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Sample records for probing intermolecular couplings

  1. Intermolecular artifacts in probe microscope images of C60 assemblies

    NASA Astrophysics Data System (ADS)

    Jarvis, Samuel Paul; Rashid, Mohammad Abdur; Sweetman, Adam; Leaf, Jeremy; Taylor, Simon; Moriarty, Philip; Dunn, Janette

    2015-12-01

    Claims that dynamic force microscopy has the capability to resolve intermolecular bonds in real space continue to be vigorously debated. To date, studies have been restricted to planar molecular assemblies with small separations between neighboring molecules. Here we report the observation of intermolecular artifacts over much larger distances in 2D assemblies of C60 molecules, with compelling evidence that in our case the tip apex is terminated by a C60 molecule (rather than the CO termination typically exploited in ultrahigh resolution force microscopy). The complete absence of directional interactions such as hydrogen or halogen bonding, the nonplanar structure of C60, and the fullerene termination of the tip apex in our case highlight that intermolecular artifacts are ubiquitous in dynamic force microscopy.

  2. Visualizing coherent intermolecular dipole–dipole coupling in real space

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J. G.

    2016-03-01

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole–dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced ‘single-molecule’ superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole–dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources.

  3. Visualizing coherent intermolecular dipole-dipole coupling in real space

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Luo, Yang; Zhang, Yao; Yu, Yun-Jie; Kuang, Yan-Min; Zhang, Li; Meng, Qiu-Shi; Luo, Yi; Yang, Jin-Long; Dong, Zhen-Chao; Hou, J. G.

    2016-03-01

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole-dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced ‘single-molecule’ superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole-dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources.

  4. Probing Intermolecular Interaction through Thermal-Lens Spectroscopy

    PubMed Central

    Bhattacharyya, Indrajit; Kumar, Pardeep; Goswami, Debabrata

    2013-01-01

    Binary liquid mixtures are studied using femtosecond pump–probe thermal-lens (TL) spectroscopy. Changes in the measured TL signals as a function of relative concentration of binary mixtures show that these result from a combined effect of physical and molecular properties of the constituent binary liquids. The experimental TL values deviate from the ones calculated from phenomenological equations. These, we argue, are due to an underestimation of the influence of molecular interactions when the TL signals are calculated by using physical parameters only. PMID:21166402

  5. Optical Activity Enhanced by Strong Inter-molecular Coupling in Planar Chiral Metamaterials

    PubMed Central

    Kim, Teun-Teun; Oh, Sang Soon; Park, Hyun-Sung; Zhao, Rongkuo; Kim, Seong-Han; Choi, Wonjune; Min, Bumki; Hess, Ortwin

    2014-01-01

    The polarization of light can be rotated in materials with an absence of molecular or structural mirror symmetry. While this rotating ability is normally rather weak in naturally occurring chiral materials, artificial chiral metamaterials have demonstrated extraordinary rotational ability by engineering intra-molecular couplings. However, while in general, chiral metamaterials can exhibit strong rotatory power at or around resonances, they convert linearly polarized waves into elliptically polarized ones. Here, we demonstrate that strong inter-molecular coupling through a small gap between adjacent chiral metamolecules can lead to a broadband enhanced rotating ability with pure rotation of linearly polarized electromagnetic waves. Strong inter-molecular coupling leads to nearly identical behaviour in magnitude, but engenders substantial difference in phase between transmitted left and right-handed waves. PMID:25209452

  6. Intermolecular electronic coupling in organic molecular thin films measured by temperature modulation spectroscopy

    SciTech Connect

    Yadav, Abhishek; Jin, Y; Chan, P. K. L.; Shtein, Max; Pipe, Kevin P.

    2010-01-01

    Temperature modulation spectroscopy is used to obtain the temperature dependences of oscillator strength, exciton transition energy, and line width for a copper phthalocyanine thin film. With increasing temperature, the oscillator strength exhibits a pronounced decrease for charge transfer (CT) excitons, making this technique suitable for differentiating exciton types. From the measured magnitude and temperature dependence of the CT oscillator strength, we obtain estimates for the intermolecular electronic coupling and its exponential decay coefficient.

  7. Coupled effects of substrate adhesion and intermolecular forces on polymer thin film glass-transition behavior.

    PubMed

    Xia, Wenjie; Keten, Sinan

    2013-10-15

    Intermolecular noncovalent forces between polymer chains influence the mobility and glass-transition temperature (Tg), where weaker interchain interactions, all else being the same, typically results in lower bulk polymer Tg. Using molecular dynamics simulations, here we show that this relation can become invalid for supported ultrathin films when the substrate-polymer interaction is extremely strong and the polymer-polymer interactions are much weaker. This contrasting trend is found to be due to a more pronounced substrate-induced appreciation of the film Tg for polymers with weaker intermolecular interactions and low bulk Tg. We show that optimizing this coupling between substrate adhesion and bulk Tg maximizes thin film Tg, paving the way for tuning film properties through interface nanoengineering.

  8. The Origins of - and Inter-Molecular Vibrational Couplings: a Case Study of H_2O-Ar on Full and Reduced-Dimensional Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-06-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H_2O-Ar, which explicitly incorporates interdependence on the intramolecular normal-mode coordinates of the H_2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (νb{1},νb{2},νb{3})=(0,0,0),(0,0,1),(1,0,0),(0,1,0) states of H_2O to the three-dimensional Morse/long-range potential function. The resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with RMS discrepancies smaller than 0.02 wn for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H_2O in H_2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. J. Chem. Phys., 144, 014301 (2016)

  9. 15N-15N spin-spin coupling constants through intermolecular hydrogen bonds in the solid state.

    PubMed

    Claramunt, Rosa M; Pérez-Torralba, Marta; María, Dolores Santa; Sanz, Dionisia; Elena, Bénédicte; Alkorta, Ibon; Elguero, José

    2010-10-01

    A 2hJNN intermolecular spin-spin coupling constant (SSCC) of 10.2±0.4 Hz has been measured for the powdered tetrachlorogallate salt of pyridinium solvated by pyridine (pyridine-H+⋯pyridine cation 3). Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d,p) level reproduced this value and two others reported in the literature for 2hJ intermolecular SSCCs, which were measured for complexes in solution.

  10. Intermolecular Electronic Coupling of Organic Units for Efficient Persistent Room‐Temperature Phosphorescence

    PubMed Central

    Yang, Zhiyong; Mao, Zhu; Zhang, Xuepeng; Ou, Depei; Mu, Yingxiao; Zhao, Cunyuan; Liu, Siwei; Xu, Jiarui; Wu, Yuan‐Chun; Lu, Po‐Yen; Lien, Alan

    2016-01-01

    Abstract Although persistent room‐temperature phosphorescence (RTP) emission has been observed for a few pure crystalline organic molecules, there is no consistent mechanism and no universal design strategy for organic persistent RTP (pRTP) materials. A new mechanism for pRTP is presented, based on combining the advantages of different excited‐state configurations in coupled intermolecular units, which may be applicable to a wide range of organic molecules. By following this mechanism, we have developed a successful design strategy to obtain bright pRTP by utilizing a heavy halogen atom to further increase the intersystem crossing rate of the coupled units. RTP with a remarkably long lifetime of 0.28 s and a very high quantum efficiency of 5 % was thus obtained under ambient conditions. This strategy represents an important step in the understanding of organic pRTP emission. PMID:26836346

  11. Intermolecular Electronic Coupling of Organic Units for Efficient Persistent Room-Temperature Phosphorescence.

    PubMed

    Yang, Zhiyong; Mao, Zhu; Zhang, Xuepeng; Ou, Depei; Mu, Yingxiao; Zhang, Yi; Zhao, Cunyuan; Liu, Siwei; Chi, Zhenguo; Xu, Jiarui; Wu, Yuan-Chun; Lu, Po-Yen; Lien, Alan; Bryce, Martin R

    2016-02-01

    Although persistent room-temperature phosphorescence (RTP) emission has been observed for a few pure crystalline organic molecules, there is no consistent mechanism and no universal design strategy for organic persistent RTP (pRTP) materials. A new mechanism for pRTP is presented, based on combining the advantages of different excited-state configurations in coupled intermolecular units, which may be applicable to a wide range of organic molecules. By following this mechanism, we have developed a successful design strategy to obtain bright pRTP by utilizing a heavy halogen atom to further increase the intersystem crossing rate of the coupled units. RTP with a remarkably long lifetime of 0.28 s and a very high quantum efficiency of 5 % was thus obtained under ambient conditions. This strategy represents an important step in the understanding of organic pRTP emission. PMID:26836346

  12. First-order exchange energy of intermolecular interactions from coupled cluster density matrices and their cumulants.

    PubMed

    Korona, Tatiana

    2008-06-14

    A new method for the calculation of the first-order intermolecular exchange energy is proposed. It is based on the partition of two-particle density matrices of monomers into the antisymmetrized product of one-particle density matrices and the remaining cumulant part. This partition is used to modify the formula for the first-order exchange energy developed by Moszynski et al. [J. Chem. Phys. 100, 5080 (1994)]. The new expression has been applied for the case of monomer density matrices derived from the expectation value expression for the coupled cluster singles and doubles wave function. In this way an accurate method of calculation of the first-order exchange energy for many-electron systems has been obtained, where both monomers are described on the coupled cluster level. Numerical results are presented for several benchmark van der Waals systems to illustrate the performance of the new approach.

  13. Spatio-spectral infrared vibrational nano-imaging of intermolecular coupling

    NASA Astrophysics Data System (ADS)

    Pollard, Benjamin; Muller, Eric; Raschke, Markus

    2014-03-01

    Molecular self-assembly, the function of biomembranes, and the performance of organic solar cells rely on molecular interactions on the nanoscale. The understanding and design of such heterogeneous functional soft matter has long been impeded by a lack of spectroscopic tools with sufficient nanometer spatial resolution, attomolar sensitivity, and intermolecular spectroscopic specificity. We implement vibrational scattering-scanning near-field optical microscopy (s-SNOM) in a multi-spectral modality to investigate the structure-function relationship in PS- b-PMMA block copolymers. Using a vibrational resonance as a sensitive reporter of local structure, coupling, and dynamics, we resolve spectral Stark shifts and line broadening correlated with molecular-scale morphologies. By creating images of solvatochromic vibrational shifts we discriminate local variations in electric fields between nanoscale bulk and interface regions, with quantitative agreement to dielectric continuum models. This new nano-chemometric ability to directly resolve nanoscale morphology and associated intermolecular interactions can form a basis for the systematic control of functionality in multicomponent soft matter systems.

  14. Cross-dehydrogenative coupling for the intermolecular C–O bond formation

    PubMed Central

    Krylov, Igor B; Vil’, Vera A

    2015-01-01

    Summary The present review summarizes primary publications on the cross-dehydrogenative C–O coupling, with special emphasis on the studies published after 2000. The starting compound, which donates a carbon atom for the formation of a new C–O bond, is called the CH-reagent or the C-reagent, and the compound, an oxygen atom of which is involved in the new bond, is called the OH-reagent or the O-reagent. Alcohols and carboxylic acids are most commonly used as O-reagents; hydroxylamine derivatives, hydroperoxides, and sulfonic acids are employed less often. The cross-dehydrogenative C–O coupling reactions are carried out using different C-reagents, such as compounds containing directing functional groups (amide, heteroaromatic, oxime, and so on) and compounds with activated C–H bonds (aldehydes, alcohols, ketones, ethers, amines, amides, compounds containing the benzyl, allyl, or propargyl moiety). An analysis of the published data showed that the principles at the basis of a particular cross-dehydrogenative C–O coupling reaction are dictated mainly by the nature of the C-reagent. Hence, in the present review the data are classified according to the structures of C-reagents, and, in the second place, according to the type of oxidative systems. Besides the typical cross-dehydrogenative coupling reactions of CH- and OH-reagents, closely related C–H activation processes involving intermolecular C–O bond formation are discussed: acyloxylation reactions with ArI(O2CR)2 reagents and generation of O-reagents in situ from C-reagents (methylarenes, aldehydes, etc.). PMID:25670997

  15. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  16. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface.

    PubMed

    Hou, Dan; Ma, Yong-Tao; Zhang, Xiao-Long; Li, Hui

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm(-1), and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.

  17. Probing the contribution of different intermolecular forces to the adsorption of spheroproteins onto hydrophilic surfaces.

    PubMed

    Borges, João; Campiña, José M; Silva, A Fernando

    2013-12-27

    Protein adsorption is a delicate process, which results from the balance between the properties of proteins and their solid supports. Although the relevance of some of these parameters has been already unveiled, the precise involvement of electrostatics and other weaker intermolecular forces requires further comprehension. Aiming to contribute to this task, this work explores the attachment, rearrangement, and surface aggregation of a model spheroprotein, such as bovine β-lactoglobulin (β-LG), onto hydrophilic substrates prefunctionalized with different alkylthiol films. Thereby, a variety of electrostatic scenarios for the adsorption of β-LG could be recreated through the variation of the pH and the functional chemistry of the surfaces. The changes in surface mass density (plus associated water) and film flexibility were followed in situ with quartz crystal microbalance with dissipation monitoring. Film packing and aggregation were assessed by faradaic electrochemical measurements and ex situ atomic force microscopy and field effect scanning electron microscopy. In contrast to previous hypotheses arguing that electrostatic interactions between charged substrates and proteins would be the only driving force, a complex interplay between Coulombic and non-Coulombic intermolecular forces (which would depend upon the experimental conditions) has been suggested to explain the results.

  18. Similarity-transformed perturbation theory on top of truncated local coupled cluster solutions: Theory and applications to intermolecular interactions

    SciTech Connect

    Azar, Richard Julian Head-Gordon, Martin

    2015-05-28

    Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the “(2)”-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order.

  19. Strong intermolecular vibrational coupling through cyclic hydrogen-bonded structures revealed by ultrafast continuum mid-IR spectroscopy.

    PubMed

    Stingel, Ashley M; Calabrese, Carmella; Petersen, Poul B

    2013-12-12

    Cyclic hydrogen-bonded structures are common motifs in biological systems, providing structural stability and mediating proton transfer for redox reactions. The mechanism of proton transfer across hydrogen-bonded interfaces depends on the strength of the intermolecular coupling between bridging OH/NH vibrational modes. Here we present a novel ultrafast continuum mid-IR spectroscopy experiment to study the vibrational dynamics of the 7-azaindole-acetic acid (7AI-Ac) heterodimer as a model system for asymmetric cyclic hydrogen-bonded structures. In addition to spreading of the excitation across the whole OH band within the time resolution of the experiment, excitation of a 300 cm(-1) region of the ∼1000 cm(-1) broad OH stretching mode of the acetic acid monomer leads to a frequency shift in the NH stretching mode of the 7AI monomer. This indicates that the NH and OH stretching modes located on the two monomers are strongly coupled despite being separated by 750 cm(-1). The strong coupling further causes the OH and NH bands to decay with a common decay time of ∼2.5 ps. This intermolecular coupling is mediated through the hydrogen-bonded structure of the 7AI-Ac heterodimer and is likely a general property of cyclic hydrogen-bonded structures. Characterizing the vibrational dynamics of and the coupling between the high-frequency OH/NH modes will be important for understanding proton transfer across such molecular interfaces.

  20. Evaluation of coupling terms between intra- and intermolecular vibrations in coarse-grained normal-mode analysis: does a stronger acid make a stiffer hydrogen bond?

    PubMed

    Houjou, Hirohiko

    2011-10-21

    Using theory of harmonic normal-mode vibration analysis, we developed a procedure for evaluating the anisotropic stiffness of intermolecular forces. Our scheme for coarse-graining of molecular motions is modified so as to account for intramolecular vibrations in addition to relative translational/rotational displacement. We applied this new analytical scheme to four carboxylic acid dimers, for which coupling between intra- and intermolecular vibrations is crucial for determining the apparent stiffness of the intermolecular double hydrogen bond. The apparent stiffness constant was analyzed on the basis of a conjunct spring model, which defines contributions from true intermolecular stiffness and molecular internal stiffness. Consequently, the true intermolecular stiffness was in the range of 43-48 N m(-1) for all carboxylic acids studied, regardless of the molecules' acidity. We concluded that the difference in the apparent stiffness can be attributed to differences in the internal stiffness of the respective molecules.

  1. Probing Intramolecular versus Intermolecular CO2 Adsorption on Amine-Grafted SBA-15.

    PubMed

    Yoo, Chun-Jae; Lee, Li-Chen; Jones, Christopher W

    2015-12-15

    A mesoporous silica SBA-15 is modified with an array of amine-containing organosilanes including (i) propylamine, SiCH2CH2CH2NH2 (MONO), (ii) propylethylenediamine, SiCH2CH2CH2NHCH2CH2NH2 (DI), (iii) propyldiethylenetriamine, SiCH2CH2CH2NHCH2CH2NHCH2CH2NH2 (TRI), and (iv) propyltriethylenetetramine, SiCH2CH2CH2NHCH2CH2N(CH2CH2NH2)2 (TREN) and the low loading silane adsorbents (∼0.45 mmol silane/g) are evaluated for their CO2 adsorption properties, with a focus on gaining insight into the propensity for intramolecular vs intermolecular CO2 adsorption. Adsorption isotherms at low CO2 coverages are measured while simultaneously recording the heat evolved via a Tian-Calvet calorimeter. The results are compared on a silane molecule efficiency basis (mol CO2 adsorbed/mol silane) to assess the potential for intramolecular CO2 adsorption, employing two amine groups in a single silane molecule. As the number of amines in the silane molecule increases (MONO < DI < TREN ∼ TRI), the silane molecule efficiency is enhanced owing to the ability to intramolecularly capture CO2. Analysis of the CO2 uptake for samples with the surface silanols removed by capping demonstrates that cooperative uptake due to amine-CO2-silanol interactions is also possible over these adsorbents and is the primary mode of sorption for the MONO material at the studied low silane loading. As the propensity for intramolecular CO2 capture increases due to the presence of multiple amines in a single silane molecule (MONO < DI < TREN ∼ TRI), the measured heat of adsorption also increases. This study of various amine-containing silanes at low coverage is the first to provide significant, direct evidence for intramolecular CO2 capture in a single silane molecule. Furthermore, it provides evidence for the relative heats of adsorption for physisorption on a silanol laden surface (ca. 37 kJ/mol), a silanol-capped surface (ca. 25 kJ/mol), via amine-CO2-silanol interactions (ca. 46 kJ/mol), and via amine-CO2

  2. Vibrational nano-spectroscopic imaging correlating structure with intermolecular coupling and dynamics

    PubMed Central

    Pollard, Benjamin; Muller, Eric A.; Hinrichs, Karsten; Raschke, Markus B.

