lymphocytes, we examined whether human thymic epithelial cells (TEC) expressed HLA-DP molecules. We present evidence that TEC obtained from short time culture express low but significant levels of HLA-DP molecules. The expression of HLA-DP molecules was comparable to or higher than the expression...... of HLA-DQ but lower than that of HLA-DR. Upon IFN-gamma treatment, HLA-DP expression was strongly upregulated. Since HLA-DQ and DR expression was upregulated in parallel, the hierarchy between MHC class II isotypes remained unchanged following interferon treatment. TEC elicited significant...

  13. Adsorption Geometry Determination of Single Molecules by Atomic Force Microscopy

    Schuler, Bruno; Liu, Wei; Tkatchenko, Alexandre; Moll, Nikolaj; Meyer, Gerhard; Mistry, Anish; Fox, David; GROSS, Leo

    2013-01-01

    We measured the adsorption geometry of single molecules with intramolecular resolution using noncontact atomic force microscopy with functionalized tips. The lateral adsorption position was determined with atomic resolution, adsorption height differences with a precision of 3 pm, and tilts of the molecular plane within 0.2 degrees. The method was applied to five pi-conjugated molecules, including three molecules from the olympicene family, adsorbed on Cu(111). For the olympicenes, we found th...

  14. Cold and Ultracold Molecules: Science, Technology, and Applications

    Carr, Lincoln D.; DeMille, David; Krems, Roman V.; Ye, Jun

    2009-01-01

    This article presents a review of the current state of the art in the research field of cold and ultracold molecules. It serves as an introduction to the Special Issue of the New Journal of Physics on Cold and Ultracold Molecules and describes new prospects for fundamental research and technological development. Cold and ultracold molecules may revolutionize physical chemistry and few body physics, provide techniques for probing new states of quantum matter, allow for precision measurements o...

  15. Bone marrow origin of Ia molecules purified from epidermal cells

    Using radiation bone marrow chimeras, we have shown that Ia molecules purified from epidermal cell preparations of the mouse reflect the Ia phenotype of the bone marrow donor. This result strongly suggests that Ia molecules are synthesized by a bone-marrow-derived cell in the epidermis. Furthermore, results of peptide map analysis of immunoprecipitated biosynthetically labeled Ia suggest that the Ia molecules found in skin are identical to those found on B lymphocytes. These results support biochemical as well as serologic identity

  16. Biophysical characterization of DNA binding from single molecule force measurements

    Chaurasiya, Kathy R.; Paramanathan, Thayaparan; McCauley, Micah J.; Williams, Mark C.

    2010-01-01

    Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as hig...

  17. Dynamic scanning probe microscopy of adsorbed molecules on graphite

    Berdunov, N.; Pollard, A J; Beton, P. H.

    2008-01-01

    We have used a combined dynamic scanning tunneling and atomic force microscope to study the organisation of weakly bound adsorbed molecules on a graphite substrate. Specifically we have acquired images of islands of the perylene derivative molecules. These weakly bound molecules may be imaged in dynamic STM, in which the probe is oscillated above the surface. We show that molecular resolution may be readily attained and that a similar mode of imaging may be realised using conventional STM arr...

  18. The electroluminescence and scanning tunneling microscopy of single molecules

    Buker, John William

    2009-01-01

    The scanning tunneling microscopy (STM) of single molecules has become a prominent experimental method in the field of molecular electronics. It has been found that in STM experiments, when an electric current flows through a single molecule, the molecule may luminesce. This electroluminescence, in conjunction with traditional STM data, provides a potentially important additional degree of freedom for understanding nanoscale systems. This thesis describes exploratory theoretical work on the n...

  19. Reversible Photomechanical Switching of Individual Engineered Molecules at a Surface

    Comstock, Matthew J.; Levy, Niv; Kirakosian, Armen; Cho, Jongweon; Lauterwasser, Frank; Harvey, Jessica H.; Strubbe, David A; Frechet, Jean M. J.; Trauner, Dirk; Louie, Steven G.; Crommie, Michael F.

    2006-01-01

    We have observed reversible light-induced mechanical switching for a single organic molecule bound to a metal surface. Scanning tunneling microscopy (STM) was used to image the features of an individual azobenzene molecule on Au(111) before and after reversibly cycling its mechanical structure between trans and cis states using light. Azobenzene molecules were engineered to increase their surface photomechanical activity by attaching varying numbers of tert-butyl (TB) ligands ("legs") to the ...

  20. Transport of polar molecules by an alternating gradient guide

    Wall, T. E.; Armitage, S; Hudson, J. J.; Sauer, B. E.; Dyne, J. M.; Hinds, E. A.; Tarbutt, M.R.

    2009-01-01

    An alternating gradient electric guide provides a way to transport a wide variety of polar molecules, including those in high-field seeking states. We investigate the motion of polar molecules in such a guide by measuring the transmission of CaF molecules in their high-field seeking ground state, with the guide operating at a variety of switching frequencies and voltages. We model the guide using analytical and numerical techniques and compare the predictions of these models to the experiment...

  1. An RNA toolbox for single-molecule force spectroscopy studies

    2007-01-01

    Precise, controllable single-molecule force spectroscopy studies of RNA and RNA-dependent processes have recently shed new light on the dynamics and pathways of RNA folding and RNA-enzyme interactions. A crucial component of this research is the design and assembly of an appropriate RNA construct. Such a construct is typically subject to several criteria. First, single-molecule force spectroscopy techniques often require an RNA construct that is longer than the RNA molecules used for bulk bio...

  2. Small molecule annotation for the Protein Data Bank

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M.; Chen, Minyu; Conroy, Matthew J.; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P.; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100 000 structures contain more than 20 000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present...

  3. Deceleration of neutral molecules in macroscopic traveling traps

    A decelerator is presented where polar neutral molecules are guided and decelerated using the principle of traveling electric potential wells, such that molecules are confined in stable three-dimensional traps throughout. We compare this decelerator with that of Scharfenberg et al. [Phys. Rev. A 79, 023410 (2009)] and we show that the current decelerator provides a substantially larger phase-space acceptance, even at higher acceleration. The mode of operation is described and experimentally demonstrated by guiding and decelerating CO molecules.

  4. Single Molecule Raman Detection of Enkephalin on Silver Colloidal Particles

    Kneipp, Katrin; Kneipp, Holger; Abdali, Salim; Berg, Rolf W.; Bohr, Henrik

    2004-01-01

    Raman signal the enkephalin molecules have been attached to silver colloidal cluster structures. The experiments demonstrate that the SERS signal of the strongly enhanced ring breathing vibration of phenylalanine at 1000 cm-1 can be used as “intrinsic marker” for detecting a single enkephalin molecule...... and for monitoring its diffusion on the surface of the silver colloidal cluster without using a specific label molecule....

  5. Single Molecule Spectroscopy for Studying Conformational Dynamics of Short Oligonucleotides

    Lin, Ron Reuven

    2012-01-01

    Understanding biology at the molecular level has been driving technological advances in biological and medical science for many years. Methods for probing molecular systems are often dependent on sampling the concerted actions of large assemblies of molecules rather than for studying individual molecules operating in isolation. Most methods used in experimental biology are largely insensitive to the activity of a single molecule. Over the past twenty five years, advances in a variety of di...

  6. Nanostructure sensor of presence and concentration of a target molecule

    Schipper, John F. (Inventor)

    2009-01-01

    Method and system (i) to determine when a selected target molecule is present or absent in a fluid, (2) to estimate concentration of the target molecule in the fluid and (3) estimate possible presence of a second (different) target molecule in the fluid, by analyzing differences in resonant frequencies of vibration of a thin beam suspended in the fluid, after the fluid has moved across the beam.