    2014-01-01

    Molecular self-assembly, the function of biomembranes and the performance of organic solar cells rely on nanoscale molecular interactions. Understanding and control of such materials have been impeded by difficulties in imaging their properties with the desired nanometre spatial resolution, attomolar sensitivity and intermolecular spectroscopic specificity. Here we implement vibrational scattering-scanning near-field optical microscopy with high spectral precision to investigate the structure–function relationship in nano-phase separated block copolymers. A vibrational resonance is used as a sensitive reporter of the local chemical environment and we image, with few nanometre spatial resolution and 0.2 cm−1 spectral precision, solvatochromic Stark shifts and line broadening correlated with molecular-scale morphologies. We discriminate local variations in electric fields between nano-domains with quantitative agreement with dielectric continuum models. This ability to directly resolve nanoscale morphology and associated intermolecular interactions can form a basis for the systematic control of functionality in multicomponent soft matter systems. PMID:24721995

  3. Computational IR spectroscopy of water: OH stretch frequencies, transition dipoles, and intermolecular vibrational coupling constants

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2013-05-01

    The Hessian matrix reconstruction method initially developed to extract the basis mode frequencies, vibrational coupling constants, and transition dipoles of the delocalized amide I, II, and III vibrations of polypeptides and proteins from quantum chemistry calculation results is used to obtain those properties of delocalized O-H stretch modes in liquid water. Considering the water symmetric and asymmetric O-H stretch modes as basis modes, we here develop theoretical models relating vibrational frequencies, transition dipoles, and coupling constants of basis modes to local water configuration and solvent electric potential. Molecular dynamics simulation was performed to generate an ensemble of water configurations that was in turn used to construct vibrational Hamiltonian matrices. Obtaining the eigenvalues and eigenvectors of the matrices and using the time-averaging approximation method, which was developed by the Skinner group, to calculating the vibrational spectra of coupled oscillator systems, we could numerically simulate the O-H stretch IR spectrum of liquid water. The asymmetric line shape and weak shoulder bands were quantitatively reproduced by the present computational procedure based on vibrational exciton model, where the polarization effects on basis mode transition dipoles and inter-mode coupling constants were found to be crucial in quantitatively simulating the vibrational spectra of hydrogen-bond networking liquid water.

  4. Intermolecular bonding of hemin in solution and in solid state probed by N K-edge X-ray spectroscopies.

    PubMed

    Golnak, Ronny; Xiao, Jie; Atak, Kaan; Stevens, Joanna S; Gainar, Adrian; Schroeder, Sven L M; Aziz, Emad F

    2015-11-21

    X-ray absorption/emission spectroscopy (XAS/XES) at the N K-edge of iron protoporphyrin IX chloride (FePPIX-Cl, or hemin) has been carried out for dissolved monomers in DMSO, dimers in water and for the solid state. This sequence of samples permits identification of characteristic spectral features associated with the hemin intermolecular bonding. These characteristic features are further analyzed and understood at the molecular orbital (MO) level based on the DFT calculations.

  5. Strong intermolecular exciton couplings in solid-state circular dichroism of aryl benzyl sulfoxides.

    PubMed

    Padula, Daniele; Di Pietro, Sebastiano; Capozzi, Maria Annunziata M; Cardellicchio, Cosimo; Pescitelli, Gennaro

    2014-09-01

    A series of 13 enantiopure aryl benzyl sulfoxides () with different substituents on the two aromatic rings has been previously analyzed by means of electronic circular dichroism (CD) spectroscopy. Most of these compounds are crystalline and their X-ray structure is established. For almost one-half of the series, CD spectra measured in the solid state were quite different from those in acetonitrile solution. We demonstrate that the difference is due to strong exciton couplings between molecules packed closely together in the crystal. The computational approach consists of time-dependent density functional theory (TDDFT) calculations run on "dimers" composed of nearest neighbors found in the lattice. Solid-state CD spectra are well reproduced by the average of all possible pairwise terms. The relation between the crystal space group and conformation, and the appearance of solid-state CD spectra, is also discussed.

  6. Probing anomalous gauge boson couplings at LEP

    SciTech Connect

    Dawson, S.; Valencia, G.

    1994-12-31

    We bound anomalous gauge boson couplings using LEP data for the Z {yields} {bar {integral}}{integral} partial widths. We use an effective field theory formalism to compute the one-loop corrections resulting from non-standard model three and four gauge boson vertices. We find that measurements at LEP constrain the three gauge boson couplings at a level comparable to that obtainable at LEPII.

  7. Biomedical probe using a fiber-optic coupled scintillator.

    PubMed

    Swinth, K L; Ewins, J H

    1976-01-01

    A high-sensitivity biomedical radiation probe which employs a fiber-optic coupled NaI(Tl) scintillator as a detector is described. It was developed for in vivo counting of low-energy 239Pu photons from material located in the tracheobronchial lymph nodes.-This probe is 20 times as sensitive as a solid-state probe (avalanche diode) previously developed for this application. Tests with 99mTc show a sensitivity more than 90 times greater than biomedical probes using DcTe of GaAs; however, the improved sensitivity is largely due to an increased sensitive volume. Probes were evaluated in animals and phantoms for detection of 239Pu and for location of lung tumors labeled with 111In. PMID:1264039

  8. Energy of the quasi-free electron in H2, D2, and O2: Probing intermolecular potentials within the local Wigner-Seitz model

    NASA Astrophysics Data System (ADS)

    Evans, C. M.; Krynski, Kamil; Streeter, Zachary; Findley, G. L.

    2015-12-01

    We present for the first time the quasi-free electron energy V0(ρ) for H2, D2, and O2 from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V0(ρ) accurately in strongly absorbing fluids (e.g., O2) and fluids with extremely low critical temperatures (e.g., H2 and D2). We also show that the isotropic local Wigner-Seitz model for V0(ρ) — when coupled with thermodynamic data for the fluid — can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths.

  9. Energy of the quasi-free electron in hydrogen, deuterium and oxygen: Probing intermolecular potentials within the local Wigner-Seitz model

    NASA Astrophysics Data System (ADS)

    Krynski, Kamil; Streeter, Zachary; Evans, Cherice; Findley, Gary L.

    We present for the first time the quasi-free electron energy V0 (ρ) for H2, D2 and O2 from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V0 (ρ) accurately in strongly optically absorbing fluids (e.g., O2) and fluids with extremely low critical temperatures (e.g., H2 and D2). We also show that the isotropic local Wigner-Seitz model for V0 (ρ) - when coupled with thermodynamic data for the fluid - can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths. All measurements were performed at the University of Wisconsin Synchrotron Radiation Center. This work was supported by a grant from the National Science Foundation (NSF CHE-0956719).

  10. Two-dimensional probe absorption in coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Liu, Ningwu; Zhang, Yan; Kang, Chengxian; Wang, Zhiping; Yu, Benli

    2016-07-01

    We investigate the two-dimensional (2D) probe absorption in coupled quantum dots. It is found that, due to the position-dependent quantum interference effect, the 2D optical absorption spectrum can be easily controlled via adjusting the system parameters. Thus, our scheme may provide some technological applications in solid-state quantum communication.

  11. Rotationally inelastic scattering of ND3 with H2 as a probe of the intermolecular potential energy surface

    NASA Astrophysics Data System (ADS)

    Tkáč, Ondřej; Saha, Ashim K.; Loreau, Jérôme; Ma, Qianli; Dagdigian, Paul J.; Parker, David H.; van der Avoird, Ad; Orr-Ewing, Andrew J.

    2015-12-01

    Differential cross sections (DCSs) are reported for rotationally inelastic scattering of ND3 with H2, measured using a crossed molecular beam apparatus with velocity map imaging (VMI). ND3 molecules were quantum-state selected in the ground electronic and vibrational levels and, optionally, in the j±k = 11- rotation-inversion level prior to collisions. Inelastic scattering of state-selected ND3 with H2 was measured at the mean collision energy of 580 cm-1 by resonance-enhanced multiphoton ionisation spectroscopy and VMI of ND3 in selected single final j'±k' levels. Comparison of experimental DCSs with close-coupling quantum-mechanical scattering calculations serves as a test of a recently reported ab initio potential energy surface. Calculated integral cross sections reveal the propensities for scattering into various final j'±k' levels of ND3 and differences between scattering by ortho and para H2. Integral and differential cross sections are also computed at a mean collision energy of 430 cm-1 and compared to our recent results for inelastic scattering of state-selected ND3 with He.

  12. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  13. An energy decomposition analysis for intermolecular interactions from an absolutely localized molecular orbital reference at the coupled-cluster singles and doubles level.

    PubMed

    Azar, R Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C(s)-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  14. Probing scalar coupling differences via long-lived singlet states

    NASA Astrophysics Data System (ADS)

    DeVience, Stephen J.; Walsworth, Ronald L.; Rosen, Matthew S.

    2016-01-01

    We probe small scalar coupling differences via the coherent interactions between two nuclear spin singlet states in organic molecules. We show that the spin-lock induced crossing (SLIC) technique enables the coherent transfer of singlet order between one spin pair and another. The transfer is mediated by the difference in syn and anti vicinal or long-range J couplings among the spins. By measuring the transfer rate, we calculate a J coupling difference of 8 ± 2 mHz in phenylalanine-glycine-glycine and 2.57 ± 0.04 Hz in glutamate. We also characterize a coherence between two singlet states in glutamate, which may enable the creation of a long-lived quantum memory.

  15. H2 and (H2)2 molecules with an ab initio optimization of wave functions in correlated state: electron-proton couplings and intermolecular microscopic parameters

    NASA Astrophysics Data System (ADS)

    Kądzielawa, Andrzej P.; Bielas, Agata; Acquarone, Marcello; Biborski, Andrzej; Maśka, Maciej M.; Spałek, Józef

    2014-12-01

    The hydrogen molecules H2 and {{≤ft( {{H}2} \\right)}2} are analyzed with electronic correlations taken into account between the 1s electrons in an exact manner. The optimal single-particle Slater orbitals are evaluated in the correlated state of H2 by combining their variational determination with the diagonalization of the full Hamiltonian in the second-quantization language. All electron-ion coupling constants are determined explicitly and their relative importance is discussed. Sizable zero-point motion amplitude and the corresponding energy are then evaluated by taking into account the anharmonic contributions up to the ninth order in the relative displacement of the ions from their static equilibrium value. The applicability of the model to solid molecular hydrogen is briefly analyzed by calculating intermolecular microscopic parameters for the 2× {{H}2} rectangular configuration, as well its ground state energy.

  16. Langmuir Probe Distortions and Probe Compensation in an Inductively Coupled Plasma

    NASA Technical Reports Server (NTRS)

    Ji, J. S.; Cappelli, M. A.; Kim, J. S.; Rao, M. V. V. S.; Sharma, S. P.

    1999-01-01

    In many RF discharges, Langmuir probe measurements are usually made against a background of sinusoidal (and not so sinusoidal) fluctuations in the plasma parameters such as the plasma potential (Vp), the electron number density (ne), and the electron temperature (Te). The compensation of sinusoidal fluctuations in Vp has been extensively studied and is relatively well understood. Less attention has been paid to the possible distortions introduced by small fluctuations in plasma density and/or plasma temperature, which may arise in the sheath and pre-sheath regions of RF discharges. Here, we present the results of a model simulation of probe characteristics subject to fluctuations in both Vp and ne. The modeling of probe distortion due to possible fluctuations in Te is less straightforward. A comparison is presented of calculations with experimental measurements using a compensated and uncompensated Langmuir probe in an inductively coupled GEC reference cell plasma, operating on Ar and Ar/CF4 mixtures. The plasma parameters determined from the compensated probe characteristics are compared to previous measurements of others made in similar discharges, and to our own measurements of the average electron density derived from electrical impedance measurements.

  17. A fiber-optically coupled positron-sensitive surgical probe

    SciTech Connect

    Raylman, R.R.; Wahl, R.L.

    1994-05-01

    Positron-emitting radiopharmaceuticals such as {sup 18}F-labeled 2-deoxy-D-glucose (FDG) have considerable utility in the noninvasive imaging of cancers due to their rapid and excellent tumor-localizing properties. In addition, the relatively short range of positrons in tissue facilitates the precise delineation of FDG-avid tumors. Therefore, FDG used in conjunction with a positron-sensitive probe may be capable of guiding surgical procedures. Many of the current probe systems, however, are sensitive to the intense flux of background photons produced by positron annihilation. The authors describe the design, manufacture and initial in vitro and in vivo testing of a probe well-suited to the detection of positron-emitting isotopes in a high-photon background. The device consists of a small piece of plastic scintillator coupled by fiber-optic cable to a photomultiplier tube. Measurements of resolution and detector sensitivity were obtained. In addition, the reduction in resolution caused by the effects of various levels of background photon flux was determined. These measurements indicate that resolution is degraded minimally ({approximately}5% with a background-to-source ratio of 2:1) due to annihilation photon background. Sensitivity for positrons is good, detecting amounts of radioactivity as low as 10.2 nCi of FDG in vitro. In rats given FDG subcutaneously, lymph nodes containing as little as 11 nCi of FDG could be detected above the background activity levels present in normal surrounding tissues. A plastic scintillator probe system has been devised which may be highly suitable for intraoperative FDG-guided (or other positron or beta emitting-tracer) surgery. 29 refs., 7 figs.

  18. Driving Forces for Covalent Assembly of Porphyrins by Selective C-H Bond Activation and Intermolecular Coupling on a Copper Surface.

    PubMed

    Floris, Andrea; Haq, Sam; In't Veld, Mendel; Amabilino, David B; Raval, Rasmita; Kantorovich, Lev

    2016-05-11

    Recent synthesis of covalent organic assemblies at surfaces has opened the promise of producing robust nanostructures for functional interfaces. To uncover how this new chemistry works at surfaces and understand the underlying mechanisms that control bond-breaking and bond-making processes at specific positions of the participating molecules, we study here the coupling reaction of tetra(mesityl)porphyrin molecules, which creates covalently connected networks on the Cu(110) surface by utilizing the 4-methyl groups as unique connection points. Using scanning tunneling microscopy (STM), state-of-the-art density functional theory (DFT), and Nudged Elastic Band (NEB) calculations, we show that the unique directionality of the covalent bonding is found to stem from a chain of highly selective C-H activation and dehydrogenation processes, followed by specific intermolecular C-C coupling reactions that are facilitated by the surface, by steric constraints, and by anisotropic molecular diffusion. These insights provide the first steps toward developing synthetic rules for complex two-dimensional covalent organic chemistry that can be enacted directly at a surface to deliver specific macromolecular structures designed for specific functions.

  19. Coupling Electrochemistry with Probe Electrospray Ionization Mass Spectrometry.

    PubMed

    Cai, Yi; Liu, Pengyuan; Held, Michael A; Dewald, Howard D; Chen, Hao

    2016-04-18

    A new coupling of electrochemistry with mass spectrometry (MS) using probe electrospray ionization (PESI) is presented. Due to the high salt tolerance of PESI, the detection of electrochemical reaction products in room-temperature ionic liquids (RTILs) is realized for the first time. Furthermore, PESI-MS allows the analysis of electrochemical reaction products on different or multiple electrode surfaces. In addition, peptides and proteins fractionated through isoelectric focusing (IEF) in the presence of an external electric field can also be directly analyzed by using PESI-MS, suggesting a new and rapid characterization means for the IEF technique. This study reveals the versatility of EC/PESI-MS, which could have an impact in electrochemistry and bioanalysis fields.

  20. Second-order exchange-induction energy of intermolecular interactions from coupled cluster density matrices and their cumulants.

    PubMed

    Korona, Tatiana

    2008-11-21

    A new formulation of the second-order exchange-induction energy of symmetry-adapted perturbation theory is presented. In the proposed formalism the exchange-induction energy is expressed through one- and two-particle reduced density matrices of monomers, which are of zeroth and first order with respect to the effective electrostatic potential of another monomer. The resulting expression is further modified by using the partition of two-particle density matrices into the antisymmetrized product of one-particle density matrices and the remaining cumulant part. The proposed formalism has been applied to the case of closed-shell monomers and for density matrices obtained from the expectation-value expression with coupled cluster singles and doubles wave functions. The performance of the new approach has been demonstrated on several benchmark van der Waals systems, including dimers of argon, water, and ethyne.

  1. On the intermolecular vibrational coupling, hydrogen bonding, and librational freedom of water in the hydration shell of mono- and bivalent anions.

    PubMed

    Ahmed, Mohammed; Namboodiri, V; Singh, Ajay K; Mondal, Jahur A

    2014-10-28

    The hydration energy of an ion largely resides within the first few layers of water molecules in its hydration shell. Hence, it is important to understand the transformation of water properties, such as hydrogen-bonding, intermolecular vibrational coupling, and librational freedom in the hydration shell of ions. We investigated these properties in the hydration shell of mono- (Cl(-) and I(-)) and bivalent (SO4(2-) and CO3(2-)) anions by using Raman multivariate curve resolution (Raman-MCR) spectroscopy in the OH stretch, HOH bend, and [bend+librational] combination bands of water. Raman-MCR of aqueous Na-salt (NaCl, NaI, Na2SO4, and Na2CO3) solutions provides ion-correlated spectra (IC-spectrum) which predominantly bear the vibrational characteristics of water in the hydration shell of respective anions. Comparison of these IC-spectra with the Raman spectrum of bulk water in different spectral regions reveals that the water is vibrationally decoupled with its neighbors in the hydration shell. Hydrogen-bond strength and librational freedom also vary with the nature of anion: hydrogen-bond strength, for example, decreases as CO3(2-) > SO4(2-) > bulk water ≈ Cl(-) > I(-); and the librational freedom increases as CO3(2-) ≈ SO4(2-) < bulk water < Cl(-) < I(-). It is believed that these structural perturbations influence the dynamics of coherent energy transfer and librational reorientation of water in the hydration shell of anions.

  2. Improving the Mass-Limited Performance of Routine NMR Probes using Coupled Coils

    NASA Astrophysics Data System (ADS)

    Marsden, Brian; Lim, Victor; Taber, Bob; Zens, Albert

    2016-07-01

    We report a method to convert, on demand, a general use dual-broadband probe to a high performance mass-limited probe for both high band and low band nuclei. This technology uses magnetic coupling of inductors to achieve this capability. The method offers a cost effective way of increasing the performance of routine NMR probes without having to change probes or increase the overall foot print of the spectrometer.

  3. Capacitively coupled RF voltage probe having optimized flux linkage

    DOEpatents

    Moore, James A.; Sparks, Dennis O.

    1999-02-02

    An RF sensor having a novel current sensing probe and a voltage sensing probe to measure voltage and current. The current sensor is disposed in a transmission line to link all of the flux generated by the flowing current in order to obtain an accurate measurement. The voltage sensor is a flat plate which operates as a capacitive plate to sense voltage on a center conductor of the transmission line, in which the measured voltage is obtained across a resistance leg of a R-C differentiator circuit formed by the characteristic impedance of a connecting transmission line and a capacitance of the plate, which is positioned proximal to the center conductor.

  4. Higgs coupling constants as a probe of new physics

    NASA Astrophysics Data System (ADS)

    Kanemura, Shinya; Okada, Yasuhiro; Senaha, Eibun; Yuan, C.-P.

    2004-12-01

    We study new physics effects on the couplings of weak gauge bosons with the lightest CP-even Higgs boson (h), hZZ, and the trilinear coupling of the lightest Higgs boson, hhh, at the one-loop order, as predicted by the two Higgs doublet model. Those renormalized coupling constants can deviate from the standard model (SM) predictions due to two distinct origins: the tree level mixing effect of Higgs bosons and the quantum effect of additional particles in loop diagrams. The latter can be enhanced in the renormalized hhh coupling constant when the additional particles show the nondecoupling property. Therefore, even in the case where the hZZ coupling is close to the SM value, deviation in the hhh coupling from the SM value can become as large as plus 100%, while that in the hZZ coupling is at most minus 1% level. Such large quantum effect on the Higgs trilinear coupling is distinguishable from the tree level mixing effect, and is expected to be detectable at a future linear collider.

  5. Energy of the quasi-free electron in H{sub 2}, D{sub 2}, and O{sub 2}: Probing intermolecular potentials within the local Wigner-Seitz model

    SciTech Connect

    Evans, C. M. Krynski, Kamil; Streeter, Zachary; Findley, G. L.

    2015-12-14

    We present for the first time the quasi-free electron energy V{sub 0}(ρ) for H{sub 2}, D{sub 2}, and O{sub 2} from gas to liquid densities, on noncritical isotherms and on a near critical isotherm in each fluid. These data illustrate the ability of field enhanced photoemission (FEP) to determine V{sub 0}(ρ) accurately in strongly absorbing fluids (e.g., O{sub 2}) and fluids with extremely low critical temperatures (e.g., H{sub 2} and D{sub 2}). We also show that the isotropic local Wigner-Seitz model for V{sub 0}(ρ) — when coupled with thermodynamic data for the fluid — can yield optimized parameters for intermolecular potentials, as well as zero kinetic energy electron scattering lengths.

  6. Control of the probe absorption in coupled quantum wells in two dimensions

    NASA Astrophysics Data System (ADS)

    Kang, Chengxian; Ma, Yangcheng; Wang, Zhiping; Yu, Benli

    2016-06-01

    We investigate the probe absorption of a weak probe field in two dimensions (the so-called two-dimensional probe absorption) in an asymmetric two coupled quantum wells. It is found that, due to the joint quantum interference induced by the standing-wave and coherent coupling fields, the probe absorption can be easily controlled via adjusting the system parameters in two dimensions. Most importantly, the pattern of probe absorption can be localized at a particular position and the maximal probability of finding the pattern in one period of the standing-wave fields reaches unity by properly adjusting the system parameters. Thus, our scheme may provide some technological applications in solid-state optoelectronics and quantum information science.

  7. Langmuir Probe Measurements in an Inductively Coupled GEC Reference Cell Plasma

    NASA Technical Reports Server (NTRS)

    Ji, J. S.; Kim, J. S.; Cappelli, M. A.; Sharma, S. P.; Arnold, J. O. (Technical Monitor)

    1998-01-01

    Measurements of electron number density, electron temperature, and electron energy distribution function (EEDF) using a compensated Langmuir probe have been performed on an inductively (transformer ) coupled Gaseous Electronics Conference (GEC) reference cell plasma. The plasma source is operated with CH4, CF4, or their mixtures with argon. The effect of independently driving the electrode supporting the wafer on the probe data is studied. In particular, we find that the plasma structure depends on the phase in addition to the magnitude of the power coupled to the electrode relative to that of the transformer coil. The Langmuir probe is translated in a plane parallel to the electrode to investigate the spatial structure of the plasma. The probe data is also compared with fluid model predictions.

  8. Probing strongly coupled anisotropic plasmas from higher curvature gravity

    NASA Astrophysics Data System (ADS)

    Jahnke, Viktor; Misobuchi, Anderson Seigo

    2016-06-01

    We consider five-dimensional AdS-axion-dilaton gravity with a Gauss-Bonnet term and use a black brane solution displaying spatial anisotropy as the gravity dual of a strongly coupled anisotropic plasma. We compute several observables relevant to the study of the plasma, namely, the drag force, the jet quenching parameter, the quarkonium potential, and the thermal photon production. The effects of higher derivative corrections and of the anisotropy are discussed and compared with previous results.

  9. Probing transmembrane mechanical coupling and cytomechanics using magnetic twisting cytometry

    NASA Technical Reports Server (NTRS)

    Wang, N.; Ingber, D. E.

    1995-01-01

    We recently developed a magnetic twisting cytometry technique that allows us to apply controlled mechanical stresses to specific cell surface receptors using ligand-coated ferromagnetic microbeads and to simultaneously measure the mechanical response in living cells. Using this technique, we have previously shown the following: (i) beta 1 integrin receptors mediate mechanical force transfer across the cell surface and to the cytoskeleton, whereas other transmembrane receptors (e.g., scavenger receptors) do not; (ii) cytoskeletal stiffness increases in direct proportion to the level of stress applied to integrins; and (iii) the slope of this linear stiffening response differs depending on the shape of the cell. We now show that different integrins (beta 1, alpha V beta 3, alpha V, alpha 5, alpha 2) and other transmembrane receptors (scavenger receptor, platelet endothelial cell adhesion molecule) differ in their ability to mediate force transfer across the cell surface. In addition, the linear stiffening behavior previously observed in endothelial cells was found to be shared by other cell types. Finally, we demonstrate that dynamic changes in cell shape that occur during both cell spreading and retraction are accompanied by coordinate changes in cytoskeletal stiffness. Taken together, these results suggest that the magnetic twisting cytometry technique may be a powerful and versatile tool for studies analyzing the molecular basis of transmembrane mechanical coupling to the cytoskeleton as well as dynamic relations between changes in cytoskeletal structure and alterations in cell form and function.

  10. Development of a Methodology for the Characterisation of Air-coupled Ultrasound Probes

    SciTech Connect

    Pietroni, Paolo; Marco Revel, Gian

    2010-05-28

    This study is aimed at developing a technique for the characterisation of air-coupled ultrasound probes, starting from the analysis of the mechanical behaviour of the probe membrane. The vibratory behaviour of the emission membrane is studied using laser-Doppler vibrometry techniques with high frequency demodulation system (20 MHz). The determination of the vibration provides information which are useful for the assessment of the performance of the probe, in particular concerning the Quality factor and the portion of the membrane which really contributes to the emission. During the second step the results of the vibration measurements are used to calculate, by means of numerical boundary element method, the ultrasound beam emitted in terms of intensity in space. The obtained field is compared with the direct measurements carried out by scanning with the receiver probe and a pinhole plate. This comparison allows the potential and the problems of the two different characterisation techniques to be determined, even if the pinhole technique (which is currently considered the state of the art) cannot be used as an absolute reference. This study appears to be useful for paving the way for a new methodology for the calibration of air-coupled ultrasound probes, which potentially could be used not only to improve the probe manufacturing process, but also to control conformity to specifications.

  11. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds. PMID:20673643

  12. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil.

    PubMed

    Litvak, Ilya M; Espinosa, Catalina A; Shapiro, Rebecca A; Oldham, Andrew N; Duong, Vincent V; Martin, Rachel W

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  13. Pneumatic switched angle spinning NMR probe with capacitively coupled double saddle coil

    NASA Astrophysics Data System (ADS)

    Litvak, Ilya M.; Espinosa, Catalina A.; Shapiro, Rebecca A.; Oldham, Andrew N.; Duong, Vincent V.; Martin, Rachel W.

    2010-10-01

    Switched angle spinning (SAS) experiments can be used for generating isotropic-anisotropic correlations in oriented samples in a single experiment. In order for these methods to become widespread, specialized hardware is required. Here we describe the electronic and mechanical design and performance of a double-resonance SAS probe. Unlike many previous SAS probe implementations, the focus here is on systems where the dipolar couplings are partially averaged by molecular motion. This probe has a moving double saddle coil capacitively coupled to the stationary circuit. Angle switching is accomplished by a steam engine-type pneumatic mechanism. The speed and stability of the switching hardware for SAS experiments are demonstrated using spectra of model compounds.

  14. An earth-isolated optically coupled wideband high voltage probe powered by ambient light

    NASA Astrophysics Data System (ADS)

    Zhai, Xiang; Bellan, Paul M.

    2012-10-01

    An earth-isolated optically-coupled wideband high voltage probe has been developed for pulsed power applications. The probe uses a capacitive voltage divider coupled to a fast light-emitting diode that converts high voltage into an amplitude-modulated optical signal, which is then conveyed to a receiver via an optical fiber. A solar cell array, powered by ambient laboratory lighting, charges a capacitor that, when triggered, acts as a short-duration power supply for an on-board amplifier in the probe. The entire system has a noise level ⩽0.03 kV, a DC-5 MHz bandwidth, and a measurement range from -6 to 2 kV; this range can be conveniently adjusted.

  15. An earth-isolated optically coupled wideband high voltage probe powered by ambient light

    NASA Astrophysics Data System (ADS)

    Zhai, Xiang; Bellan, Paul

    2012-10-01

    An earth-isolated optically coupled wideband high voltage probe has been developed for pulsed power applications. The probe uses a capacitive voltage divider coupled to a fast LED that converts high voltage into an amplitude-modulated optical signal, which is then conveyed to a receiver via an optical fiber. A solar cell array powered by ambient laboratory lighting charges a capacitor that, when triggered, acts as a short-duration power supply for an on-board amplifier in the probe. The entire system has a noise level <=0.03 kV, a DC-5 MHz bandwidth and a measurement range from -6 to 2 kV; this range can be conveniently adjusted.

  16. Local two-way magnetoelectric couplings in multiferroic composites via scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Xie, S. H.; Liu, Y. M.; Liu, X. Y.; Zhou, Q. F.; Shung, K. K.; Zhou, Y. C.; Li, J. Y.

    2010-09-01

    Local two-way magnetoelectric (ME) couplings of a multiferroic composite have been characterized at nanoscale using novel scanning probe microscopy techniques we developed. A bilayer multiferroic composite consisting of lead zirconate titanate (PZT) and TbDyFe (TDF) has been fabricated, and the evolution of ferroelectric domains in PZT induced by an external magnetic field is observed by piezoresponse force microscopy, while the evolution of magnetic domains in TDF induced by an external electric field is observed by magnetic force microscopy, confirming the two-way ME couplings in the multiferroic composite. The technique will be useful in characterizing nanoscale ME couplings in a wide range of multiferroic composites.

  17. Enhanced fullerene–Au(111) coupling in (2√3 × 2√3)R30° superstructures with intermolecular interactions

    PubMed Central

    Paßens, Michael; Waser, Rainer

    2015-01-01

    Summary Disordered and uniform (2√3 × 2√3)R30° superstructures of fullerenes on the Au(111) surface have been studied using scanning tunneling microscopy and spectroscopy. It is shown that the deposition and growth process of a fullerene monolayer on the Au(111) surface determine the resulting superstructure. The supply of thermal energy is of importance for the activation of a Au vacancy forming process and thus, one criterion for the selection of the respective superstructure. However, here it is depicted that a vacancy–adatom pair can be formed even at room temperature. This latter process results in C60 molecules that appear slightly more bright in scanning tunnelling microscopy images and are identified in disordered (2√3 x 2√3)R30° superstructures based on a detailed structure analysis. In addition, these slightly more bright C60 molecules form uniform (2√3 x 2√3)R30° superstructures, which exhibit intermolecular interactions, likely mediated by Au adatoms. Thus, vacancy–adatom pairs forming at room temperature directly affect the resulting C60 superstructure. Differential conductivity spectra reveal a lifting of the degeneracy of the LUMO and LUMO+1 orbitals in the uniform (2√3 x 2√3)R30° superstructure and in addition, hybrid fullerene–Au(111) surface states suggest partly covalent interactions. PMID:26199846

  18. Transient gain-absorption of the probe field in triple quantum dots coupled by double tunneling

    NASA Astrophysics Data System (ADS)

    Tian, Si-Cong; Zhang, Xiao-Jun; Wan, Ren-Gang; Zhao, Shuai; Wu, Hao; Shu, Shi-Li; Wang, Li-Jie; Tong, Cun-Zhu

    2016-06-01

    The transient gain-absorption property of the probe field in a linear triple quantum dots coupled by double tunneling is investigated. It is found that the additional tunneling can dramatically affect the transient behaviors under the transparency condition. The dependence of transient behaviors on other parameters, such as probe detuning, the pure dephasing decay rate of the quantum dots and the initial conditions of the population, are also discussed. The results can be explained by the properties of the dressed states generated by the additional tunneling. The scheme may have important application in quantum information network and communication.

  19. Tamm State-Coupled Emission: Effect of Probe Location and Emission Wavelength

    PubMed Central

    2015-01-01

    We report the effect of the probe location and wavelength on the emission spatial distribution and spectral properties of fluorophores located on structures which display Tamm states. Our structure consists of a one-dimensional photonic crystal (1DPC)—that is, a multilayer structure of alternate high and low refractive index dielectrics—and a thin top silver film. Simulations show the presence of Tamm and surface plasmon modes in the structure. The electric field intensities for the Tamm modes are located mostly in the dielectric layer below the metal film. The corresponding field intensities for the surface plamon modes are located above the metal film in the distal side. Tamm states can be in resonance with the incident light normal or near normal to the surface, within the light line, and can be accessed without the use of a coupling prism or gratings. We investigated the emission spectra and angular distribution of the emission for probes located above and below the metal film to explore the interaction of fluorophores with Tamm plasmons and surface plasmons modes. Three probes were chosen with different overlap of the emission spectra with the Tamm modes. The fluorophores below the metal film coupled predominantly with the Tamm state and displayed more intense and only Tamm state-coupled emission (TSCE). Probes above the metal film display both surface plasmon-coupled emission (SPCE) and Tamm state-coupled emission. In contrast to SPCE, which shows only KR, P-polarized emission, the Tamm states can display both S- and P-polarized emission and can be populated using both RK and KR illuminations. The TSCE angle is highly sensitive to wavelength, which suggests the use of Tamm structures to provide both directional emission and wavelength dispersion. The combination of plasmonic and photonic structures with directional emission close to surface normal offers the opportunities for new design formats for clinical testing, portable devices, and other

  20. Probing Spin-Orbit Coupling and Interlayer Coupling in Atomically Thin Molybdenum Disulfide Using Hydrostatic Pressure.