  7. Trajectory Dynamics of Gas Molecules and Galaxy Formation

    Llanos, Pedro J.; Miller, James K.; Hintz, Gerald R.

    2013-01-01

    The probability distribution of the velocity of gas molecules in a closed container is described by the kinetic theory of gases. When molecules collide or impact the walls of a container, they exchange energy and momentum in accordance with Newton's laws of motion. Between collisions, the trajectory of individual molecules is a straight line, neglecting gravity. During the formation of a galaxy, the stars are constrained to a region of space and exchange energy and momentum in a manner simila...

  8. MHCcluster, a method for functional clustering of MHC molecules

    Thomsen, Martin; Lundegaard, Claus; Buus, Søren; Lund, Ole; Nielsen, Morten

    2013-01-01

    The identification of peptides binding to major histocompatibility complexes (MHC) is a critical step in the understanding of T cell immune responses. The human MHC genomic region (HLA) is extremely polymorphic comprising several thousand alleles, many encoding a distinct molecule. The potentially unique specificities remain experimentally uncharacterized for the vast majority of HLA molecules. Likewise, for nonhuman species, only a minor fraction of the known MHC molecules have been characte...

  9. Cell adhesion molecules: detection with univalent second antibody

    1980-01-01

    Identification of cell surface molecules that play a role in cell-cell adhesion (here called cell adhesion molecules) has been achieved by demonstrating the inhibitory effect of univalent antibodies that bind these molecules in an in vitro assay of cell-cell adhesion. A more convenient reagent, intact (divalent) antibody, has been avoided because it might agglutinate the cells rather than blocking cell-cell adhesion. In this report, we show that intact rabbit immunoglobulin directed against c...

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

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

  11. Domain-based small molecule binding site annotation

    Dumontier Michel

    2006-03-01

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

  12. Spin-lattice relaxation in phosphorescent triplet state molecules

    The present thesis contains the results of a study of spin-lattice relaxation (SLR) in the photo-excited triplet state of aromatic molecules, dissolved in a molecular host crystal. It appears that SLR in phosphorescent triplet state molecules often is related to the presence of so-called (pseudo) localized phonons in the molecular mixed crystals. These local phonons can be thought to correspond with vibrations (librations) of the guest molecule in the force field of the surrounding host molecules. Since the intermolecular forces are relatively weak, the frequencies corresponding with these vibrations are relatively low and usually are of the order of 10-30 cm-1. (Auth.)

  13. Quantum effects at low-energy atom–molecule interface

    B Deb; A Rakshit; J Hazra; D Chakraborty

    2013-01-01

    The effects of quantum interference in inter-conversion between cold atoms and diatomic molecules are analysed in this study. Within the framework of Fano’s theory, continuum bound anisotropic dressed state formalism of atom–molecule quantum dynamics is presented. This formalism is applicable in photo- and magneto-associative strong-coupling regimes. The significance of Fano effect in ultracold atom–molecule transitions is discussed. Quantum effects at low-energy atom–molecule interface are important for exploring coherent phenomena in hitherto unexplored parameter regimes.

  14. Visualization of DNA molecules in time during electrophoresis

    Lubega, Seth

    1991-01-01

    For several years individual DNA molecules have been observed and photographed during agarose gel electrophoresis. The DNA molecule is clearly the largest molecule known. Nevertheless, the largest molecule is still too small to be seen using a microscope. A technique developed by Morikawa and Yanagida has made it possible to visualize individual DNA molecules. When these long molecules are labeled with appropriate fluorescence dyes and observed under a fluorescence microscope, although it is not possible to directly visualize the local ultrastructure of the molecules, yet because they are long light emitting chains, their microscopic dynamical behavior can be observed. This visualization works in the same principle that enables one to observe a star through a telescope because it emits light against a dark background. The dynamics of individual DNA molecules migrating through agarose matrix during electrophoresis have been described by Smith et al. (1989), Schwartz and Koval (1989), and Bustamante et al. (1990). DNA molecules during agarose gel electrophoresis advance lengthwise thorough the gel in an extended configuration. They display an extension-contraction motion and tend to bunch up in their leading ends as the 'heads' find new pores through the gel. From time to time they get hooked on obstacles in the gel to form U-shaped configurations before they resume their linear configuration.

  15. Molecular electronics with single molecules in solid-state devices.

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-09-01

    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule, and on how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong. PMID:19734925

  16. Counting Single Rhodamine 6G Dye Molecules in Organosilicate Nanoparticles

    Trenkmann, I.; Bok, S.; Korampally, V.; S. Gangopadhyay; Graaf, H. de; C. von Borczyskowski

    2012-01-01

    Rhodamine 6G (R6G) dye molecules have been embedded into organosilicate nanoparticles to improve thermal and chemical stability of these marker molecules. We demonstrate that the well-established method of optical single-particle microscopy can be used to determine the number of dye molecules per nanoparticle in such hybrid materials. Analysing the fluorescence intensity of R6G in single nanoparticles, we obtain an average number of 1.3 – 1.7 dye molecules per nanoparticle as compared to 1 R6...

  17. DNA entropic elasticity for short molecules attached to beads

    Li, J; Nelson, P C; Li, Jinyu; Nelson, Philip C.

    2006-01-01

    Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the...

  18. Novel approaches for single molecule activation and detection

    Benfenati, Fabio; Torre, Vincent

    2014-01-01

    How can we obtain tools able to process and exchange information at the molecular scale In order to do this, it is necessary to activate and detect single molecules under controlled conditions. This book focuses on the generation of biologically-inspired molecular devices. These devices are based on the developments of new photonic tools able to activate and stimulate single molecule machines. Additionally, new light sensitive molecules can be selectively activated by photonic tools. These technological innovations will provide a way to control activation of single light-sensitive molecules, a

  19. Electron capture by polar molecules and cluster in magnetic field

    Impact of external magnetic field on formation of a bound electron state with neutral molecular complex, consisting of polar molecules, is considered. It is shown that in case of one polar molecule with dipole moment anti ρ, positioned in the magnetic field, the electron forms the bound state therewith, if anti ρ equals to 0.318D. The polar theory of bound states in magnetic fields is developed for a cluster of polar molecules with the summarized of polar molecules with the summarized dipole moment equal to zero. The electron and cluster bound states are considered. The spectrum of such states is obtained

  20. Molecular electronics with single molecules in solid-state devices

    Moth-Poulsen, Kasper; Bjørnholm, Thomas

    2009-01-01

    The ultimate aim of molecular electronics is to understand and master single-molecule devices. Based on the latest results on electron transport in single molecules in solid-state devices, we focus here on new insights into the influence of metal electrodes on the energy spectrum of the molecule......, and how the electron transport properties of the molecule depend on the strength of the electronic coupling between it and the electrodes. A variety of phenomena are observed depending on whether this coupling is weak, intermediate or strong....

  1. Quantum Effects at Low Energy Atom-Molecule Interface

    Deb, B; Hazra, J; Chakraborty, D

    2013-01-01

    Quantum interference effects in inter-conversion between cold atoms and diatomic molecules are analysed. Within the framework of Fano's theory, continuum-bound anisotropic dressed state formalism of atom-molecule quantum dynamics is presented. This formalism is applicable in photo- and magneto-associative strong-coupling regimes. The significance of Fano effect in ultracold atom-molecule transitions is discussed. Quantum effects at low energy atom-molecule interface are important for exploring coherent phenomena in hither-to unexplored parameter regimes.