    PubMed

    Dou, Xiuming; Ding, Kun; Jiang, Desheng; Fan, Xiaofeng; Sun, Baoquan

    2016-01-26

    In two-dimensional transition-metal dichalcogenides, both spin-orbit coupling and interlayer coupling play critical roles in the electronic band structure and are desirable for the potential applications in spin electronics. Here, we demonstrate the pressure characteristics of the exciton absorption peaks (so-called excitons A, B and C) in monolayer, bilayer, and trilayer molybdenum disulfide (MoS2) by studying the reflectance spectra under hydrostatic pressure and performing the electronic band structure calculations based on density functional theory to account for the experimental observations. We find that the valence band maximum splitting at the K point in monolayer MoS2, induced by spin-orbit coupling, remains almost unchanged with increasing pressure applied up to 3.98 GPa, indicating that the spin-orbit coupling is insensitive to the pressure. For bilayer and trilayer MoS2, however, the splitting shows an increase with increasing pressure due to the pressure-induced strengthening of the interlayer coupling. The experimental results are in good agreement with the theoretical calculations. Moreover, the exciton C is identified to be the interband transition related to the van Hove singularity located at a special point which is approximately 1/4 of the total length of Γ-K away from the Γ point in the Brillouin zone. PMID:26745440

  1. Azimuthal angle probe of anomalous HWW couplings at a high energy ep collider.

    PubMed

    Biswal, Sudhansu S; Godbole, Rohini M; Mellado, Bruce; Raychaudhuri, Sreerup

    2012-12-28

    A high energy ep collider, such as the proposed LHeC, possesses the unique facility of permitting direct measurement of the HWW coupling without contamination from the HZZ coupling. At such a machine, the fusion of two W bosons through the HWW vertex would give rise to typical charged current events accompanied by a Higgs boson. We demonstrate that azimuthal angle correlations between the observable charged current final states could then be a sensitive probe of the nature of the HWW vertex and hence of the CP properties of the Higgs boson.

  2. Probing the Higgs couplings to photons in h→4ℓ at the LHC.

    PubMed

    Chen, Yi; Harnik, Roni; Vega-Morales, Roberto

    2014-11-01

    We explore the sensitivity of the Higgs decay to four leptons, the so-called golden channel, to higher dimensional loop-induced couplings of the Higgs boson to ZZ, Zγ, and γγ pairs, allowing for general CP mixtures. The larger standard model tree level coupling hZ(μ)Z(μ) is the dominant "background" for the loop-induced couplings. However, this large background interferes with the smaller loop-induced couplings, enhancing the sensitivity. We perform a maximum likelihood analysis based on analytic expressions of the fully differential decay width for h→4ℓ (4ℓ≡2e2μ,4e,4μ), including all interference effects. We find that the spectral shapes induced by Higgs couplings to photons are particularly different than the hZ(μ)Z(μ) background leading to enhanced sensitivity to these couplings. We show that even if the h→γγ and h→4ℓ rates agree with that predicted by the standard model, the golden channel has the potential to probe both the CP nature as well as the overall sign of the Higgs coupling to photons well before the end of a high-luminosity LHC.

  3. Probing the Higgs Couplings to Photons in h→4l at the LHC

    SciTech Connect

    Chen, Yi; Harnik, Roni; Vega-Morales, Roberto

    2014-11-01

    We explore the sensitivity of the Higgs decay to four leptons, the so-called golden channel, to higher dimensional loop-induced couplings of the Higgs boson to $ZZ$, $Z\\gamma$, and $\\gamma\\gamma$, allowing for general CP mixtures. The larger standard model tree level coupling $hZ^\\mu Z_\\mu$ is the dominant "background" for the loop induced couplings. However this large background interferes with the smaller loop induced couplings, enhancing the sensitivity. We perform a maximum likelihood analysis based on analytic expressions of the fully differential decay width for $h\\to 4\\ell$ ($4\\ell \\equiv 2e2\\mu, 4e, 4\\mu$) including all interference effects. We find that the spectral shapes induced by Higgs couplings to photons are particularly different than the $hZ^\\mu Z_\\mu$ background leading to enhanced sensitivity to these couplings. We show that even if the $h\\to\\gamma\\gamma$ and $h\\to 4\\ell$ rates agree with that predicted by the Standard Model, the golden channel has the potential to probe both the CP nature as well as the overall sign of the Higgs coupling to photons well before the end of high-luminosity LHC running ($\\sim$3 ab$^{-1}$).

  4. Desensitization of metastable intermolecular composites

    DOEpatents

    Busse, James R.; Dye, Robert C.; Foley, Timothy J.; Higa, Kelvin T.; Jorgensen, Betty S.; Sanders, Victor E.; Son, Steven F.

    2011-04-26

    A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

  5. Coupled Ablation, Heat Conduction, Pyrolysis, Shape Change and Spallation of the Galileo Probe

    NASA Technical Reports Server (NTRS)

    Milos, Frank S.; Chen, Y.-K.; Rasky, Daniel J. (Technical Monitor)

    1995-01-01

    The Galileo probe enters the atmosphere of Jupiter in December 1995. This paper presents numerical methodology and detailed results of our final pre-impact calculations for the heat shield response. The calculations are performed using a highly modified version of a viscous shock layer code with massive radiation coupled with a surface thermochemical ablation and spallation model and with the transient in-depth thermal response of the charring and ablating heat shield. The flowfield is quasi-steady along the trajectory, but the heat shield thermal response is dynamic. Each surface node of the VSL grid is coupled with a one-dimensional thermal response calculation. The thermal solver includes heat conduction, pyrolysis, and grid movement owing to surface recession. Initial conditions for the heat shield temperature and density were obtained from the high altitude rarefied-flow calculations of Haas and Milos. Galileo probe surface temperature, shape, mass flux, and element flux are all determined as functions of time along the trajectory with spallation varied parametrically. The calculations also estimate the in-depth density and temperature profiles for the heat shield. All this information is required to determine the time-dependent vehicle mass and drag coefficient which are necessary inputs for the atmospheric reconstruction experiment on board the probe.

  6. Fiber optic probe having fibers with endfaces formed for improved coupling efficiency and method using same

    DOEpatents

    O'Rourke, Patrick E.; Livingston, Ronald R.

    1995-01-01

    A fiber optic probe for detecting scattered light, with transmitting and receiving fibers having slanted ends and bundled together to form a bevel within the tip of the probe. The probe comprises a housing with a transparent window across its tip for protecting the transmitting and receiving fibers held therein. The endfaces of the fibers are slanted, by cutting, polishing and the like, so that they lie in a plane that is not perpendicular to the longitudinal axis of the respective fiber. The fibers are held in the tip of the probe using an epoxy and oriented so that lines normal to the slanted endfaces are divergent with respect to one another. The epoxy, which is positioned substantially between the transmitting and receiving fibers, is tapered so that the transmitting fiber, the epoxy and the receiving fiber form a bevel of not more than 20 degrees. The angled fiber endfaces cause directing of the light cones toward each other, resulting in improved light coupling efficiency. A light absorber, such as carbon black, is contained in the epoxy to reduce crosstalk between the transmitting and receiving fibers.

  7. Fiber optic probe having fibers with endfaces formed for improved coupling efficiency and method using same

    DOEpatents

    O`Rourke, P.E.; Livingston, R.R.

    1995-03-28

    A fiber optic probe is disclosed for detecting scattered light, with transmitting and receiving fibers having slanted ends and bundled together to form a bevel within the tip of the probe. The probe comprises a housing with a transparent window across its tip for protecting the transmitting and receiving fibers held therein. The endfaces of the fibers are slanted, by cutting, polishing and the like, so that they lie in a plane that is not perpendicular to the longitudinal axis of the respective fiber. The fibers are held in the tip of the probe using an epoxy and oriented so that lines normal to the slanted endfaces are divergent with respect to one another. The epoxy, which is positioned substantially between the transmitting and receiving fibers, is tapered so that the transmitting fiber, the epoxy and the receiving fiber form a bevel of not more than 20 degrees. The angled fiber endfaces cause directing of the light cones toward each other, resulting in improved light coupling efficiency. A light absorber, such as carbon black, is contained in the epoxy to reduce crosstalk between the transmitting and receiving fibers. 3 figures.

  8. Transient absorption probe of intermolecular triplet excimer of naphthalene in fluid solutions: Identification of the species based on comparison to the intramolecular triplet excimers of covalently-linked dimers

    SciTech Connect

    Wang, X.; Kofron, W.G.; Kong, S.; Rajesh, C.S.; Modarelli, D.A.; Lim, E.C.

    2000-02-24

    The authors report here the observation of the laser-induced transient absorption spectrum of intermolecular triplet excimers of naphthalene in fluid solution. This assignment is confirmed by comparison to the transient absorption spectra of the intramolecular triplet excimers of covalently linked dimers of naphthalene and quinoxaline.

  9. A sensitive DNA biosensor based on a facile sulfamide coupling reaction for capture probe immobilization.

    PubMed

    Wang, Qingxiang; Ding, Yingtao; Gao, Feng; Jiang, Shulian; Zhang, Bin; Ni, Jiancong; Gao, Fei

    2013-07-25

    A novel DNA biosensor was fabricated through a facile sulfamide coupling reaction. First, the versatile sulfonic dye molecule of 1-amino-2-naphthol-4-sulfonate (AN-SO3(-)) was electrodeposited on the surface of a glassy carbon electrode (GCE) to form a steady and ordered AN-SO3(-) layer. Then the amino-terminated capture probe was covalently grafted to the surface of SO3(-)-AN deposited GCE through the sulfamide coupling reaction between the amino groups in the probe DNA and the sulfonic groups in the AN-SO3(-). The step-by-step modification process was characterized by electrochemistry and attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy. Using Ru(NH3)6(3+) as probe, the probe density and the hybridization efficiency of the biosensor were determined to be 3.18×10(13) strands cm(-2) and 86.5%, respectively. The hybridization performance of the biosensor was examined by differential pulse voltammetry using Co(phen)3(3+/2+) (phen=1,10-phenanthroline) as the indicator. The selectivity experiments showed that the biosensor presented distinguishable response after hybridization with the three-base mismatched, non-complementary and complementary sequences. Under the optimal conditions, the oxidation peak currents of Co(phen)3(3+/2+) increased linearly with the logarithm values of the concentration of the complementary sequences in the range from 1.0×10(-13)M to 1.0×10(-8)M with a regression coefficient of 0.9961. The detection limit was estimated to be 7.2×10(-14)M based on 3σ. PMID:23845495

  10. Nanoscale resolved infrared probing of crystal structure and of plasmon-phonon coupling.

    PubMed

    Huber, A; Ocelic, N; Taubner, T; Hillenbrand, R

    2006-04-01

    We show that slight variations of a crystal lattice cause significant spectral modifications of phonon-polariton resonant near-field interaction between polar semiconductor crystals and a scanning metal tip. Exploiting the effect for near-field imaging a SiC polytype boundary, we establish infrared mapping of crystal structure and crystal defects at 20 nm spatial resolution (lambda/500). By spectroscopic probing of doped SiC polytypes, we find that phonon-polariton resonant near-field interaction is also sensitive to electronic properties due to plasmon-phonon coupling in the crystals.

  11. Intermolecular G-quadruplex-based universal quencher free molecular beacon.

    PubMed

    Zhou, Hui; Xie, Su-Jin; Li, Ji-Shan; Wu, Zai-Sheng; Shen, Guo-Li

    2012-11-11

    A simple and universal quencher-free molecular beacon (MB) with low background fluorescence is developed based on an intermolecular G-quadruplex signaling probe. Unlike previous fluorescent MB strategies, it can function without any fluorophore and quencher modifications on its hairpin sequence.

  12. Beyond Higgs couplings: probing the Higgs with angular observables at future e + e - colliders

    NASA Astrophysics Data System (ADS)

    Craig, Nathaniel; Gu, Jiayin; Liu, Zhen; Wang, Kechen

    2016-03-01

    We study angular observables in the {e}+{e}-to ZHto {ell}+{ell}-boverline{b} channel at future circular e + e - colliders such as CEPC and FCC-ee. Taking into account the impact of realistic cut acceptance and detector effects, we forecast the precision of six angular asymmetries at CEPC (FCC-ee) with center-of-mass energy sqrt{s}=240 GeV and 5 (30) ab-1 integrated luminosity. We then determine the projected sensitivity to a range of operators relevant for he Higgs-strahlung process in the dimension-6 Higgs EFT. Our results show that angular observables provide complementary sensitivity to rate measurements when constraining various tensor structures arising from new physics. We further find that angular asymmetries provide a novel means of both probing BSM corrections to the HZγ coupling and constraining the "blind spot" in indirect limits on supersymmetric scalar top partners.

  13. Soft Particle Spectrometer, Langmuir Probe, and Data Analysis for Aerospace Magnetospheric/Thermospheric Coupling Rocket Program

    NASA Technical Reports Server (NTRS)

    Sharber, J. R.; Frahm, R. A.; Scherrer, J. R.

    1997-01-01

    Under this grant two instruments, a soft particle spectrometer and a Langmuir probe, were refurbished and calibrated, and flown on three instrumented rocket payloads as part of the Magnetosphere/Thermosphere Coupling program. The flights took place at the Poker Flat Research Range on February 12, 1994 (T(sub o) = 1316:00 UT), February 2, 1995 (T(sub o) = 1527:20 UT), and November 27, 1995 (T(sub o) = 0807:24 UT). In this report the observations of the particle instrumentation flown on all three of the flights are described, and brief descriptions of relevant geophysical activity for each flight are provided. Calibrations of the particle instrumentation for all ARIA flights are also provided.

  14. The intermolecular interaction in D2 - CX4 and O2 - CX4 (X = F, Cl) systems: Molecular beam scattering experiments as a sensitive probe of the selectivity of charge transfer component

    NASA Astrophysics Data System (ADS)

    Cappelletti, David; Falcinelli, Stefano; Pirani, Fernando

    2016-10-01

    Gas phase collisions of a D2 projectile by CF4 and by CCl4 targets have been investigated with the molecular beam technique. The integral cross section, Q, has been measured for both collisional systems in the thermal energy range and oscillations due to the quantum "glory" interference have been resolved in the velocity dependence of Q. The analysis of the measured Q(v) data provided novel information on the anisotropic potential energy surfaces of the studied systems at intermediate and large separation distances. The relative role of the most relevant types of contributions to the global interaction has been characterized. Extending the phenomenology of a weak intermolecular halogen bond, the present work demonstrates that while D2 - CF4 is basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreciable intermolecular bond stabilization by charge transfer is operative in D2 - CCl4. We also demonstrated that the present analysis is consistent with that carried out for the F(2P)-D2 and Cl(2P)-D2 systems, previously characterized by scattering experiments performed with state-selected halogen atom beams. A detailed comparison of the present and previous results on O2-CF4 and O2-CCl4 systems pinpointed striking differences in the behavior of hydrogen and oxygen molecules when they interact with the same partner, mainly due to the selectivity of the charge transfer component. The present work contributes to cast light on the nature and role of the intermolecular interaction in prototype systems, involving homo-nuclear diatoms and symmetric halogenated molecules.

  15. Emissive Probe Measurements in a Dual-Frequency-Confined Capacitively-Coupled-Plasma System

    NASA Astrophysics Data System (ADS)

    Linnane, Shane; Ellingboe, Albert R.

    2002-10-01

    Dual frequency confined capacitively coupled plasmas (DFC-CCP) are increasingly used in semiconductor manufacturing for dielectric etching, allowing greater (and independent) control of ion energies and ion flux on the etched substrate. The powered electrode is driven with the summation of 27MHz and 2MHz sinusoidal voltages, while the other electrode is grounded. The electrode areas are similar in size, giving an electrode aspect ratio less than 2. Because of this low aspect ratio, there are large oscillations in the plasma potential. The expectation is for sinusoidal oscillations at the higher driving frequency, due to capacitive sheaths, while a rectified oscillation is expected at the lower driving frequency.(E. Kawamura, V. Vahedi, M. A. Lieberman and C. K. Birdsall, Plasma Sources Sci. Technology. 8 (1999) R45-R64 Work Supported by EURATOM.) Measurements of rf oscillation in the plasma potential taken with a floating emissive probe will be presented. The emissive probe and circuitry allows direct realtime measurement of plasma potential oscillation at both driving frequencies and the harmonics of each, thus allowing measurement of the actual potential on the driven electrode and ion energy incident on grounded electrode.

  16. Coupling atom probe tomography and photoluminescence spectroscopy: exploratory results and perspectives.

    PubMed

    Rigutti, Lorenzo; Vella, Angela; Vurpillot, François; Gaillard, Aurore; Sevelin-Radiguet, Nicolas; Houard, Jonathan; Hideur, Ammar; Martel, Gilles; Jacopin, Gwénolé; De Luna Bugallo, Andrés; Deconihout, Bernard

    2013-09-01

    The development of laser-assisted atom probes makes it possible, in principle, to exploit the femtosecond laser pulse not only for triggering ion evaporation from a nanometric field emission tip, but also for generating photons via the radiative recombination of electron-hole pairs in tips made of dielectric materials. In this article we demonstrate a first step towards a correlation of micro-photoluminescence (μ-PL) and laser-assisted tomographic atom probe (LA-TAP) analysis applied separately on the same objects, namely on ZnO microwires. In particular, we assess that the use of the focused ion beam (FIB) tip preparation method significantly degrades the radiative recombination yield of the analyzed microwires. We discuss the strategies to avoid the FIB-induced damage on the optical properties of the sample and how to get beyond the correlated μ-PL and LA-TAP analysis with a coupled approach allowing to perform the two analyses within the same instrument. PMID:23489908

  17. Langmuir Probe Measurements in an Inductively Coupled Ar/CF4 Plasmas

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Meyyappan, M.; Sharma, S. P.; Arnold, James O. (Technical Monitor)

    2000-01-01

    Technological advancement in the microelectronics industry requires an understanding of the physical and chemical processes occurring in plasmas of fluorocarbon gases, such as carbon tetrafluoride (CF4) which is commonly used as an etchant, and their mixtures to optimize various operating parameters. In this paper we report data on electron number density (ne), electron temperature'(Te), electron energy distribution function (EEDF), mean electron energy, ion number density (ni), and plasma potential (Vp) measured by using Langmuir probe in an inductively coupled 13.56 MHz radio frequency plasmas generated in 50%Ar:50%CF4 mixture in the GEC cell. The probe data were recorded at various radial positions providing radial profiles of these plasma parameters at 10-50 mTorr pressures and 200 W and 300 W of RF power. Present measurements indicate that the electron and ion number densities increase with increase in pressure and power. Whereas the plasma potential and electron temperature decrease with increase in pressure, and they weakly depend on RF power. The radial profiles exhibit that the electron and ion number densities and the plasma potential peak at the center of the plasma with an exponential fall away from it, while the electron temperature has a minimum at the center and it increases steadily towards the electrode edge. The EEDFs have a characteristic drop near the low energy end at all pressures and pressures and their shapes represent non-Maxwellian plasma and exhibit more like Druyvesteyn energy distribution.v

  18. Langmuir Probe Measurements of Inductively Coupled Plasmas in CF4/Ar/O2 Mixtures

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Meyyappan, M.; Sharma, S. P.

    2000-01-01

    Fluorocarbon gases, such as CF4, and their mixtures are widely used in contemporary low-pressure and high-density plasma processing techniques. In such plasmas Langmuir probe is one of the most commonly employed diagnostic techniques to obtain electron number density (ne), electron temperature (Te), electron energy distribution function (EEDF), mean electron energy (Ee), ion number density (ni), and plasma potential (Vp). In this paper we report probe data for planar inductively coupled plasmas in CF4/O2/Ar mixtures. By varying the relative concentrations in the mixture, radial profiles of ne, ni, Te, Ee, Vp, EEDF were measured in the mid-plane of the plasma at 10 mTorr and 20 mTorr of gas pressures, and 200 W and 300 W of RF powers. Data show that ne and ni decrease with increase of CF4 content and decrease of gas-pressure but they increase with increase of RF-power, whereas Vp increases with decrease of gas-pressure and remains independent of RF-power. However, they all peak at the center of the plasma and decrease towards the edge while Te follows the other way and increases a little with increase of power. The measured EEDFs exhibit Druyvesteyn-like distribution at all pressures and powers. Data are analyzed and will be presented.

  19. Probing top quark neutral couplings in the Standard Model Effective Field Theory at NLO in QCD

    NASA Astrophysics Data System (ADS)

    Bylund, Olga Bessidskaia; Maltoni, Fabio; Tsinikos, Ioannis; Vryonidou, Eleni; Zhang, Cen

    2016-05-01

    Top quark pair production in association with a Z-boson or a photon at the LHC directly probes neutral top-quark couplings. We present predictions for these two processes in the Standard Model (SM) Effective Field Theory (EFT) at next-to-leading order (NLO) in QCD. We include the full set of CP-even dimension-six operators that enter the top-quark interactions with the SM gauge bosons. For comparison, we also present predictions in the SMEFT for top loop-induced HZ production at the LHC and for toverline{t} production at the ILC at NLO in QCD. Results for total cross sections and differential distributions are obtained and uncertainties coming from missing higher orders in the strong coupling and in the EFT expansions are discussed. NLO results matched to the parton shower are available, allowing for event generation to be directly employed in an experimental analyses. Our framework provides a solid basis for the interpretation of current and future measurements in the SMEFT, with improved accuracy and precision.

  20. Perturbation analyses of intermolecular interactions.

    PubMed

    Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

    2011-08-01

    Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the

  1. Perturbation analyses of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

    2011-08-01

    Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the

  2. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

    De Marco, Luigi; Thämer, Martin; Reppert, Mike; Tokmakoff, Andrei

    2014-07-01

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N-H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  3. Direct observation of intermolecular interactions mediated by hydrogen bonding

    SciTech Connect

    De Marco, Luigi; Reppert, Mike; Thämer, Martin; Tokmakoff, Andrei

    2014-07-21

    Although intermolecular interactions are ubiquitous in physicochemical phenomena, their dynamics have proven difficult to observe directly, and most experiments rely on indirect measurements. Using broadband two-dimensional infrared spectroscopy (2DIR), we have measured the influence of hydrogen bonding on the intermolecular vibrational coupling between dimerized N-methylacetamide molecules. In addition to strong intramolecular coupling between N–H and C=O oscillators, cross-peaks in the broadband 2DIR spectrum appearing upon dimerization reveal strong intermolecular coupling that changes the character of the vibrations. In addition, dimerization changes the effects of intramolecular coupling, resulting in Fermi resonances between high and low-frequency modes. These results illustrate how hydrogen bonding influences the interplay of inter- and intramolecular vibrations, giving rise to correlated nuclear motions and significant changes in the vibrational structure of the amide group. These observations have direct impact on modeling and interpreting the IR spectra of proteins. In addition, they illustrate a general approach to direct molecular characterization of intermolecular interactions.

  4. Discovery of selective probes and antagonists for G-protein-coupled receptors FPR/FPRL1 and GPR30.

    PubMed

    Arterburn, Jeffrey B; Oprea, Tudor I; Prossnitz, Eric R; Edwards, Bruce S; Sklar, Larry A

    2009-01-01

    Recent technological advances in flow cytometry provide a versatile platform for high throughput screening of compound libraries coupled with high-content biological testing and drug discovery. The G protein-coupled receptors (GPCRs) constitute the largest class of signaling molecules in the human genome with frequent roles in disease pathogenesis, yet many examples of orphan receptors with unknown ligands remain. The complex biology and potential for drug discovery within this class provide strong incentives for chemical biology approaches seeking to develop small molecule probes to facilitate elucidation of mechanistic pathways and enable specific manipulation of the activity of individual receptors. We have initiated small molecule probe development projects targeting two distinct families of GPCRs: the formylpeptide receptors (FPR/FPRL1) and G protein-coupled estrogen receptor (GPR30). In each case the assay for compound screening involved the development of an appropriate small molecule fluorescent probe, and the flow cytometry platform provided inherently biological rich assays that enhanced the process of identification and optimization of novel antagonists. The contributions of cheminformatics analysis tools, virtual screening, and synthetic chemistry in synergy with the biomolecular screening program have yielded valuable new chemical probes with high binding affinity, selectivity for the targeted receptor, and potent antagonist activity. This review describes the discovery of novel small molecule antagonists of FPR and FPRL1, and GPR30, and the associated characterization process involving secondary assays, cell based and in vivo studies to define the selectivity and activity of the resulting chemical probes.

  5. A coupled protein and probe engineering approach for selective inhibition and activity based probe labeling of the caspases

    PubMed Central

    Xiao, Junpeng; Broz, Petr; Puri, Aaron W.; Deu, Edgar; Morell, Montse; Monack, Denise M.; Bogyo, Matthew

    2013-01-01

    Caspases are cysteine proteases that play essential roles in apoptosis and inflammation. Unfortunately, their highly conserved active sites and overlapping substrate specificities make it difficult to use inhibitors or activity-based probes to study the function, activation, localization and regulation of individual members of this family. Here we describe a strategy to engineer a caspase to contain a latent nucleophile that can be targeted by a probe containing a suitably placed electrophile, thereby allowing specific, irreversible inhibition and labeling of only the engineered protease. To accomplish this, we have identified a non-conserved residue on the small subunit of all caspases that is near the substrate-binding pocket and that can be mutated to a non-catalytic cysteine residue. We demonstrate that an active site probe containing an irreversible binding acrylamide electrophile can specifically target this cysteine residue. Here we validate the approach using the apoptotic mediator, caspase-8 and the inflammasome effector, caspase-1. We show that the engineered enzymes are functionally identical to the wild type enzymes and that the approach allows specific inhibition and direct imaging of the engineered targets in cells. Therefore, this method can be used to image localization and activation as well as the functional contributions of individual caspase proteases to the process of cell death or inflammation. PMID:23701470

  6. Protein-Coupled Fluorescent Probe To Visualize Potassium Ion Transition on Cellular Membranes.

    PubMed

    Hirata, Tomoya; Terai, Takuya; Yamamura, Hisao; Shimonishi, Manabu; Komatsu, Toru; Hanaoka, Kenjiro; Ueno, Tasuku; Imaizumi, Yuji; Nagano, Tetsuo; Urano, Yasuteru

    2016-03-01

    K(+) is the most abundant metal ion in cells, and changes of [K(+)] around cell membranes play important roles in physiological events. However, there is no practical method to selectively visualize [K(+)] at the surface of cells. To address this issue, we have developed a protein-coupled fluorescent probe for K(+), TLSHalo. TLSHalo is responsive to [K(+)] in the physiological range, with good selectivity over Na(+) and retains its K(+)-sensing properties after covalent conjugation with HaloTag protein. By using cells expressing HaloTag on the plasma membrane, we successfully directed TLSHalo specifically to the outer surface of target cells. This enabled us to visualize localized extracellular [K(+)] change with TLSHalo under a fluorescence microscope in real time. To confirm the experimental value of this system, we used TLSHalo to monitor extracellular [K(+)] change induced by K(+) ionophores or by activation of a native Ca(2+)-dependent K(+) channel (BK channel). Further, we show that K(+) efflux via BK channel induced by electrical stimulation at the bottom surface of the cells can be visualized with TLSHalo by means of total internal reflection fluorescence microscope (TIRFM) imaging. Our methodology should be useful to analyze physiological K(+) dynamics with high spatiotemporal resolution. PMID:26894407

  7. Probing Protein Surface with a Solvent Mimetic Carbene Coupled to Detection by Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Gómez, Gabriela E.; Mundo, Mariana R.; Craig, Patricio O.; Delfino, José M.

    2012-01-01

    Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH2). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites.

  8. Beyond Higgs couplings: Probing the Higgs with angular observables at future e$$^{+}$$e$$^{-}$$ colliders

    DOE PAGES

    Craig, Nathaniel; Gu, Jiayin; Liu, Zhen; Wang, Kechen

    2016-03-09

    Here, we study angular observables in themore » $$ {e}^{+}{e}^{-}\\to ZH\\to {\\ell}^{+}{\\ell}^{-}b\\overline{b} $$ channel at future circular e$$^{+}$$ e$$^{-}$$ colliders such as CEPC and FCC-ee. Taking into account the impact of realistic cut acceptance and detector effects, we forecast the precision of six angular asymmetries at CEPC (FCC-ee) with center-of-mass energy $$ \\sqrt{s}=240 $$ GeV and 5 (30) ab$$^{-1}$$ integrated luminosity. We then determine the projected sensitivity to a range of operators relevant for he Higgs-strahlung process in the dimension-6 Higgs EFT. Our results show that angular observables provide complementary sensitivity to rate measurements when constraining various tensor structures arising from new physics. We further find that angular asymmetries provide a novel means of both probing BSM corrections to the HZγ coupling and constraining the “blind spot” in indirect limits on supersymmetric scalar top partners.« less

  9. Experimental study of spatial nonuniformities in 100 MHz capacitively coupled plasma using optical probe

    SciTech Connect

    Volynets, V. N.; Ushakov, A. G.; Sung, D.; Tolmachev, Y. N.; Pashkovsky, V. G.; Lee, J. B.; Kwon, T. Y.; Jeong, K. S.

    2008-05-15

    Plasma spatial nonuniformities in the 100 MHz rf driven capacitively coupled reactor used for reactive ion etching of 300 mm substrates were experimentally studied using a linear scanning optical emission spectroscopy probe. Radial profiles of plasma emission intensity were measured both in argon and fluorocarbon-containing gas mixtures in the pressure interval of 10-80 mTorr and the rf power range of 500-1250 W. It was demonstrated that the plasma emission profiles strongly depend on the working gas composition and pressure. The profiles have a bell-like shape at pressures about 10 mTorr for all gases. As the pressure increases, the profile shape becomes more complex with the central and peripheral peaks, and the amplitudes of the peaks strongly depend on the working gas composition. It is suggested that the emission profiles show plasma spatial nonuniformities that can influence the etching rate profiles obtained with such systems. According to the existing theoretical models, the most probable reasons for these plasma nonuniformities are charged particle radial diffusion at low pressures (about 10 mTorr), as well as the standing wave and skin and edge effects at higher pressures. Using the experimental emission profiles, the working conditions have been found that allow one to achieve the most uniform plasma for discharges in argon and fluorocarbon-containing gas mixtures.

  10. Probing biased/partial agonism at the G protein-coupled A(2B) adenosine receptor.

    PubMed

    Gao, Zhan-Guo; Balasubramanian, Ramachandran; Kiselev, Evgeny; Wei, Qiang; Jacobson, Kenneth A

    2014-08-01

    G protein-coupled A(2B) adenosine receptor (AR) regulates numerous important physiological functions, but its activation by diverse A(2B)AR agonists is poorly profiled. We probed potential partial and/or biased agonism in cell lines expressing variable levels of endogenous or recombinant A(2B)AR. In cAMP accumulation assays, both 5'-substituted NECA and C2-substituted MRS3997 are full agonists. However, only 5'-substituted adenosine analogs are full agonists in calcium mobilization, ERK1/2 phosphorylation and β-arrestin translocation. A(2B)AR overexpression in HEK293 cells markedly increased the agonist potency and maximum effect in cAMP accumulation, but less in calcium and ERK1/2. A(2B)AR siRNA silencing was more effective in reducing the maximum cAMP effect of non-nucleoside agonist BAY60-6583 than NECA's. A quantitative 'operational model' characterized C2-substituted MRS3997 as either balanced (cAMP accumulation, ERK1/2) or strongly biased agonist (against calcium, β-arrestin). N⁶-substitution biased against ERK1/2 (weakly) and calcium and β-arrestin (strongly) pathways. BAY60-6583 is ERK1/2-biased, suggesting a mechanism distinct from adenosine derivatives. BAY60-6583, as A(2B)AR antagonist in MIN-6 mouse pancreatic β cells expressing low A(2B)AR levels, induced insulin release. This is the first relatively systematic study of structure-efficacy relationships of this emerging drug target.

  11. DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation

    PubMed Central

    Mishamandani, Sara; Gutierrez, Tony; Aitken, Michael D.

    2014-01-01

    Marine hydrocarbon-degrading bacteria perform a fundamental role in the oxidation and ultimate removal of crude oil and its petrochemical derivatives in coastal and open ocean environments. Those with an almost exclusive ability to utilize hydrocarbons as a sole carbon and energy source have been found confined to just a few genera. Here we used stable isotope probing (SIP), a valuable tool to link the phylogeny and function of targeted microbial groups, to investigate hydrocarbon-degrading bacteria in coastal North Carolina sea water (Beaufort Inlet, USA) with uniformly labeled [13C]n-hexadecane. The dominant sequences in clone libraries constructed from 13C-enriched bacterial DNA (from n-hexadecane enrichments) were identified to belong to the genus Alcanivorax, with ≤98% sequence identity to the closest type strain—thus representing a putative novel phylogenetic taxon within this genus. Unexpectedly, we also identified 13C-enriched sequences in heavy DNA fractions that were affiliated to the genus Methylophaga. This is a contentious group since, though some of its members have been proposed to degrade hydrocarbons, substantive evidence has not previously confirmed this. We used quantitative PCR primers targeting the 16S rRNA gene of the SIP-identified Alcanivorax and Methylophaga to determine their abundance in incubations amended with unlabeled n-hexadecane. Both showed substantial increases in gene copy number during the experiments. Subsequently, we isolated a strain representing the SIP-identified Methylophaga sequences (99.9% 16S rRNA gene sequence identity) and used it to show, for the first time, direct evidence of hydrocarbon degradation by a cultured Methylophaga sp. This study demonstrates the value of coupling SIP with cultivation methods to identify and expand on the known diversity of hydrocarbon-degrading bacteria in the marine environment. PMID:24578702

  12. Langmuir Probe and Mass Spectroscopic Measurements in Inductively Coupled CF4 Plasmas

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Sharma, Surendra; Cruden, B. A.; Meyyappan, M.

    2001-01-01

    Abstract Electron and ion energy distribution functions and other plasma parameters such as plasma potential (V(sub p)) , electron temperature (T(sub e)), and electron and ion number densities (n (sub e) and n(sub i)) in low pressure CF4 plasmas have been measured. The experiments were conducted in a GEC cell using an inductively coupled plasma (ICP) device powered by a 13.56 MHz radio-frequency (rf) power source. The measurements were made at 300 W of input rf power at 10, 30 and 50 mTorr gas pressures. Langmuir probe measurements suggest that n(sub e), n(sub i) and V(sub p) remain constant over 60% of the central electrode area, beyond which they decrease. Within the limits of experimental error (+/- 0.25 eV), T(sub e) remains nearly constant over the electrode area. T(sub e) and V(sub p) increase with a decrease in pressure. n(sub e) and n(sub i) are not affected as significantly as T(sub e) or V(sub p) by variation in the gas pressure. The electron energy distribution function (EEDF) measurements indicate a highly non-Maxwellian plasma. CF3+ is the most dominant ion product of the plasma, followed by CF2+ and CF+. The concentrations of CF2+ and CF+ are much larger than that is possible from direct electron impact ionization of the parent gas. The cross-section data suggest that the direct electron impact ionization of fragment neutrals and negative ion production by electron attachment may be responsible for increase of the minor ions.

  13. User's guide for the computer code COLTS for calculating the coupled laminar and turbulent flow over a Jovian entry probe

    NASA Technical Reports Server (NTRS)

    Kumar, A.; Graeves, R. A.