  2. Observation of individual molecules trapped on a nanostructured insulator

    Nony, L; Baratoff, A; Alkauskas, A; Bennewitz, R P; Pfeiffer, O; Maier, S; Wezel, A; Meyer, E; Gerber, C E; Nony, Laurent; Gnecco, Enrico Dr.; Baratoff, Alexis; Alkauskas, Audrius; Bennewitz, Roland; Pfeiffer, Oliver; Maier, Sabine; Wezel, Adrian; Meyer, Ernst; Gerber, Christophe

    2004-01-01

    For the first time, ordered polar molecules confined in monolayer-deep rectangular pits produced on an alkali halide surface by electron irradiation have been resolved at room temperature by non-contact atomic force microscopy. Molecules self-assemble in a specific fashion inside pits of width smaller than 15 nm. By contrast no ordered aggregates of molecules are observed on flat terraces. Conclusions regarding nucleation and ordering mechanisms are drawn. Trapping in pits as small as 2 nm opens a route to address single molecules.

  3. Multiple packets of neutral molecules revolving for over a mile

    Zieger, Peter C; Heiner, Cynthia E; Bethlem, Hendrick L; van Roij, André J A; Meijer, Gerard

    2010-01-01

    The level of control that one has over neutral molecules in beams dictates their possible applications. Here we experimentally demonstrate that state-selected, neutral molecules can be kept together in a few mm long packet for a distance of over one mile. This is accomplished in a circular arrangement of 40 straight electrostatic hexapoles through which the molecules propagate over 1000 times. Up to 19 packets of molecules have simultaneously been stored in this ring structure. This brings the realization of a molecular low-energy collider within reach.

  4. Enantiomer-Specific State Transfer of Chiral Molecules

    Eibenberger, Sandra; Patterson, David

    2016-01-01

    State-selective enantiomeric excess is realized using microwave-driven coherent population transfer. The method selectively promotes either R- or S- molecules to a higher rotational state by phase-controlled microwave pulses that drive electric-dipole allowed rotational transitions. We demonstrate the method using a racemic mixture of 1,2-propanediol. This method of chiral enrichment can be applied to nearly any chiral molecule that can be vaporized and cooled to the point where rotationally resolved spectroscopy is possible, including molecules that rapidly racemize. The rapid chiral switching demonstrated here allows for new applications in high-precision spectroscopic searches for parity violation in chiral molecules.

  5. The photodissociation and reaction dynamics of vibrationally excited molecules

    Crim, F.F. [Univ. of Wisconsin, Madison (United States)

    1993-12-01

    This research determines the nature of highly vibrationally excited molecules, their unimolecular reactions, and their photodissociation dynamics. The goal is to characterize vibrationally excited molecules and to exploit that understanding to discover and control their chemical pathways. Most recently the author has used a combination of vibrational overtone excitation and laser induced fluorescence both to characterize vibrationally excited molecules and to study their photodissociation dynamics. The author has also begun laser induced grating spectroscopy experiments designed to obtain the electronic absorption spectra of highly vibrationally excited molecules.

  6. An optical nanofiber-based interface for single molecules

    Skoff, Sarah M; Schauffert, Hardy; Rauschenbeutel, Arno

    2016-01-01

    Optical interfaces for quantum emitters are a prerequisite for implementing quantum networks. Here, we couple single molecules to the guided modes of an optical nanofiber. The molecules are embedded within a crystal that provides photostability and due to its inhomogeneous environment, a means to spectrally address single molecules. Single molecules are excited and detected solely via the nanofiber interface without the requirement of additional optical access. In this way, we realize a fully fiber-integrated system that is scalable and may become a versatile constituent for quantum hybrid systems.

  7. Origin of subdiffusion of water molecules on cell membrane surfaces

    Yamamoto, Eiji; Yasui, Masato; Yasuoka, Kenji

    2014-01-01

    Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using all-atom molecular dynamics simulations, we show that translational and rotational diffusion of water molecules on lipid membrane surfaces exhibit subdiffusion. Moreover, we provide evidence that both divergent mean trapping time (continuous-time random walk) and long-correlated noise (fractional Brownian motion) contribute to this subdiffusion. These results suggest that subdiffusion on cell membranes causes the water retardation, an enhancement of cell membrane stability, and a higher reaction efficiency.

  8. Electron attachment to biological relevant molecules

    Full text: The interaction of low energy electrons with compounds of DNA/RNA leading to negative ions gives insight into radiation damage processes in human cells. We demonstrate that electrons at sub excitation energies (- with X = T, C, U or G. This observation has significant consequences for the molecular picture of radiation damage, i.e. genotoxic effects or damage of living cells due to the secondary component of high energy radiation. The present experiment is performed in a crossed electron/neutral molecule beam arrangement. A highly monochromatized electron beam, generated by an electrostatic hemispherical electron monochromator, interacts with an effusive molecular beam of biomolecules. Negative ions are extracted from the collision region and focused into a quadrupole mass spectrometer, where they are mass analyzed and detected by single pulse counting electronics. In the present measurements the dominant negative ions formed via electron attachment (EA) reaction to T, C, U and G, are (T-H)-, (C-H)-, (U-H)- and (G-H)-. Using a simple calibration procedure, values for the respective partial EA cross section for (T-H)-, (C-H)-, (U-H)-, and (G-H)- could be determined yielding a peak value of σ (1.05 eV) = 1.2 x 10-19 m2, σ (1.54 eV) = 2.3 x 10-20 m2, σ (1.0 eV) = 3 x 10-20 m2, σ (1.3 eV) = 5 x 10-20 m2 , respectively. At higher electron energies, we observe further product anions, but at significantly lower cross sections. (author)

  9. Mean field theory for long chain molecules

    Pereira, Gerald G.

    1996-06-01

    We provide a mathematical formalism for a self-consistent mean field treatment of long chain molecules. The formalism is applied to the case of a neutral polymer under the excluded volume interaction. Upon scaling the problem in the N→∞ limit we find the natural scaling length RN, of the polymer, which is made up of (N+1) monomers or beads, is RN˜N3/5, the well known Flory result. The asymptotics of the problem is dominated by the neighborhood of the turning point, so that a uniformly valid Green's function solution of the differential equations is necessary. In the neighborhood of a point y* the scaled polymer density fN(x), is found to decay sharply. If we let x denote the scaled distance from one end of the chain to a point in space we obtain, for y*-x≳O(N-2/15), a closed form expression for the polymer density viz., fN(x)˜{1/2x2[fN(x)-fN(y*)]1/2} while for x-y*≳O(N-2/15) the density is shown to be, to leading order, zero. Although our results imply the rate of decay of the density at y* is O(N1/5) we are unable to verify this explicitly by calculating fN'(y*). We believe this is due to the inability of the WKB theory to correctly approximate solutions in regions of rapid variation. We suggest remedies for this, so that a complete self-consistent solution may be obtained.

  10. Planctomycetes as Novel Source of Bioactive Molecules

    Graça, Ana P.; Calisto, Rita; Lage, Olga M.

    2016-01-01

    strains from Rhodopirellula lusitana, R. rubra, R. baltica, Roseimaritima ulvae, and Planctomyces brasiliensis. This study confirms the bioactive capacity of Planctomycetes to produce antimicrobial compounds and encourages further studies envisaging molecule isolation and characterization for the possible discovery of new drugs.