    1980-01-01

    A user's guide for a computer code 'COLTS' (Coupled Laminar and Turbulent Solutions) is provided which calculates the laminar and turbulent hypersonic flows with radiation and coupled ablation injection past a Jovian entry probe. Time-dependent viscous-shock-layer equations are used to describe the flow field. These equations are solved by an explicit, two-step, time-asymptotic finite-difference method. Eddy viscosity in the turbulent flow is approximated by a two-layer model. In all, 19 chemical species are used to describe the injection of carbon-phenolic ablator in the hydrogen-helium gas mixture. The equilibrium composition of the mixture is determined by a free-energy minimization technique. A detailed frequency dependence of the absorption coefficient for various species is considered to obtain the radiative flux. The code is written for a CDC-CYBER-203 computer and is capable of providing solutions for ablated probe shapes also.

  14. Electric probe measurements of inductively coupled Ar/O2/Ar-O2 plasmas: comparison by the interpretation methods of the probe data

    NASA Astrophysics Data System (ADS)

    Chung, Tae Hun; Seo, Min Woo

    2013-09-01

    Properties of low-pressure inductively coupled argon, oxygen, and Ar-O2 mixture plasmas are investigated using an rf-compensated Langmuir probe measurement. In each gas discharge, the electron energy probability function (EEPF), the plasma density and the electron temperature were obtained by using the probe. The estimates of plasma density determined by using different methods to interpret the probe current-voltage curve are compared. The results show a good agreement between the plasma density values measured in ion saturation current at the floating potential and values measured using other classical methods. Especially, in low-pressure oxygen discharges, the plasma density determined from OML theory compares well with the densities obtained by other methods. At high rf powers, the measured EEPFs for argon, oxygen, and Ar-O2 mixture plasmas were observed to be Maxwellian in the pressure range of 1 - 40 mTorr. The electron temperature was observed to decrease with increasing power and pressure and observed to remain not much changed with increasing Ar content in Ar-O2plasmas. This work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (Grant No 20120005928, Fusion Core Research Center Program).

  15. Full counting statistics as a probe of quantum coherence in a side-coupled double quantum dot system

    SciTech Connect

    Xue, Hai-Bin

    2013-12-15

    We study theoretically the full counting statistics of electron transport through side-coupled double quantum dot (QD) based on an efficient particle-number-resolved master equation. It is demonstrated that the high-order cumulants of transport current are more sensitive to the quantum coherence than the average current, which can be used to probe the quantum coherence of the considered double QD system. Especially, quantum coherence plays a crucial role in determining whether the super-Poissonian noise occurs in the weak inter-dot hopping coupling regime depending on the corresponding QD-lead coupling, and the corresponding values of super-Poissonian noise can be relatively enhanced when considering the spins of conduction electrons. Moreover, this super-Poissonian noise bias range depends on the singly-occupied eigenstates of the system, which thus suggests a tunable super-Poissonian noise device. The occurrence-mechanism of super-Poissonian noise can be understood in terms of the interplay of quantum coherence and effective competition between fast-and-slow transport channels. -- Highlights: •The FCS can be used to probe the quantum coherence of side-coupled double QD system. •Probing quantum coherence using FCS may permit experimental tests in the near future. •The current noise characteristics depend on the quantum coherence of this QD system. •The super-Poissonian noise can be enhanced when considering conduction electron spin. •The side-coupled double QD system suggests a tunable super-Poissonian noise device.

  16. Attaching Biological Probes to Silica Optical Biosensors Using Silane Coupling Agents

    PubMed Central

    Soteropulos, Carol E.; Hunt, Heather K.

    2012-01-01

    pair, e.g. antibodies / antigens) through surface modification.2 Although WGM optical resonators can be fabricated in several geometries from a variety of material systems, the silica microsphere is the most common. These microspheres are generally fabricated on the end of an optical fiber, which provides a "stem" by which the microspheres can be handled during functionalization and detection experiments. Silica surface chemistries may be applied to attach probe molecules to their surfaces; however, traditional techniques generated for planar substrates are often not adequate for these three-dimensional structures, as any changes to the surface of the microspheres (dust, contamination, surface defects, and uneven coatings) can have severe, negative consequences on their detection capabilities. Here, we demonstrate a facile approach for the surface functionalization of silica microsphere WGM optical resonators using silane coupling agents to bridge the inorganic surface and the biological environment, by attaching biotin to the silica surface.8,16 Although we use silica microsphere WGM resonators as the sensor system in this report, the protocols are general and can be used to functionalize the surface of any silica device with biotin. PMID:22588224

  17. Theoretical study on the effect of solvent and intermolecular fluctuations in proton transfer reactions: General theory

    SciTech Connect

    Kato, Nobuhiko; Ida, Tomonori; Endo, Kazunaka

    2004-04-30

    We present a theory of proton transfer reactions which incorporate the modulation of the proton's potential surface by intermolecular vibrations and the effect of coupling to solvent degree of freedom. The proton tunnels between states corresponding to it being localized in the wells of a double minimum potential. The resulting tunnel splitting depends on the intermolecular separation. The solvent response to the proton's charge is modeled as that of a continuous distribution of harmonic oscillators and the intermolecular stretching mode is also damped because of the interaction with solvent degree of freedom. The transition rate is given by the Fermi Gorlden Rule expression.

  18. Non-Covalent Fluorescent Labeling of Hairpin DNA Probe Coupled with Hybridization Chain Reaction for Sensitive DNA Detection.

    PubMed

    Song, Luna; Zhang, Yonghua; Li, Junling; Gao, Qiang; Qi, Honglan; Zhang, Chengxiao

    2016-04-01

    An enzyme-free signal amplification-based assay for DNA detection was developed using fluorescent hairpin DNA probes coupled with hybridization chain reaction (HCR). The hairpin DNAs were designed to contain abasic sites in the stem moiety. Non-covalent labeling of the hairpin DNAs was achieved when a fluorescent ligand was bound to the abasic sites through hydrogen bonding with the orphan cytosine present on the complementary strand, accompanied by quench of ligand fluorescence. As a result, the resultant probes, the complex formed between the hairpin DNA and ligand, showed almost no fluorescence. Upon hybridization with target DNA, the probe underwent a dehybridization of the stem moiety containing an abasic site. The release of ligand from the abasic site to the solution resulted in an effective fluorescent enhancement, which can be used as a signal. Compared with a sensing system without HCR, a 20-fold increase in the sensitivity was achieved using the sensing system with HCR. The fluorescent intensity of the sensing system increased with the increase in target DNA concentration from 0.5 nM to 100 nM. A single mismatched target ss-DNA could be effectively discriminated from complementary target DNA. Genotyping of a G/C single-nucleotide polymorphism of polymerase chain reaction (PCR) products was successfully demonstrated with the sensing system. Therefore, integrating HCR strategy with non-covalent labeling of fluorescent hairpin DNA probes provides a sensitive and cost-effective DNA assay.

  19. Fluorescence photoactivation by intermolecular proton transfer.

    PubMed

    Swaminathan, Subramani; Petriella, Marco; Deniz, Erhan; Cusido, Janet; Baker, James D; Bossi, Mariano L; Raymo, Françisco M

    2012-10-11

    We designed a strategy to activate fluorescence under the influence of optical stimulations based on the intermolecular transfer of protons. Specifically, the illumination of a 2-nitrobenzyl derivative at an activating wavelength is accompanied by the release of hydrogen bromide. In turn, the photogenerated acid encourages the opening of an oxazine ring embedded within a halochromic compound. This structural transformation extends the conjugation of an adjacent coumarin fluorophore and enables its absorption at an appropriate excitation wavelength. Indeed, this bimolecular system offers the opportunity to activate fluorescence in liquid solutions, within rigid matrixes and inside micellar assemblies, relying on the interplay of activating and exciting beams. Furthermore, this strategy permits the permanent imprinting of fluorescent patterns on polymer films, the monitoring of proton diffusion within such materials in real time on a millisecond time scale, and the acquisition of images with spatial resolution at the nanometer level. Thus, our operating principles for fluorescence activation can eventually lead to the development of valuable photoswitchable probes for imaging applications and versatile mechanisms for the investigation of proton transport. PMID:22994311

  20. Near-field examination of perovskite-based superlenses and superlens-enhanced probe-object coupling

    PubMed Central

    Kehr, S.C.; Liu, Y.M.; Martin, L.W.; Yu, P.; Gajek, M.; Yang, S.-Y.; Yang, C.-H.; Wenzel, M.T.; Jacob, R.; von Ribbeck, H.-G.; Helm, M.; Zhang, X.; Eng, L.M.; Ramesh, R.

    2011-01-01

    A planar slab of negative-index material works as a superlens with sub-diffraction-limited resolution, as propagating waves are focused and, moreover, evanescent waves are reconstructed in the image plane. Here we demonstrate a superlens for electric evanescent fields with low losses using perovskites in the mid-infrared regime. The combination of near-field microscopy with a tunable free-electron laser allows us to address precisely the polariton modes, which are critical for super-resolution imaging. We spectrally study the lateral and vertical distributions of evanescent waves around the image plane of such a lens, and achieve imaging resolution of λ/14 at the superlensing wavelength. Interestingly, at certain distances between the probe and sample surface, we observe a maximum of these evanescent fields. Comparisons with numerical simulations indicate that this maximum originates from an enhanced coupling between probe and object, which might be applicable for multifunctional circuits, infrared spectroscopy and thermal sensors. PMID:21427720

  1. Probing the Dipolar Coupling in a Heterospin Endohedral Fullerene-Phthalocyanine Dyad.

    PubMed

    Zhou, Shen; Yamamoto, Masanori; Briggs, G Andrew D; Imahori, Hiroshi; Porfyrakis, Kyriakos

    2016-02-01

    Paramagnetic endohedral fullerenes and phthalocyanine (Pc) complexes are promising building blocks for molecular quantum information processing, for which tunable dipolar coupling is required. We have linked these two spin qubit candidates together and characterized the resulting electron paramagnetic resonance properties, including the spin dipolar coupling between the fullerene spin and the copper spin. Having interpreted the distance-dependent coupling strength quantitatively and further discussed the antiferromagnetic aggregation effect of the CuPc moieties, we demonstrate two ways of tuning the dipolar coupling in such dyad systems: changing the spacer group and adjusting the solution concentration. PMID:26745202

  2. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

    Busse, James R.; Dye, Robert C.; Foley, Timothy J.; Higa, Kelvin T.; Jorgensen, Betty S.; Sanders, Victor E.; Son, Steven F.

    2010-09-07

    A method to substantially desensitize a metastable intermolecular composite material to electrostatic discharge and friction comprising mixing the composite material with an organic diluent and removing enough organic diluent from the mixture to form a mixture with a substantially putty-like consistency, as well as a concomitant method of recovering the metastable intermolecular composite material.

  3. Pump-probe optical switching in prism-coupled Au :SiO2 nanocomposite waveguide film

    NASA Astrophysics Data System (ADS)

    Lee, Kyeong-Seok; Lee, Taek-Sung; Kim, Won-Mok; Cho, Sunghun; Lee, Soonil

    2007-10-01

    The resonance properties due to the surface plasmon excitation of metal nanoparticles make the nanocomposite films promising for various applications such as optical switching devices. In spite of the well-known ultrasensitive operation of optical switches based on a guided wave, the application of nanocomposite film has inherent limitation originating from the excessive optical loss related to the surface plasmon resonance. In this study, we address this problem and present the experimental and theoretical analyses on the pump-probe optical switching in prism-coupled Au(1vol%):SiO2 nanocomposite waveguide film.

  4. Transient grating study of the intermolecular dynamics of liquid nitrobenzene

    NASA Astrophysics Data System (ADS)

    Wu, Hong-Lin; Song, Yun-Fei; Yu, Guo-Yang; Yang, Yan-Qiang

    2016-10-01

    Femtosecond time-resolved transient grating (TG) technique is used to study the intermolecular dynamics in liquid phase. Non-resonant excitation of the sample by two crossing laser pulses results in a transient Kerr grating, and the molecular motion of liquid can be detected by monitoring the diffraction of a third time-delayed probe pulse. In liquid nitrobenzene (NB), three intermolecular processes are observed with lifetimes of 37.9±1.4 ps, 3.28±0.11 ps, and 0.44±0.03 ps, respectively. These relaxations are assigned to molecular orientational diffusion, dipole/induced dipole interaction, and libration in liquid cage, respectively. Such a result is slightly different from that obtained from OKE experiment in which the lifetime of the intermediate process is measured to be 1.9 ps. The effects of electric field on matter are different in TG and optical Kerr effect (OKE) experiments, which should be responsible for the difference between the results of these two types of experiments. The present work demonstrates that TG technique is a useful alternative in the study of intermolecular dynamics. Project supported by the National Natural Science Foundation of China (Grant Nos. 11304058 and 11404307) and NSAF (Grant No. U1330106).

  5. Direct analyte-probed nanoextraction coupled to nanospray ionization-mass spectrometry of drug residues from latent fingerprints.

    PubMed

    Clemons, Kristina; Wiley, Rachel; Waverka, Kristin; Fox, James; Dziekonski, Eric; Verbeck, Guido F

    2013-07-01

    Here, we present a method of extracting drug residues from fingerprints via Direct Analyte-Probed Nanoextraction coupled to nanospray ionization-mass spectrometry (DAPNe-NSI-MS). This instrumental technique provides higher selectivity and lower detection limits over current methods, greatly reducing sample preparation, and does not compromise the integrity of latent fingerprints. This coupled to Raman microscopy is an advantageous supplement for location and identification of trace particles. DAPNe uses a nanomanipulator for extraction and differing microscopies for localization of chemicals of interest. A capillary tip with solvent of choice is placed in a nanopositioner. The surface to be analyzed is placed under a microscope, and a particle of interest is located. Using a pressure injector, the solvent is injected onto the surface where it dissolves the analyte, and then extracted back into the capillary tip. The solution is then directly analyzed via NSI-MS. Analyses of caffeine, cocaine, crystal methamphetamine, and ecstasy have been performed successfully.

  6. Characterization of an inductively coupled nitrogen-argon plasma by Langmuir probe combined with optical emission spectroscopy

    SciTech Connect

    Song, M. A.; Lee, Y. W.; Chung, T. H.

    2011-02-15

    The properties of low-pressure inductively coupled nitrogen-argon plasmas were investigated by using a Langmuir probe combined with optical emission spectroscopy (OES) under the conditions of pressures in the range of 1-30 mTorr and applied rf powers of 200-600 W. In the experiments, the argon was introduced as an actinometer and as an adding gas. The effect of the argon content in the gas mixture was examined in the range of 5%-80%. The electron energy probability function (EEPF), the electron density, and the electron temperature were obtained by using an rf-compensated Langmuir probe. The dissociation fractions were obtained from the OES actinometry. The electron temperature was also obtained by OES corona model and compared with that measured by the probe. The second positive and first negative systems of spectral bands from nitrogen molecules were analyzed to estimate the vibrational and rotational temperatures. The effects of the control parameters on the plasma parameters and dissociation fraction were investigated. While the calculated nitrogen atom density increased with power, it exhibited a maximum value near the Ar content of 30%.

  7. Thin-layer chromatography and mass spectrometry coupled using proximal probe thermal desorption with electrospray or atmospheric pressure chemica lionization

    SciTech Connect

    Ovchinnikova, Olga S; Van Berkel, Gary J

    2010-01-01

    An atmospheric pressure proximal probe thermal desorption sampling method coupled with secondary ionization by electrospray or atmospheric pressure chemical ionization was demonstrated for the mass spectrometric analysis of a diverse set of compounds (dyestuffs, pharmaceuticals, explosives and pesticides) separated on various high-performance thin-layer chromatography plates. Line scans along or through development lanes on the plates were carried out by moving the plate relative to a stationary heated probe positioned close to or just touching the stationary phase surface. Vapors of the compounds thermally desorbed from the surface were drawn into the ionization region of a combined electrospray ionization/atmospheric pressure chemical ionization source where they merged with reagent ions and/or charged droplets from a corona discharge or an electrospray emitter and were ionized. The ionized components were then drawn through the atmospheric pressure sampling orifice into the vacuum region of a triple quadrupole mass spectrometer and detected using full scan, single ion monitoring, or selected reaction monitoring mode. Studies of variable parameters and performance metrics including the proximal probe temperature, gas flow rate into the ionization region, surface scan speed, read-out resolution, detection limits, and surface type are discussed.

  8. Reprint of : Correlated voltage probe model of relaxation in two Coulomb-coupled edge channels

    NASA Astrophysics Data System (ADS)

    Nigg, Simon E.

    2016-08-01

    A phenomenological correlated voltage probe model is introduced to mimic the effects of inelastic scattering between particles in different conduction channels of a phase coherent conductor. As an illustration, the non-equilibrium distribution functions of two noisy co-propagating chiral edge channels of the integer quantum Hall effect are calculated and compared with recent experiments. The method is further applied to calculate the linear response current noise through an interacting Mach-Zehnder interferometer.

  9. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

    PubMed Central

    Jarvis, Samuel Paul

    2015-01-01

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions. PMID:26307976

  10. Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy.

    PubMed

    Jarvis, Samuel Paul

    2015-08-21

    A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H2 molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

  11. Probing the Charm Quark Yukawa Coupling in Higgs+Charm Production.

    PubMed

    Brivio, Ilaria; Goertz, Florian; Isidori, Gino

    2015-11-20

    We propose a new method for determining the coupling of the Higgs boson to charm quarks, via Higgs production in association with a charm-tagged jet: pp→hc. As a first estimate, we find that at the LHC with 3000 fb^{-1}, it should be possible to derive a constraint of order one, relative to the standard model (SM) value of the charm Yukawa coupling. As a by-product of this analysis, we present an estimate of the exclusive pp→hD^{(*)} electroweak cross section. Within the SM, the latter turns out to be not accessible at the LHC even in the high-luminosity phase.

  12. Probing the Charm Quark Yukawa Coupling in Higgs+Charm Production.

    PubMed

    Brivio, Ilaria; Goertz, Florian; Isidori, Gino

    2015-11-20

    We propose a new method for determining the coupling of the Higgs boson to charm quarks, via Higgs production in association with a charm-tagged jet: pp→hc. As a first estimate, we find that at the LHC with 3000 fb^{-1}, it should be possible to derive a constraint of order one, relative to the standard model (SM) value of the charm Yukawa coupling. As a by-product of this analysis, we present an estimate of the exclusive pp→hD^{(*)} electroweak cross section. Within the SM, the latter turns out to be not accessible at the LHC even in the high-luminosity phase. PMID:26636844

  13. Probing the Excitations of a Lieb-Liniger Gas from Weak to Strong Coupling.

    PubMed

    Meinert, F; Panfil, M; Mark, M J; Lauber, K; Caux, J-S; Nägerl, H-C

    2015-08-21

    We probe the excitation spectrum of an ultracold one-dimensional Bose gas of cesium atoms with a repulsive contact interaction that we tune from the weakly to the strongly interacting regime via a magnetic Feshbach resonance. The dynamical structure factor, experimentally obtained using Bragg spectroscopy, is compared to integrability-based calculations valid at arbitrary interactions and finite temperatures. Our results unequivocally underlie the fact that holelike excitations, which have no counterpart in higher dimensions, actively shape the dynamical response of the gas. PMID:26340191

  14. Visualizing the orientational dependence of an intermolecular potential

    NASA Astrophysics Data System (ADS)

    Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

    2016-02-01

    Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard-Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation.

  15. Visualizing the orientational dependence of an intermolecular potential

    PubMed Central

    Sweetman, Adam; Rashid, Mohammad A.; Jarvis, Samuel P.; Dunn, Janette L.; Rahe, Philipp; Moriarty, Philip

    2016-01-01

    Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C60) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard–Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation. PMID:26879386

  16. Long-lived coherence in pentafluorobenzene as a probe of ππ(*) - πσ(*) vibronic coupling.

    PubMed

    Hüter, O; Sala, M; Neumann, H; Zhang, S; Studzinski, H; Egorova, D; Temps, F

    2016-07-01

    The dynamics of pentafluorobenzene after femtosecond laser excitation to the optically bright ππ(*) first excited electronic state have been investigated by femtosecond time-resolved time-of-flight mass spectrometry and femtosecond time-resolved photoelectron imaging spectroscopy. The observed temporal profiles exhibit a bi-exponential decay behavior with a superimposed, long-lived, large-amplitude oscillation with a frequency of νosc = 78-74 cm(-1) and a damping time of τD = 5-2 ps. On the basis of electronic structure and quantum dynamics calculations, the oscillations have been shown to arise due to vibronic coupling between the optically bright ππ(*) state and the energetically close-lying optically dark πσ(*) state. The coupling leads to a pronounced double-well character of the lowest excited adiabatic potential energy surface along several out-of-plane modes of b1 symmetry. The optical electronic excitation initiates periodic wavepacket motion along these modes. In the out-of-plane distorted molecular configuration, the excited state acquires substantial πσ(*) character, thus modulating the ionization probability. The photoelectron spectra and the anisotropy of their angular distribution confirm the periodically changing electronic character. The ionizing probe laser pulse directly maps the coupled electron-nuclear motion into the observed signal oscillations. PMID:27394103

  17. Investigation of falsified documents via direct analyte-probed nanoextraction coupled to nanospray mass spectrometry, fluorescence microscopy, and Raman spectroscopy.

    PubMed

    Huynh, V; Williams, K C; Golden, T D; Verbeck, G F

    2015-10-01

    Microscopy with direct analyte-probed nanoextraction coupled to nanospray ionization mass spectrometry (DAPNe-NSI-MS) is a direct extraction technique that extracts ultra-trace amounts of analyte. It has been proven to extract ink from documents with little to no physical or chemical footprint. In this study, DAPNe has been coupled to Raman spectroscopy, fluorescence microscopy, and NSI-MS to determine if an ink entry from a document was falsified. A handwritten number was altered using a different ink pen to test if the aforementioned techniques could discriminate the original number from the altered number, qualitatively and/or quantitatively. Chemical species from part of the original number, altered number, and a point at which both inks intersect were successfully differentiated by all techniques when using different pens. DAPNe coupled to fluorescence microscopy and Raman spectroscopy was not able to discriminate the forged ink entry when the exact same pen was used to modify the text (due to the same ink formula). However, DAPNe-NSI-MS successfully discerned that the pen was dispensed on different days by quantitating the oxidation process. PMID:26179027

  18. Long-lived coherence in pentafluorobenzene as a probe of ππ* - πσ* vibronic coupling

    NASA Astrophysics Data System (ADS)

    Hüter, O.; Sala, M.; Neumann, H.; Zhang, S.; Studzinski, H.; Egorova, D.; Temps, F.

    2016-07-01

    The dynamics of pentafluorobenzene after femtosecond laser excitation to the optically bright ππ* first excited electronic state have been investigated by femtosecond time-resolved time-of-flight mass spectrometry and femtosecond time-resolved photoelectron imaging spectroscopy. The observed temporal profiles exhibit a bi-exponential decay behavior with a superimposed, long-lived, large-amplitude oscillation with a frequency of νosc = 78-74 cm-1 and a damping time of τD = 5-2 ps. On the basis of electronic structure and quantum dynamics calculations, the oscillations have been shown to arise due to vibronic coupling between the optically bright ππ* state and the energetically close-lying optically dark πσ* state. The coupling leads to a pronounced double-well character of the lowest excited adiabatic potential energy surface along several out-of-plane modes of b1 symmetry. The optical electronic excitation initiates periodic wavepacket motion along these modes. In the out-of-plane distorted molecular configuration, the excited state acquires substantial πσ* character, thus modulating the ionization probability. The photoelectron spectra and the anisotropy of their angular distribution confirm the periodically changing electronic character. The ionizing probe laser pulse directly maps the coupled electron-nuclear motion into the observed signal oscillations.

  19. Nonplanar 4-Jets in Quarkonium Decays as a Probe for 3-Gluon Coupling

    NASA Astrophysics Data System (ADS)

    Muta, T.; Niuya, T.

    1982-11-01

    We calculate the acoplanarity (à la Fox-Wolfram) distribution of 4 jets generated by orthoquarkonium decays: 3S1(Qbar{Q})→ GGGG, GGqbar{q}. The result shows that the deviation from planar event due to 4 jets is significantly large showing the importance of the effect of 3-gluon couplings in quantum chromodynamics. The average acoplanarity is calculated to be =(0.45+0.153Nf)αs/π with Nf the number of flavors of produced quarks and αs the QCD coupling strength. As a by-product we calculated the decay rate of the parapositronium into 4 photons which results in Γ4γ=(0.0139±0.0001)α7 me with me the electron mass.

  20. Mode coupling in a hanging-fiber AFM used as a rheological probe

    NASA Astrophysics Data System (ADS)

    Devailly, C.; Laurent, J.; Steinberger, A.; Bellon, L.; Ciliberto, S.

    2014-06-01

    We analyze the advantages and drawbacks of a method which measures the viscosity of liquids at microscales, using a thin glass fiber fixed on the tip of a cantilever of an ultra-low-noise Atomic Force Microscope (AFM). When the fiber is dipped into a liquid, the dissipation of the cantilever-fiber system, which is linked to the liquid viscosity, can be computed from the power spectral density of the thermal fluctuations of the cantilever deflection. The high sensitivity of the AFM allows us to show the existence and to develop a model of the coupling between the dynamics of the fiber and that of the cantilever. This model, which accurately fits the experimental data, gives also more insights into the dynamics of coupled microdevices in a viscous environment.

  1. Probing phonon-rotation coupling in helium nanodroplets: Infrared spectroscopy of CO and its isotopomers

    SciTech Connect

    Haeften, Klaus von; Rudolph, Stephan; Simanovski, Iaroslav; Havenith, Martina; Zillich, Robert E.; Whaley, K. Birgitta

    2006-02-01

    We have recorded the R(0){nu}{sub CO}=1(leftarrow)0 IR spectrum of CO and its isotopomers in superfluid helium nanodroplets. For droplets with average size N > or approx. 2000 helium atoms, the transition exhibits a Lorentzian shaped linewidth of 0.034 cm{sup -1}, indicating a homogeneous broadening mechanism. The rotational constants could be deduced and were found to be reduced to about 60% of the corresponding gas-phase values (63% for the reference {sup 12}C {sup 16}O species). Accompanying calculations of the pure rotational spectra were carried out using the method of correlated basis functions in combination with diffusion Monte Carlo (CBF/DMC). These calculations show that both the reduction of the rotational B constant and the line broadening can be attributed to phonon-rotation coupling. The reduction in B is confirmed by path integral correlation function calculations for a cluster of 64 {sup 4}He atoms, which also reveal a non-negligible effect of finite size on the collective modes. The phonon-rotation coupling strength is seen to depend strongly on the strength and anisotropy of the molecule-helium interaction potential. Comparison with other light rotors shows that this coupling is particularly high for CO. The CBF/DMC analysis shows that the J=1 rotational state couples effectively to phonon states, which are only present in large helium droplets or bulk. In particular, they are not present in small clusters with n{<=}20, thereby accounting for the much narrower linewidths and larger B constant measured for these sizes.

  2. Intramolecular anodic olefin coupling reactions: using competition studies to probe the mechanism of oxidative cyclization reactions.

    PubMed

    Xu, Hai-Chao; Moeller, Kevin D

    2010-04-16

    A competition experiment was designed so that the relative rates of anodic cyclization reactions under various electrolysis conditions can be determined. Reactions with ketene dithioacetal and enol ether-based substrates that use lithium methoxide as a base were shown to proceed through radical cation intermediates that were trapped by a sulfonamide anion. Results for the oxidative coupling of a vinyl sulfide with a sulfonamide anion using the same conditions were consistent with the reaction proceeding through a nitrogen-radical.

  3. Antibodies to probe endogenous G protein-coupled receptor heteromer expression, regulation, and function

    PubMed Central

    Gomes, Ivone; Gupta, Achla; Bushlin, Ittai; Devi, Lakshmi A.

    2014-01-01

    Over the last decade an increasing number of studies have focused on the ability of G protein-coupled receptors to form heteromers and explored how receptor heteromerization modulates the binding, signaling and trafficking properties of individual receptors. Most of these studies were carried out in heterologous cells expressing epitope tagged receptors. Very little information is available about the in vivo physiological role of G protein-coupled receptor heteromers due to a lack of tools to detect their presence in endogenous tissue. Recent advances such as the generation of mouse models expressing fluorescently labeled receptors, of TAT based peptides that can disrupt a given heteromer pair, or of heteromer-selective antibodies that recognize the heteromer in endogenous tissue have begun to elucidate the physiological and pathological roles of receptor heteromers. In this review we have focused on heteromer-selective antibodies and describe how a subtractive immunization strategy can be successfully used to generate antibodies that selectively recognize a desired heteromer pair. We also describe the uses of these antibodies to detect the presence of heteromers, to study their properties in endogenous tissues, and to monitor changes in heteromer levels under pathological conditions. Together, these findings suggest that G protein-coupled receptor heteromers represent unique targets for the development of drugs with reduced side-effects. PMID:25520661

  4. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling.

    PubMed

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; de la Fuente, César; Arnaudas, José Ignacio

    2015-01-01

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths. PMID:26333417

  5. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling.

    PubMed

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; de la Fuente, César; Arnaudas, José Ignacio

    2015-09-03

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths.

  6. Antiferromagnetic Spin Coupling between Rare Earth Adatoms and Iron Islands Probed by Spin-Polarized Tunneling

    PubMed Central

    Coffey, David; Diez-Ferrer, José Luis; Serrate, David; Ciria, Miguel; Fuente, César de la; Arnaudas, José Ignacio

    2015-01-01

    High-density magnetic storage or quantum computing could be achieved using small magnets with large magnetic anisotropy, a requirement that rare-earth iron alloys fulfill in bulk. This compelling property demands a thorough investigation of the magnetism in low dimensional rare-earth iron structures. Here, we report on the magnetic coupling between 4f single atoms and a 3d magnetic nanoisland. Thulium and lutetium adatoms deposited on iron monolayer islands pseudomorphically grown on W(110) have been investigated at low temperature with scanning tunneling microscopy and spectroscopy. The spin-polarized current indicates that both kind of adatoms have in-plane magnetic moments, which couple antiferromagnetically with their underlying iron islands. Our first-principles calculations explain the observed behavior, predicting an antiparallel coupling of the induced 5d electrons magnetic moment of the lanthanides with the 3d magnetic moment of iron, as well as their in-plane orientation, and pointing to a non-contribution of 4f electrons to the spin-polarized tunneling processes in rare earths. PMID:26333417

  7. Probing variations of the Rashba spin-orbit coupling at the nanometre scale

    NASA Astrophysics Data System (ADS)

    Bindel, Jan Raphael; Pezzotta, Mike; Ulrich, Jascha; Liebmann, Marcus; Sherman, Eugene Ya.; Morgenstern, Markus

    2016-10-01

    As the Rashba effect is an electrically tunable spin-orbit interaction, it could form the basis for a multitude of applications, such as spin filters, spin transistors and quantum computing using Majorana states in nanowires. Moreover, this interaction can determine the spin dephasing and antilocalization phenomena in two dimensions. However, the real space pattern of the Rashba parameter, which critically influences spin transistors using the spin-helix state and the otherwise forbidden electron backscattering in topologically protected channels, is difficult to probe. Here, we map this pattern down to nanometre length scales by measuring the spin splitting of the lowest Landau level using scanning tunnelling spectroscopy. We reveal strong fluctuations correlated with the local electrostatic potential for an InSb inversion layer with a large Rashba coefficient (~1 eV Å). This type of Rashba field mapping enables a more comprehensive understanding of its fluctuations, which might be decisive towards robust semiconductor-based spintronic devices.

  8. Direct coupling of a flow-flow electromembrane extraction probe to LC-MS.

    PubMed

    Fuchs, David; Gabel-Jensen, Charlotte; Jensen, Henrik; Rand, Kasper D; Pedersen-Bjergaard, Stig; Hansen, Steen Honoré; Petersen, Nickolaj Jacob

    2016-01-28

    A fully integrated and automated electromembrane extraction LC-MS (EME-LC-MS) system has been developed and characterized. Hyphenation of a flow-flow EME probe to LC-MS was accomplished by using an in-built 10-port switching valve of the LC-MS system. The 10-port switching valve decoupled the high pressure of the UHPLC-system from the low pressure required for operation of the EME-probe by automated switching between a sample extraction/analysis and a sample load position. In the sample load position the extracted analytes were loaded into a HPLC sample loop. By switching the valve to the sample extraction/analysis position the setup allowed simultaneous analysis of previously loaded analytes while extracting a new sample. Performance of the system was characterized with respect to precision and linearity (RSD < 2.5%, R(2): 0.998) and the setup was applied for studying the in-vitro metabolism of methadone by rat liver microsomes. As the metabolic reaction proceeded, methadone and its metabolites were extracted and analyzed in parallel by LC-MS using either isocratic or gradient elution. Compared to a conventional in-vitro metabolism analysis based on protein precipitation followed by LC-MS analysis the fully automated EME-LC-MS system offers a significant time saving and in addition demonstrates increased sensitivity as the analytes were automatically enriched during the extraction process. The experiment revealed 6 to 16 times higher S/N ratios of the EME-LC-MS method compared to protein precipitation followed by LC-MS and thus concomitantly lower LOD and LOQ. The setup integrates a complete analytical workflow of rapid extraction, enrichment, separation and detection of analytes in a fully automated manner. These attributes make the developed system a powerful alternative approach for a wide range of analytical applications. PMID:26755142

  9. Design and technical evaluation of fibre-coupled Raman probes for the image-guided discrimination of cancerous skin

    NASA Astrophysics Data System (ADS)

    Schleusener, J.; Reble, C.; Helfmann, J.; Gersonde, I.; Cappius, H.-J.; Glanert, M.; Fluhr, J. W.; Meinke, M. C.

    2014-03-01

    Two different designs for fibre-coupled Raman probes are presented that are optimized for discriminating cancerous and normal skin by achieving high epithelial sensitivity to detect a major component of the Raman signal from the depth range of the epithelium. This is achieved by optimizing Raman spot diameters to the range of ≈200 µm, which distinguishes this approach from the common applications of either Raman microspectroscopy (1-5 µm) or measurements on larger sampling volume using spot sizes of a few mm. Video imaging with a depicted area in the order of a few cm, to allow comparing Raman measurements to the location of the histo-pathologic findings, is integrated in both designs. This is important due to the inhomogeneity of cancerous lesions. Video image acquisition is achieved using white light LED illumination, which avoids ambient light artefacts. The design requirements focus either on a compact light-weight configuration, for pen-like handling, or on a video-visible measurement spot to enable increased positioning accuracy. Both probes are evaluated with regard to spot size, Rayleigh suppression, background fluorescence, depth sensitivity, clinical handling and ambient light suppression. Ex vivo measurements on porcine ear skin correlates well with findings of other groups.