  11. Immune receptors and adhesion molecules in human pulmonary leptospirosis.

    Del Carlo Bernardi, Fabiola; Ctenas, Bruno; da Silva, Luiz Fernando Ferraz; Nicodemo, Antonio Carlos; Saldiva, Paulo Hilário Nascimento; Dolhnikoff, Marisa; Mauad, Thais

    2012-10-01

    Pulmonary involvement in leptospirosis has been increasingly reported in the last 20 years, being related to the severity and mortality of the disease. The pathogenesis of pulmonary hemorrhage in leptospirosis is not understood. Lung endothelial cells have been proposed as targets in the pathogenesis of lung involvement in leptospirosis through the activation of Toll-like receptor 2 or the complement system, which stimulates the release of cytokines that lead to the activation of adhesion molecules. The aim of this study was to investigate the involvement of immune pathways and of the intercellular and vascular cell adhesion molecules (intercellular adhesion molecule and vascular cell adhesion molecule, respectively) in the lungs of patients with pulmonary involvement of leptospirosis. We studied the lungs of 18 patients who died of leptospirosis and compared them with 2 groups of controls: normal and noninfectious hemorrhagic lungs. Using immunohistochemistry and image analysis, we quantified the expression of the C3a anaphylatoxin receptor, intercellular adhesion molecule, vascular cell adhesion molecule, and Toll-like receptor 2 in small pulmonary vessels and in the alveolar septa. There was an increased expression of intercellular adhesion molecule (P < .03) and C3a anaphylatoxin receptor (P < .008) in alveolar septa in the leptospirosis group compared with the normal and hemorrhagic controls. In the vessels of the leptospirosis group, there was an increased expression of intercellular adhesion molecule (P = .004), vascular cell adhesion molecule (P = .030), and Toll-like receptor 2 (P = .042) compared with the normal group. Vascular cell adhesion molecule expression in vessels was higher in the leptospirosis group compared with the hemorrhagic group (P = .015). Our results indicate that immune receptors and adhesion molecules participate in the phenomena leading to pulmonary hemorrhage in leptospirosis. PMID:22436623

  12. Influence of conformational changes in complex molecules on photon statistics of single molecule fluorescence

    A single complex molecule with conformational changes (conformations 0 and 2) is considered. When such a molecule is irradiated by cw-laser light it can randomly change the intensity or polarization of its fluorescence due to jumps from one conformation to another. In fact, the molecule manifests itself either like the 0-type or the 2-type emitter. An expression for the matrix sαβ(t) called the start-stop correlator (waiting time distribution) in which α=0,2 and β=0,2 is derived. An expression for the matrix pαβ(t) called the full correlator is derived as well. It determines the density of the probability of finding an event of α type and an event of β type separated by time interval t. A relation between matrices sαβ(t) and pαβ(t) is found. A mathematical expression for the distribution wN(T) of events measured in time interval T is derived. It is expressed solely via the matrix sαβ(t). Numerical calculations of the event distribution function for various rates of intra- and interconformational jumps are carried out with the help of the formula for wN(T) and by the Monte Carlo method. Both methods of the calculation yield identical distributions. Fluctuating fluorescence intensity I(t) for a bin time of 5 ms is calculated for slow and fast interconformational jumps. A relation is found between the autocorrelation function g(2)(t) of fluorescence measurable in experiments and the matrix pαβ(t) calculated theoretically.

  13. Single-molecule conductance of redox molecules in electrochemical scanning tunneling microscopy

    Haiss, W.; Albrecht, Tim; van Zalinge, H.;

    2007-01-01

    Experimental data and theoretical notions are presented for 6-[1'-(6-mercapto-hexyl)-[4,4']bipyridinium]-hexane-1-thiol iodide (6V6) "wired" between a gold electrode surface and tip in an in situ scanning tunneling microscopy configuration. The viologen group can be used to "gate" charge transport...... analysis and reproduces in all important respects the 6V6 data for physically sound values of the appropriate parameters. This study demonstrates that fluctuations of isolated configurationally "soft" molecules can dominate charge transport patterns and that theoretical frameworks for compact monolayers...

  14. Soluble adhesion molecules in human cancers: sources and fates.

    Kilsdonk, J.W.J. van; Kempen, L.C.L.T. van; Muijen, G.N.P. van; Ruiter, D.J.; Swart, G.W.

    2010-01-01

    Adhesion molecules endow tumor cells with the necessary cell-cell contacts and cell-matrix interactions. As such, adhesion molecules are involved in cell signalling, proliferation and tumor growth. Rearrangements in the adhesion repertoire allow tumor cells to migrate, invade and form metastases. Be

  15. Electrochemical Single-Molecule Transistors with Optimized Gate Coupling

    Osorio, Henrry M.; Catarelli, Samantha; Cea, Pilar;

    2015-01-01

    Electrochemical gating at the single molecule level of viologen molecular bridges in ionic liquids is examined. Contrary to previous data recorded in aqueous electrolytes, a clear and sharp peak in the single molecule conductance versus electrochemical potential data is obtained in ionic liquids....

  16. Single-molecule binding experiments on long time scales

    Elenko, Mark P.; Szostak, Jack W.; van Oijen, Antoine M.

    2010-01-01

    We describe an approach for performing single-molecule binding experiments on time scales from hours to days, allowing for the observation of slower kinetics than have been previously investigated by single-molecule techniques. Total internal reflection fluorescence microscopy is used to image the b

  17. Fluorescence Emission from Small Molecules Containing Amino Group

    2006-01-01

    After the treatment of oxygen gas, the small molecules containing amine group could emit fluorescence. Oxidation was believed to play an important role in the formation of fluorescence centers. Compared to previous results, both small molecules and macromolecules might have the same fluorescence centers.

  18. Synchrotron radiation VUV double photoionization of some small molecules

    The VUV double photoionizations of small molecules (NO, CO, CO2, CS2, OSC and NH3) were investigated with photoionization mass spectroscopy using synchrotron radiation. The double ionization energies of molecules were determined with photoionization efficiency spectroscopy. The total energies of these molecules and their parent dications (NO2+, CO2+, CO2+2, CS2+2, OSC2+ and NH2+3) were calculated using the Gaussian 03 program and Gaussian 2 calculations. Then, the adiabatic double ionization energies of the molecules were predicated by using high accuracy energy mode. The experimental double ionization energies of these small molecules were all in reasonable agreement with their respective calculated adiabatic double ionization energies. The mechanisms of double photoionization of these molecules were discussed based on a comparison of our experimental results with those predicted theoretically. The equilibrium geometries and harmonic vibrational frequencies of molecules and their parent dications were calculated by using the MP2 (full) method. The differences in configurations between these molecules and their parent dications were also discussed on the basis of theoretical calculations. (atomic and molecular physics)

  19. Rotation of a single molecule within a supramolecular bearing

    Gimzewski, J.K.; Joachim, C.; Schlittler, R.R.;

    1998-01-01

    Experimental visualization and verification of a single-molecule rotor operating within a supramolecular bearing is reported. Using a scanning tunneling microscope, single molecules were observed to exist in one of two spatially defined states Laterally separated by 0.26 nanometers. One was...

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

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

    1993-12-01

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

  1. Reversible switching of ultrastrong light-molecule coupling

    Schwartz, T; Hutchison, J A; Genet, C;

    2011-01-01

    We demonstrate that photochromic molecules enable switching from the weak- to ultrastrong-coupling regime reversibly, by using all-optical control. This switch is achieved by photochemically inducing conformational changes in the molecule. Remarkably, a Rabi splitting of 700 meV is measured at room...

  2. Single-Molecule FRET Study of DNA G-Quadruplex

    2002-01-01

    The DNA G-quadruplex formed by the human telomeric sequence is a potential target for novel anticancer drugs. We have investigated an intramolecular DNA G-quadruplex using single-molecule fluorescence resonance energy transfer and shown that individual folded quadruplexes can be identified. The mean proximity ratio measured at the single-molecule level was consistent with ensemble measurement.

  3. Degenerate atom-molecule mixture in a cold Fermi gas

    We show that the atom-molecule mixture formed in a degenerate atomic Fermi gas with interspecies repulsion near a Feshbach resonance constitutes a peculiar system where the atomic component is almost nondegenerate but quantum degeneracy of molecules is important. We develop a thermodynamic approach for studying this mixture, explain experimental observations, and predict optimal conditions for achieving molecular Bose-Einstein condensation

  4. Degenerate Atom-Molecule Mixture in a Cold Fermi Gas

    Kokkelmans, S.J.J.M.F.; Shlyapnikov, G. V.; Salomon, R.

    2004-01-01

    We show that the atom-molecule mixture formed in a degenerate atomic Fermi gas with interspecies repulsion near a Feshbach resonance, constitutes a peculiar system where the atomic component is almost non-degenerate but quantum degeneracy of molecules is important. We develop a thermodynamic approach for studying this mixture, explain experimental observations and predict optimal conditions for achieving molecular BEC.

  5. A single molecule DNA flow stretching microscope for undergraduates

    Williams, Kelly; Grafe, Brendan; Burke, Kathryn M.; Tanner, Nathan; van Oijen, Antoine M.; Loparo, Joseph; Price, Allen C.

    2011-01-01

    The design of a simple, safe, and inexpensive single molecule flow stretching instrument is presented. The instrument uses a low cost upright microscope coupled to a webcam for imaging single DNA molecules that are tethered in an easy to construct microfluidic flow cell. The system requires no speci

  6. Looking at the photodynamics of individual fluorescent molecules and proteins

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

    2001-01-01

    The photodynamics of individual molecules and fluorescent proteins has been investigated in real time. In the case of organic molecules, both the triplet state lifetime and intersystem crossing yield appear to vary in time and space. In the case of autofluorescent proteins, light-driven "on-off" flu

  7. Formation of Prebiotic Molecules in Interstellar and Cometary Ices

    Bernstein, Max P.; Sandford, Scott A.; Allamandola, Louis J.; Dworkin, Jason; Gilette, J. Seb; Zare, Richard N.; DeVincenzi, D. (Technical Monitor)

    2000-01-01

    We report here on our lab studies of ice photochemistry of large organic molecules under cometary conditions. We focus on polycyclic aromatic hydrocarbons (PAHs), their photoproducts, and their similarities to molecules seen in living systems today. We note that these kinds of compounds are seen in meteorites and we propose an explanation for both their formation and their observed deuterium enrichments.

  8. Performance of Bioactive Molecules on Cotton and Other Textiles

    Four types of biologically active molecules were examined for their structure/activity relationships as applied to textile functionalization. Bio-molecules including enzymes, peptides, carbohydrates, and lipids have been found to retain their activity when linked to cotton fabrics. Wound dressing pr...

  9. Full Alignment of Molecules Using Elliptically Polarized Light

    Larsen, Jakob Juul; Hald, Kasper; Seideman, Tamar;

    When a molecule with an anisotropic polarizability is placed in a strong nonresonant laser field the interaction occurs through the induced dipole moment. The outcome is that the molecule experiences an angular dependent potential energy. It is now well established that a linearly polarized laser...

  10. DNA analysis by single molecule stretching in nanofluidic biochips

    Abad, E.; Juarros, A.; Retolaza, A.;

    2011-01-01

    Imprint Lithography (NIL) technology combined with a conventional anodic bonding of the silicon base and Pyrex cover. Using this chip, we have performed single molecule imaging on a bench-top fluorescent microscope system. Lambda phage DNA was used as a model sample to characterize the chip. Single molecules of λ...

  11. Formation and properties of isolated molecules in copper

    Isolated molecules of SbFx, SbOx and SbClx in copper have been prepared by ion implantation and annealing treatments and studied by 119Sn Moessbauer spectroscopy. The uniqueness of this technique for the investigation of isolated intracrystalline molecules is demonstrated. (Auth.)

  12. Organic Optoelectronic Devices Employing Small Molecules

    Fleetham, Tyler Blain

    Organic optoelectronic devices have remained a research topic of great interest over the past two decades, particularly in the development of efficient organic photovoltaics (OPV) and organic light emitting diodes (OLED). In order to improve the efficiency, stability, and materials variety for organic optoelectronic devices a number of emitting materials, absorbing materials, and charge transport materials were developed and employed in a device setting. Optical, electrical, and photophysical studies of the organic materials and their corresponding devices were thoroughly carried out. Two major approaches were taken to enhance the efficiency of small molecule based OPVs: developing material with higher open circuit voltages or improved device structures which increased short circuit current. To explore the factors affecting the open circuit voltage (VOC) in OPVs, molecular structures were modified to bring VOC closer to the effective bandgap, DeltaE DA, which allowed the achievement of 1V VOC for a heterojunction of a select Ir complex with estimated exciton energy of only 1.55eV. Furthermore, the development of anode interfacial layer for exciton blocking and molecular templating provide a general approach for enhancing the short circuit current. Ultimately, a 5.8% PCE was achieved in a single heterojunction of C60 and a ZnPc material prepared in a simple, one step, solvent free, synthesis. OLEDs employing newly developed deep blue emitters based on cyclometalated complexes were demonstrated. Ultimately, a peak EQE of 24.8% and nearly perfect blue emission of (0.148,0.079) was achieved from PtON7dtb, which approaches the maximum attainable performance from a blue OLED. Furthermore, utilizing the excimer formation properties of square-planar Pt complexes, highly efficient and stable white devices employing a single emissive material were demonstrated. A peak EQE of over 20% for pure white color (0.33,0.33) and 80 CRI was achieved with the tridentate Pt complex, Pt

  13. Small Molecule Chemical Probes of MicroRNA Function

    Velagapudi, Sai Pradeep; Vummidi, Balayeshwanth R.; Disney, Matthew D.

    2015-01-01

    MicroRNAs (miRNAs) are small, non-coding RNAs that control protein expression. Aberrant miRNA expression has been linked to various human diseases, and thus miRNAs have been explored as diagnostic markers and therapeutic targets. Although it is challenging to target RNA with small molecules in general, there have been successful campaigns that have identified small molecule modulators of miRNA function by targeting various pathways. For example, small molecules that modulate transcription and target nuclease processing sites in miRNA precursors have been identified. Herein, we describe challenges in developing chemical probes that target miRNAs and highlight aspects of miRNA cellular biology elucidated by using small molecule chemical probes. We expect that this area will expand dramatically in the near future as strides are made to understand small molecule recognition of RNA from a fundamental perspective. PMID:25500006

  14. Massively parallel single-molecule manipulation using centrifugal force

    Halvorsen, Ken

    2009-01-01

    Precise manipulation of single molecules has already led to remarkable insights in physics, chemistry, biology and medicine. However, widespread adoption of single-molecule techniques has been impeded by equipment cost and the laborious nature of making measurements one molecule at a time. We have solved these issues with a new approach: massively parallel single-molecule force measurements using centrifugal force. This approach is realized in a novel instrument that we call the Centrifuge Force Microscope (CFM), in which objects in an orbiting sample are subjected to a calibration-free, macroscopically uniform force-field while their micro-to-nanoscopic motions are observed. We demonstrate high-throughput single-molecule force spectroscopy with this technique by performing thousands of rupture experiments in parallel, characterizing force-dependent unbinding kinetics of an antibody-antigen pair in minutes rather than days. Additionally, we verify the force accuracy of the instrument by measuring the well-est...

  15. Positron-molecule interactions: resonant attachment, annihilation, and bound states

    Gribakin, G F; Surko, C M; 10.1103/RevModPhys.82.2557

    2010-01-01

    This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecules (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom. While the details are as yet unclear, intr...

  16. A proposal for sympathetically cooling neutral molecules using cold ions

    Robicheaux, F

    2014-01-01

    We describe a method for cooling neutral molecules that have magnetic and electric dipole moments using collisions with cold ions. An external magnetic field is used to split the ground rovibrational energy levels of the molecule. The highest energy state within the ground rovibrational manifold increases in energy as the distance to the ion decreases leading to a repelling potential. At low energy, inelastic collisions are strongly suppressed due to the large distance of closest approach. Thus, a collision between a neutral molecule and a cold ion will lead to a decrease in the molecule's kinetic energy with no change in internal energy. We present results for the specific case of OH molecules cooled by Be$^+$, Mg$^+$, or Ca$^+$ ions.

  17. Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications

    Annamaria eRuscito

    2016-05-01

    Full Text Available Aptamers are single-stranded, synthetic oligonucleotides that fold into 3-dimensional shapes capable of binding non-covalently with high affinity and specificity to a target molecule. They are generated via an in vitro process known as the Systematic Evolution of Ligands by EXponential enrichment, from which candidates are screened and characterized, and then applied in aptamer-based biosensors for target detection. Aptamers for small molecule targets such as toxins, antibiotics, molecular markers, drugs, and heavy metals will be the focus of this review. Their accurate detection is ultimately needed for the protection and wellbeing of humans and animals. However, issues such as the drastic difference in size of the aptamer and small molecule make it challenging to select, characterize, and apply aptamers for the detection of small molecules. Thus, recent (since 2012 notable advances in small molecule aptamers, which have overcome some of these challenges, are presented here, while defining challenges that still exist are discussed

  18. Adsorbed molecules in external fields: Effect of confining potential.

    Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

    2016-12-01

    We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials. PMID:27387127

  19. Detecting and identifying small molecules in a nanopore flux capacitor

    Bearden, Samuel; McClure, Ethan; Zhang, Guigen

    2016-02-01

    A new method of molecular detection in a metallic-semiconductor nanopore was developed and evaluated with experimental and computational methods. Measurements were made of the charging potential of the electrical double layer (EDL) capacitance as charge-carrying small molecules translocated the nanopore. Signals in the charging potential were found to be correlated to the physical properties of analyte molecules. From the measured signals, we were able to distinguish molecules with different valence charge or similar valence charge but different size. The relative magnitude of the signals from different analytes was consistent over a wide range of experimental conditions, suggesting that the detected signals are likely due to single molecules. Computational modeling of the nanopore system indicated that the double layer potential signal may be described in terms of disruption of the EDL structure due to the size and charge of the analyte molecule, in agreement with Huckel and Debye’s analysis of the electrical atmosphere of electrolyte solutions.

  20. Regularities in positronium formation for atoms and molecules

    Machacek, J. R.; Blanco, F.; Garcia, G.; Buckman, S. J.; Sullivan, J. P.

    2016-03-01

    In an effort to aid the modelling of positron and positronium (Ps) transport in biological media we have compiled recent experimental results for the total Ps formation in positron scattering from atoms and molecules. A simple function was found to adequately describe the total Ps formation cross section for both atoms and molecules. The parameters of this function describe the magnitude and shape of the Ps formation cross section and are compared to physical characteristics of the target atoms and molecules. A general trend in the magnitude of the total Ps formation cross section is observed as a function of the target atom/molecule dipole polarisability. The functional form may enable quick estimation of the Ps cross section for molecules for which experimental measurements or theoretical estimates do not exist.

  1. Computer systems for annotation of single molecule fragments

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  2. Functionalized molecules studied by STM: motion, switching and reactivity

    Functionalized molecules represent the central issue of molecular nanotechnology. Scanning tunnelling microscopy (STM) is a powerful method to investigate such molecules, because it allows us to image them with sub-molecular resolution when adsorbed on a surface and can be used at the same time as a tool to manipulate single molecules in a controlled way. Such studies permit deep insight into the conformational, mechanical and electronic structure and thus functionalities of the molecules. In this review, recent experiments on specially designed molecules, acting as model systems for molecular nanotechnology, are reviewed. The presented studies focus on key functionalities: lateral rolling and hopping motion on a supporting surface, the switching behaviour of azobenzene derivatives by using the STM tip and the controlled reactivity of molecular side groups, which enable the formation of covalently bound molecular nanoarchitectures. (topical review)

  3. Cold molecules: Formation, ro-vibrational cooling and electronic conversion

    Horchani, R.

    2016-05-01

    The possibility of controlling all the motion as well as the internal quantum state of a sample of molecules is a long term goal in the cold molecules field. Although many different techniques have been used to produce ultra-cold molecules, in this paper, we will concentrate on the optical pumping technique successfully used to achieve rotational and vibrational cooling of Cs2 molecules. We will review the different photo-association schemes for molecule formation, the detection schemes through photoionization, the ro-vibrational cooling into a single level and finally the electronic conversion. In addition, we will present a theoretical model for both ro-vibrational cooling and electronic conversion that can be used for the preparation of different experiments.

  4. Decelerating and trapping molecules in a traveling wave decelerator

    Quintero-Pérez, Marina; Wall, Thomas E; van der Berg, Joost E; Hoekstra, Steven; Bethlem, Hendrick L

    2013-01-01

    We present experiments on decelerating and trapping ammonia molecules using a combination of a Stark decelerator and a traveling wave decelerator. In the traveling wave decelerator a moving potential is created by a series of ring-shaped electrodes to which oscillating high voltages are applied. By lowering the frequency of the applied voltages, the molecules confined in the moving trap are decelerated and brought to a standstill. As the molecules are con?ned in a true 3D well, this new kind of deceleration has practically no losses, resulting in a great improvement on the usual Stark deceleration techniques. The necessary voltages are generated by amplifying the output of an arbitrary wave generator using fast HV-amplifiers, giving us great control over the trapped molecules. We illustrate this by experiments in which we adiabatically cool trapped NH3 and ND3 molecules and resonantly excite their motion.

  5. Structural characterization of chiral molecules using vibrational circular dichroism spectroscopy

    Lassen, Peter Rygaard

    2006-01-01

    Chiral molecules, i.e., molecules with handedness, are essential to biology, because most amino acids and sugars are chiral. A pair of molecules which are mirror images of each other have identical physical properties, but they differ in their interaction with other chiral molecules. This is the...... cornerstone of biological specificity. Chiral molecules also interact differently with different polarization states of electromagnetic radiation, because the absorption coefficient depends on the state of polarization. This is called dichroism and gives rise to several spectroscopic techniques targeting...... compounds of pharmaceutical interest. Others are transition metal complexes relevant for the search for parity-violation effects in vibrational spectroscopy (rhenium complexes), for asymmetric catalysis (Schiff-base complexes), or as model systems for metal centres in biology (Schiff-bases and heme...

  6. Friction mediated by redox-active supramolecular connector molecules.

    Bozna, B L; Blass, J; Albrecht, M; Hausen, F; Wenz, G; Bennewitz, R

    2015-10-01

    We report on a friction study at the nanometer scale using atomic force microscopy under electrochemical control. Friction arises from the interaction between two surfaces functionalized with cyclodextrin molecules. The interaction is mediated by connector molecules with (ferrocenylmethyl)ammonium end groups forming supramolecular complexes with the cyclodextrin molecules. With ferrocene connector molecules in solution, the friction increases by a factor of up to 12 compared to control experiments without connector molecules. The electrochemical oxidation of ferrocene to ferrocenium causes a decrease in friction owing to the lower stability of ferrocenium-cyclodextrin complex. Upon switching between oxidative and reduction potentials, a change in friction by a factor of 1.2-1.8 is observed. Isothermal titration calorimetry reveals fast dissociation and rebinding kinetics and thus an equilibrium regime for the friction experiments. PMID:26367352

  7. Dynamics of thermal Casimir-Polder forces on polar molecules

    We study the influence of thermal Casimir-Polder forces on the near-surface trapping of cold polar molecules, with emphasis on LiH and YbF near a Au surface at room temperature. We show that even for a molecule initially prepared in its electronic and rovibrational ground state, the Casimir-Polder force oscillates with the molecule-wall separation. The nonresonant force and the evanescent part of the resonant force almost exactly cancel at high temperature which results in a saturation of the (attractive) force in this limit. This implies that the Casimir-Polder force on a fully thermalized molecule can differ dramatically from that obtained using a naive perturbative expansion of the Lifshitz formula based on the molecular ground-state polarizability. A dynamical calculation reveals how the spatial oscillations die out on a typical time scale of several seconds as thermalization of the molecule with its environment sets in.

  8. Controlled Ensembles of Formaldehyde Molecules at Ultracold Temperatures

    Zeppenfeld, Martin; Prehn, Alexander; Ibrügger, Martin; Glöckner, Rosa; Rempe, Gerhard

    2016-05-01

    Applications of ultracold molecules such as quantum information processing and quantum controlled chemistry require the preparation of ultracold molecule ensembles with a high level of control over all molecular degrees of freedom. Due to the inability to apply standard atom cooling techniques such as laser cooling to most molecule species, developing new methods is essential. We present a toolbox of techniques developed in our group for controlling molecules. A microstructured electric trap allows us to trap molecules in predominantly homogeneous electric fields with trapping times of up to a minute. Optical pumping on a vibrational transition allows us to transfer the population from a large number of rotational states to a single rotational M-sublevel. Our experiment provides excellent conditions for precision spectroscopy and investigation of ultracold collisions.

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

    Hybertsen M. S.

    2013-04-11

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

  10. Small-Molecule Binding Aptamers: Selection Strategies, Characterization, and Applications

    Ruscito, Annamaria; DeRosa, Maria

    2016-05-01

    Aptamers are single-stranded, synthetic oligonucleotides that fold into 3-dimensional shapes capable of binding non-covalently with high affinity and specificity to a target molecule. They are generated via an in vitro process known as the Systematic Evolution of Ligands by EXponential enrichment, from which candidates are screened and characterized, and then applied in aptamer-based biosensors for target detection. Aptamers for small molecule targets such as toxins, antibiotics, molecular markers, drugs, and heavy metals will be the focus of this review. Their accurate detection is ultimately needed for the protection and wellbeing of humans and animals. However, issues such as the drastic difference in size of the aptamer and small molecule make it challenging to select, characterize, and apply aptamers for the detection of small molecules. Thus, recent (since 2012) notable advances in small molecule aptamers, which have overcome some of these challenges, are presented here, while defining challenges that still exist are discussed

  11. Small molecule annotation for the Protein Data Bank.

    Sen, Sanchayita; Young, Jasmine; Berrisford, John M; Chen, Minyu; Conroy, Matthew J; Dutta, Shuchismita; Di Costanzo, Luigi; Gao, Guanghua; Ghosh, Sutapa; Hudson, Brian P; Igarashi, Reiko; Kengaku, Yumiko; Liang, Yuhe; Peisach, Ezra; Persikova, Irina; Mukhopadhyay, Abhik; Narayanan, Buvaneswari Coimbatore; Sahni, Gaurav; Sato, Junko; Sekharan, Monica; Shao, Chenghua; Tan, Lihua; Zhuravleva, Marina A

    2014-01-01

    The Protein Data Bank (PDB) is the single global repository for three-dimensional structures of biological macromolecules and their complexes, and its more than 100,000 structures contain more than 20,000 distinct ligands or small molecules bound to proteins and nucleic acids. Information about these small molecules and their interactions with proteins and nucleic acids is crucial for our understanding of biochemical processes and vital for structure-based drug design. Small molecules present in a deposited structure may be attached to a polymer or may occur as a separate, non-covalently linked ligand. During curation of a newly deposited structure by wwPDB annotation staff, each molecule is cross-referenced to the PDB Chemical Component Dictionary (CCD). If the molecule is new to the PDB, a dictionary description is created for it. The information about all small molecule components found in the PDB is distributed via the ftp archive as an external reference file. Small molecule annotation in the PDB also includes information about ligand-binding sites and about covalent and other linkages between ligands and macromolecules. During the remediation of the peptide-like antibiotics and inhibitors present in the PDB archive in 2011, it became clear that additional annotation was required for consistent representation of these molecules, which are quite often composed of several sequential subcomponents including modified amino acids and other chemical groups. The connectivity information of the modified amino acids is necessary for correct representation of these biologically interesting molecules. The combined information is made available via a new resource called the Biologically Interesting molecules Reference Dictionary, which is complementary to the CCD and is now routinely used for annotation of peptide-like antibiotics and inhibitors. PMID:25425036

  12. A quantum gas of polar molecules in an optical lattice

    Moses, Steven A.

    Ultracold polar molecules, because of their long-range, spatially anisotropic interactions, are a new quantum system in which to study novel many-body phenomena. In our lab, we have produced the first quantum gas of 40K 87Rb polar molecules. These molecules were found to undergo exothermic chemical reactions, and this led to interesting studies of chemistry near absolute zero. By creating the molecules at individual sites of a 3D optical lattice, we completely suppress these chemical reactions, and the polar molecule gas becomes stable and lives for tens of seconds. This thesis documents our efforts to explore coherent, many-body phenomena resulting from long-range dipolar interactions in the lattice. By encoding a spin-1/2 system in the rotational states of the molecules, we were able to realize spin-exchange interactions based on a spin Hamiltonian, which is one of the first steps in studying quantum magnetism with polar molecules. While this study was the first realization of such coherent dipolar interactions with polar molecules in a lattice, its full potential was limited by the low lattice filling fractions. Using our ability to exquisitely control the initial atomic gas mixture, we loaded a Mott insulator of Rb and a band insulator of K into the lattice. This quantum synthesis approach led to significantly higher molecular filling fractions and represents the first fully connected system of polar molecules in an optical lattice. This low-entropy quantum gas of polar molecules opens the door to interesting quantum simulations, which should be attainable in the next generation of the experiment.

  13. Electronic transport in benzodifuran single-molecule transistors

    Xiang, An; Li, Hui; Chen, Songjie; Liu, Shi-Xia; Decurtins, Silvio; Bai, Meilin; Hou, Shimin; Liao, Jianhui

    2015-04-01

    Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices.Benzodifuran (BDF) single-molecule transistors have been fabricated in electromigration break junctions for electronic measurements. The inelastic electron tunneling spectrum validates that the BDF molecule is the pathway of charge transport. The gating effect is analyzed in the framework of a single-level tunneling model combined with transition voltage spectroscopy (TVS). The analysis reveals that the highest occupied molecular orbital (HOMO) of the thiol-terminated BDF molecule dominates the charge transport through Au-BDF-Au junctions. Moreover, the energy shift of the HOMO caused by the gate voltage is the main reason for conductance modulation. In contrast, the electronic coupling between the BDF molecule and the gold electrodes, which significantly affects the low-bias junction conductance, is only influenced slightly by the applied gate voltage. These findings will help in the design of future molecular electronic devices. Electronic supplementary information (ESI) available: The fabrication procedure for BDF single-molecule

  14. Angiogenic Effect of Intercellular Adhesion Molecule-1

    DENG Chenguo; ZHANG Duanlian; SHAN Shengguo; WU Jingwen; YANG Hong; YU Ying

    2007-01-01

    In order to investigate the angiogenic effect of intercellular adhesion molecule-1 (ICAM-1), two parts of experiment were performed. Chick embryo chorioallantoic membrane (CAM) assay was used for in vivo angiogenic research. The chick embryos were divided into 4 groups: ICAM-1 group (divided into 3 subgroups, Ⅰ, Ⅱ and Ⅲ) for screening the angiogenic effect of ICAM-1 by adding different concentrations of ICAM-1 (0.1, 0.2 and 0.3 μg/μL) 5 μL into the chick embryo CAMs on the day 10 after incubation for every subgroup; Anti-ICAM-1 group A (divided into 2 subgroups, Ⅰ and Ⅱ) by adding different concentrations of Anti-ICAM-1 (1:100, 1:50) 5 μL into the chick embryo CAMs on the day 10 after incubation for every subgroup to evaluate the effect of ICAM-1 on the survival of microvessels through observing whether Anti-ICAM-1 could induce involution of the microvessels on CAMs; Anti-ICAM-1 group B (divided into 2 subgroups, Ⅰ and Ⅱ ) by adding different concentrations of Anti-ICAM-1 (1:100, 1:50) 5 μL into the chick embryo CAMs on the day 6 after incubation for every subgroup to evaluate whether ICAM-1 involved in embryonic angiogenesis through observing the growth of microvessels on CAMs; Control group: ICAM-1 or Anti-ICAM-1 was substituted by PBS 5 μL on the day 10 or day 6 after incubation. Three days later, the CAMs were photographed in vivo, excised, sectioned and the number of microvessels was counted. In ICAM-1 group, there was increased number of microvessels arranged radially with "spoked-wheel" pattern around the gelatin sponges. The new microvessels growing perpendicularly to gelatin sponges were observed. The number of the microvessels growing in the CAM mesenchymes around the sponges in 3 subgroups was higher than that in control group (P<0.01), however, there was no significant difference among the 3 subgroups (P>0.05). In anti-ICAM-1 group A, the radially arranged microvessels were very unclear around the sponges contrast to that of ICAM

  15. The influence of tobacco smoking on adhesion molecule profiles

    Palmer RM

    2002-01-01

    Full Text Available Abstract Sequential interactions between several adhesion molecules and their ligands regulate lymphocyte circulation and leukocyte recruitment to inflammatory foci. Adhesion molecules are, therefore, central and critical components of the immune and inflammatory system. We review the evidence that tobacco smoking dysregulates specific components of the adhesion cascade, which may be a common factor in several smoking-induced diseases. Smoking causes inappropriate leukocyte activation, leukocyte-endothelial adhesion, and neutrophil entrapment in the microvasculature, which may help initiate local tissue destruction. Appropriate inflammatory reactions may thus be compromised. In addition to smoke-induced alterations to membrane bound endothelial and leukocyte adhesion molecule expression, which may help explain the above phenomena, smoking has a profound influence on circulating adhesion molecule profiles, most notably sICAM-1 and specific sCD44 variants. Elevated concentrations of soluble adhesion molecules may simply reflect ongoing inflammatory processes. However, increasing evidence suggests that specific soluble adhesion molecules are immunomodulatory, and that alterations to soluble adhesion molecule profiles may represent a significant risk factor for several diverse diseases. This evidence is discussed herein.

  16. Kinetics of Hydrogen Molecules in MAGNUM-PSI

    M.BAEVA; W.J.GOEDHEER; N.J.LOPES CARDOZO

    2008-01-01

    Results from simulations of plasma and neutrals under conditions predictively characterizing the detached plasma regime in the linear machine MAGNUM-PSI are presented. The relaxation of the vibrationally excited hydrogen molecules is investigated in order to establish a relation between their relaxation and dwell times, and the role of the various mechanisms of the molecular vibrational kinetics. The results obtained show that the individual vibrational states have to be included in the transport code for neutrals as distinct species, since the relaxation time of the vibrational states is sufficiently longer than the typical dwell time of hydrogen molecules in the detached plasma region. The parameters of plasma and neutrals are affected by the transport of the vibrationally excited hydrogen molecules. Furthermore, the rate of molecular recombination is overestimated by a factor of~5 provided that the transport of hydrogen molecules only in their ground vibrational state is considered. The role of the various processes of vibrational kinetics is studied. The vibrational excitation through singlet electronic states has a strong influence on the molecular densities for levels with vibrational quantum numbers v≥ 5. Vibration-vibration (V-V) collisions between vibrationally excited hydrogen molecules and vibration-translation (V-T) collisions between vibrationally excited hydrogen molecules and ground state molecules and atoms are of minor importance in MAGNUM-PSI.

  17. Anti-Stokes-enhanced tunnelling ionization of polar molecules

    We generalize the correct account for molecule vibrational motion in tunnelling ionization, proposed earlier (Kornev and Zon 2012 Phys. Rev. A 86 043401), to the case of polar molecules. We consider the tunnel effect in both dc and ac fields, taking into account perturbation of vibrational motion by an external field. We develop a method for accounting for dipole moment on the base of the electronic wave function expansion over dipole-spherical functions instead of ordinary spherical functions. The change of polar molecule ionization probability compared to non-polar molecule ionization is mainly due to constant change in the asymptotic form of the valence electron wave function, both in the dc and ac fields. We present numerical results for HF and HCl molecules of various isotopic proportions for specific orientations of the molecule axis relative to the electric field strength. The maximum rate of the tunnel effect for these molecules is achieved if the internuclear axis is oriented perpendicularly to the electric field. (paper)

  18. FIELD IONIZATION OF MOLECULES IN AN INTENSE LASER FIELD

    吴成印; 龚旗煌

    2001-01-01

    In order to predict the field ionization probabilities, the accurate ab initio electrostatic potential of molecules has to be calculated. However, the calculation of the full ab initio electrostatic potential of molecules is complicated,even impossible for some larger molecules with low symmetry. Here, we present a semi-empirical model to treat the field ionization of molecules in an intense laser field. In this model, a modified Coulomb potential is used to take the place of the complicated ab initio electrostatic potential of molecules. The analytic equations of the Keldysh adiabatic parameter using the Coulomb potential and the modified Coulomb potential have first been given. Using our semiempirical model, we have calculated the field ionization probabilities and the Keldysh adiabatic parameters of O2,N2, SO2, C2H4, CH3CN and C6H6 in an intense laser field. The results agree excellently with the calculations using the ab initio electrostatic potential of molecules. As the modified parameter for the Coulomb potential can be found from experimental measurements, the field ionization mechanism of molecules can be immediately predicted with our semi-empirical model.

  19. Free enthalpies of replacing water molecules in protein binding pockets.

    Riniker, Sereina; Barandun, Luzi J; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH(3) group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH(3) at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design. PMID:23247390

  20. Formation of Complex Molecules via radiative association reactions

    Acharyya, Kinsuk; Herbst, Eric

    2016-07-01

    The detection of increasing numbers of complex organic molecules in the various phases of star formation plays a key role since they follow the same chemical rules of carbon-based chemistry that are observed in our planet Earth. Many of these molecules are believed to be formed on the surfaces of grains, and can then be released to the gas phase when these grains are heated. This is evident when we observe a rich chemistry in hot core regions. However, recently complex organic molecules have also been observed in cold clouds. Therefore, it is necessary to re-examine various pathways for the formation of these molecules in the gas phase. In this presentation, I will discuss role of radiative association reactions in the formation of complex molecules in the gas phase and at low temperature. We will compare abundance of assorted molecules with and without new radiative association reactions and will show that the abundance of a few complex molecules such as HCOOCH3, CH3OCH3 etc. can go up due to introduction of these reactions, which can help to explain their observed abundances.