  10. Characterization of inductively coupled Ar and Ar/CH4 plasma using tuned single Langmuir probe and fluid simulation

    NASA Astrophysics Data System (ADS)

    Cha, Ju-Hong; Han, Moon-Ki; Seo, Kwon-Sang; Kim, Dong-Hyun; Lee, Hae June; Lee, Ho-Jun

    2015-09-01

    An inductively coupled plasma source driven by 13.56 MHz was prepared for the deposition of a-C:H and hydro-fluorocarbon thin film. Properties of the plasma source are investigated by fluid simulation including Navier-Stokes equations and home-made tuned single Langmuir probe. Signal attenuation ratios of the Langmuir probe at first and second harmonic frequency were 49dB and 46dB respectively. Dependencies of plasma parameters on process parameters were well agreed with simulation results. It was found that gas flow field significantly affect spatial distribution of electron density and temperature even in inert gas feeding case. Higher electron density and lower temperature was observed near the gas inlet area. Ar/CH4 plasma simulation results shown that hydrocarbon radical densities have their lowest value at the vicinity of gas feeding line due to high flow velocity. For input power density of 0.07 W/cm3 , CH radical density follows electron density distribution. On the other hand, central region of the chamber become deficient in CH3 radical due to high dissociation rate accompanied with high electron density. The result suggest that optimization of discharge power is important for controlling deposition film quality in high density plasma sources.

  11. Intramolecular screening of intermolecular forces

    NASA Astrophysics Data System (ADS)

    Liang, Ying Q.; Hunt, K. L. C.

    1993-03-01

    By use of nonlocal polarizability densities, we analyze the intramolecular screening of intermolecular fields. For two interacting molecules A and B with weak or negligible charge overlap, we show that the reaction field and the field due to the unperturbed charge distribution of the neighboring molecule are screened identically via the Sternheimer shielding tensor and its generalizations to nonuniform fields and nonlinear response. The induction force on nucleus I in molecule A, derived from perturbation theory, results from linear screening of the reaction field due to B and nonlinear screening of the field from the permanent charge distribution of B. In general, at first or second order in the molecular interaction, the screening-tensor expressions for the force on nucleus I involve susceptibilities of one order higher than the expressions derived from perturbation theory. The first-order force from perturbation theory involves permanent charge moments, while the first-order screened force involves linear response tensors; and the second-order screened force depends on hyperpolarizabilities, while second-order induction effects are specified in terms of static, lowest-order susceptibilities. The equivalence of the two formulations for these forces, order by order, is a new illustration of the interrelations we have found among permanent moments, linear-response tensors, and nonlinear response. This work also provides new insight into the dispersion forces on an individual nucleus I in molecule A by separating the forces into two distinct terms—the first term results from changes in the reaction of A to the fluctuating charge distribution of the neighboring molecule B, when nucleus I shifts infinitesimally, and the second term stems from changes in correlations of the fluctuating charge distribution of A itself. Changes in the fluctuation correlations are determined by changes in the classical Coulomb field of nucleus I and by the imaginary part of the

  12. Magnetoencephalography with a two-color pump-probe, fiber-coupled atomic magnetometer

    NASA Astrophysics Data System (ADS)

    Johnson, Cort; Schwindt, Peter D. D.; Weisend, Michael

    2010-12-01

    The authors have detected magnetic fields from the human brain with a compact, fiber-coupled rubidium spin-exchange-relaxation-free magnetometer. Optical pumping is performed on the D1 transition and Faraday rotation is measured on the D2 transition. The beams share an optical axis, with dichroic optics preparing beam polarizations appropriately. A sensitivity of <5 fT/√Hz is achieved. Evoked responses resulting from median nerve and auditory stimulation were recorded with the atomic magnetometer. Recordings were validated by comparison with those taken by a commercial magnetoencephalography system. The design is amenable to arraying sensors around the head, providing a framework for noncryogenic, whole-head magnetoencephalography.

  13. Coherent coupling of magneto-excitons probed by two-dimensional Fourier transform spectroscopy

    NASA Astrophysics Data System (ADS)

    Paul, Jagannath; Liu, Cunming; McGill, Stephen; Hilton, David; Karaiskaj, Denis

    We present the coherent two dimensional Fourier Transform (2DFT) spectra of magneto-excitons in undoped GaAs quantum wells at high magnetic field up to 10 Tesla. The 2DFT data reveal strong coherent coupling between resonances and line shapes which are strikingly different from the zero field spectra. 2DFT spectra measured using co-linear and co-circular polarizations at low temperatures will be discussed. The work at USF and UAB was supported by the National Science Foundation under Grant Number DMR-1409473. The work at NHMFL, Florida State University was supported by the National Science Foundation under Grant Numbers DMR-1157490 and DMR-1229217.

  14. Probing triple Higgs couplings of the two Higgs doublet model at a linear collider

    SciTech Connect

    Arhrib, Abdesslam; Benbrik, Rachid; Chiang, C.-W.

    2008-06-01

    We study double Higgs production at the future linear collider in the framework of the two Higgs doublet models through the following channels: e{sup +}e{sup -}{yields}{phi}{sub i}{phi}{sub j}Z, {phi}{sub i}=h{sup 0}, H{sup 0}, A{sup 0}, H{sup {+-}}. All these processes are sensitive to triple Higgs couplings. Hence observations of them provide information on the triple Higgs couplings that help reconstructing the scalar potential. We also discuss the double Higgs-Strahlung e{sup +}e{sup -}{yields}h{sup 0}h{sup 0}Z in the decoupling limit where h{sup 0} mimics the standard model Higgs boson. The processes e{sup +}e{sup -}{yields}h{sup 0}h{sup 0}Z and e{sup +}e{sup -}{yields}h{sup 0}H{sup 0}Z are also discussed in the fermiophobic limit where distinctive signatures such as 4{gamma}+X, 2{gamma}+X, and 6{gamma}+X are expected in the Type-I two Higgs doublet model.

  15. Trajectory-probed instability and statistics of desynchronization events in coupled chaotic systems

    NASA Astrophysics Data System (ADS)

    de Oliveira, Gilson F.; Chevrollier, Martine; Passerat de Silans, Thierry; Oriá, Marcos; de Souza Cavalcante, Hugo L. D.

    2015-11-01

    Complex systems, such as financial markets, earthquakes, and neurological networks, exhibit extreme events whose mechanisms of formation are not still completely understood. These mechanisms may be identified and better studied in simpler systems with dynamical features similar to the ones encountered in the complex system of interest. For instance, sudden and brief departures from the synchronized state observed in coupled chaotic systems were shown to display non-normal statistical distributions similar to events observed in the complex systems cited above. The current hypothesis accepted is that these desynchronization events are influenced by the presence of unstable object(s) in the phase space of the system. Here, we present further evidence that the occurrence of large events is triggered by the visitation of the system's phase-space trajectory to the vicinity of these unstable objects. In the system studied here, this visitation is controlled by a single parameter, and we exploit this feature to observe the effect of the visitation rate in the overall instability of the synchronized state. We find that the probability of escapes from the synchronized state and the size of those desynchronization events are enhanced in attractors whose shapes permit the chaotic trajectories to approach the region of strong instability. This result shows that the occurrence of large events requires not only a large local instability to amplify noise, or to amplify the effect of parameter mismatch between the coupled subsystems, but also that the trajectories of the system wander close to this local instability.

  16. Probing Nonadiabaticity in the Proton-Coupled Electron Transfer Reaction Catalyzed by Soybean Lipoxygenase

    PubMed Central

    2014-01-01

    Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vibronic nonadiabaticity between the electron–proton quantum subsystem and the classical nuclei, as well as the electron–proton nonadiabaticity between the electrons and proton(s) within the quantum subsystem. Herein these diagnostics are applied to a model of the active site of the enzyme soybean lipoxygenase, which catalyzes a PCET reaction that exhibits unusually high deuterium kinetic isotope effects at room temperature. Both semiclassical and electronic charge density diagnostics illustrate vibronic and electron–proton nonadiabaticity for this PCET reaction, supporting the use of the Golden rule nonadiabatic rate constant expression with a specific form of the vibronic coupling. This type of characterization will be useful for theoretical modeling of a broad range of PCET processes. PMID:25258676

  17. Probing the holographic principle using dynamical gauge effects from open spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Zhao, Jianshi; Price, Craig; Liu, Qi; Gemelke, Nathan

    2016-05-01

    Dynamical gauge fields result from locally defined symmetries and an effective over-labeling of quantum states. Coupling atoms weakly to a reservoir of laser modes can create an effective dynamical gauge field purely due to the disregard of information in the optical states. Here we report measurements revealing effects of open spin-orbit coupling in a system where an effective model can be formed from a non-abelian SU(2) × U(1) field theory following the Yang-Mills construct. Forming a close analogy to dynamical gauge effects in quantum chromodynamics, we extract a measure of atomic motion which reveals the analog of a closing mass gap for the relevant gauge boson, shedding insight on long standing open problems in gauge-fixing scale anomalies. Using arguments following the holographic principle, we measure scaling relations which can be understood by quantifying information present in the local potential. New prospects using these techniques for developing fractionalization of multi-particle and macroscopic systems using dissipative and non-abelian gauge fields will also be discussed. We acknowledge support from NSF Award No. 1068570, and the Charles E. Kaufman Foundation.

  18. Trajectory-probed instability and statistics of desynchronization events in coupled chaotic systems

    SciTech Connect

    Oliveira, Gilson F. de Chevrollier, Martine; Oriá, Marcos; Passerat de Silans, Thierry; Souza Cavalcante, Hugo L. D. de

    2015-11-15

    Complex systems, such as financial markets, earthquakes, and neurological networks, exhibit extreme events whose mechanisms of formation are not still completely understood. These mechanisms may be identified and better studied in simpler systems with dynamical features similar to the ones encountered in the complex system of interest. For instance, sudden and brief departures from the synchronized state observed in coupled chaotic systems were shown to display non-normal statistical distributions similar to events observed in the complex systems cited above. The current hypothesis accepted is that these desynchronization events are influenced by the presence of unstable object(s) in the phase space of the system. Here, we present further evidence that the occurrence of large events is triggered by the visitation of the system's phase-space trajectory to the vicinity of these unstable objects. In the system studied here, this visitation is controlled by a single parameter, and we exploit this feature to observe the effect of the visitation rate in the overall instability of the synchronized state. We find that the probability of escapes from the synchronized state and the size of those desynchronization events are enhanced in attractors whose shapes permit the chaotic trajectories to approach the region of strong instability. This result shows that the occurrence of large events requires not only a large local instability to amplify noise, or to amplify the effect of parameter mismatch between the coupled subsystems, but also that the trajectories of the system wander close to this local instability.

  19. Probing the C₆₀ triplet state coupling to nuclear spins inside and out.

    PubMed

    Filidou, Vasileia; Mamone, Salvatore; Simmons, Stephanie; Karlen, Steven D; Anderson, Harry L; Kay, Christopher W M; Bagno, Alessandro; Rastrelli, Federico; Murata, Yasujiro; Komatsu, Koichi; Lei, Xuegong; Li, Yongjun; Turro, Nicholas J; Levitt, Malcolm H; Morton, John J L

    2013-09-13

    The photoexcitation of functionalized fullerenes to their paramagnetic triplet electronic state can be studied by pulsed electron paramagnetic resonance (EPR) spectroscopy, whereas the interactions of this state with the surrounding nuclear spins can be observed by a related technique: electron nuclear double resonance (ENDOR). In this study, we present EPR and ENDOR studies on a functionalized exohedral fullerene system, dimethyl[9-hydro (C60-Ih)[5,6]fulleren-1(9H)-yl]phosphonate (DMHFP), where the triplet electron spin has been used to hyperpolarize, couple and measure two nuclear spins. We go on to discuss the extension of these methods to study a new class of endohedral fullerenes filled with small molecules, such as H₂@C₆₀, and we relate the results to density functional calculations. PMID:23918718

  20. Coupled effect of salt and pH on proteins probed with NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kukic, Predrag; O'Meara, Fergal; Hewage, Chandralal; Erik Nielsen, Jens

    2013-07-01

    The coupled effect of ionic strength (50-400 mM) and pH (2-8) on ionization and conformation equilibria of lysozyme was studied using NMR spectroscopy. Observed changes in pKa values of the ionizable groups were found to originate from perturbations in the geometry of hydrogen bonds rather than screening of electric fields. Moreover, at the ionic strengths used here, salt-induced local conformational changes had a dominant effect on chemical shifts measured on 1HN and 15N amide nuclei. Accurate modeling of these localized perturbations in structure-based energy calculations is a necessary prerequisite on the way to complete understanding of any salt-induced processes in proteins.

  1. Magnetoelectric coupling of multiferroic chromium doped barium titanate thin film probed by magneto-impedance spectroscopy

    SciTech Connect

    Shah, Jyoti Kotnala, Ravinder K. E-mail: rkkotnala@gmail.com

    2014-04-07

    Thin film of BaTiO{sub 3} doped with 0.1 at. % Cr (Cr:BTO) has been prepared by pulsed laser deposition technique. Film was deposited on Pt/SrTiO{sub 3} substrate at 500 °C in 50 mTorr Oxygen gas pressure using KrF (298 nm) laser. Polycrystalline growth of single phase Cr:BTO thin film has been confirmed by grazing angle X-ray diffraction. Cr:BTO film exhibited remnant polarization 6.4 μC/cm{sup 2} and 0.79 MV/cm coercivity. Magnetization measurement of Cr:BTO film showed magnetic moment 12 emu/cc. Formation of weakly magnetic domains has been captured by magnetic force microscopy. Theoretical impedance equation fitted to experimental data in Cole-Cole plot for thin film in presence of transverse magnetic field resolved the increase in grain capacitance from 4.58 × 10{sup −12} to 5.4 × 10{sup −11} F. Film exhibited high value 137 mV/cm-Oe magneto-electric (ME) coupling coefficient at room temperature. The high value of ME coupling obtained can reduce the typical processing steps involved in multilayer deposition to obtain multiferrocity in thin film. Barium titanate being best ferroelectric material has been tailored to be multiferroic by non ferromagnetic element, Cr, doping in thin film form opens an avenue for more stable and reliable spintronic material for low power magnetoelectric random excess memory applications.

  2. Observed Coupling Between the International Space Station PCU Plasma and a FPMU Langmuir Probe Facilitated by the Geomagnetic Field

    NASA Technical Reports Server (NTRS)

    Hartman, William; Koontz, Steven L.

    2010-01-01

    Electrical charging of the International Space Station (ISS) is a matter of serious concern resulting from the possibility of vehicle arcing and electrical shock hazard to crew during extravehicular activity (EVA). A Plasma Contactor Unit (PCU) was developed and integrated into ISS in order to control the ISS floating potential, thereby, minimize vehicle charging and associated hazards. One of the principle factors affecting ISS electrical charging is the ionosphere plasma state (i.e., electron temperature and density). To support ISS electrical charging studies a Floating Potential Monitoring Unit (FPMU) is also integrated into ISS in order to measure the ionosphere properties using Langmuir probes (LP). The FPMU was located on the Starboard side of ISS. The PCU is located near the center of ISS with its plasma exhaust pointed to port. From its integration on ISS in 2006 through November of 2009, the FPMU data exhibited nominal characteristics during PCU operation. On November 21, 2009 the FPMU was relocated from the Starboard location to a new Port location. After relocation significant enhanced noise was observed in both the LP current-voltage sweeps and the derived electron temperature data. The enhanced noise only occurred when the PCU was in discharge and at unique and repeatable locations of the ISS orbit. The cause of this enhanced noise was investigated. It was found that there is coupling occurring between the PCU plasma and the FPMU LP. In this paper we shall 1) present the on-orbit data and the presence of enhanced noise, 2) demonstrate that the coupling of the PCU plasma and the FPMU measurements is geomagnetically organized, 3) show that coupling of the PCU plasma and the FPMU is primarily due to and driven by particle-wave interaction and 4) show that the ionosphere conditions are adequate for Alfven waves to be generated by the PCU plasma.

  3. Combination Bands of the Nonpolar OCS Dimer Involving Intermolecular Modes

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2012-06-01

    Spectra of the nonpolar carbonyl sulfide in the region of the OCS ν_1 fundamental band were observed in a supersonic slit-jet apparatus. The expansion gas was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Three bands centered at 2085.906, 2103.504, and 2114.979 cm-1 were observed and anlysed. The rotational assignment and fitting of the bands were made by fixing the lower state parameters to those for the ground state of nonpolar (OCS)_2, thus confirming that they were indeed combination bands of the of the most stable isomer of OCS dimer. The band centered at 2085.906 cm-1 is a combination of the forbidden A_g intramolecular mode plus the geared bend intermolecular mode and that centered at 2114.979 cm-1 is a combination of the allowed B_u intramolecular mode plus the intermolecular van der Waals stretch. The combination at 2103.504 cm-1 can be assigned as a band whose upper state involves four quanta of the intramolecular bend or the B_u intramolecular mode plus two quanta of the intermolecular torsional mode. Isotopic work is needed to conclusively identify the vibrational assignment of this band. Our experimental frequencies for the geared bend and van der Waals modes are in good agreement with a recent high level ab initio calculation by Brown et al. J. Brown, Xiao-Gang Wang, T. Carrington Jr. and Richard Dawes, Journal of Chemical Physics, submitted.

  4. Langmuir Probe Measurements of Inductively Coupled Plasma in CF4/AR/O2 Mixtures

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Cruden, Brett; Sharma, Surendra; Meyyappan, Meyya

    2001-01-01

    Inductively coupled plasmas of CF4:Ar:O2, which have been of importance to material processing, were studied in the GEC cell at 80:10:10, 60:20:20, and 40:30:30 mixture ratios. Radial distributions of plasma potential (V(sub p)), electron and ion number densities (n(sub e) and n(sub i)), electron temperature (T(sub e)), and electron energy distribution functions (EEDFs) were measured in the mid-plane of plasma across the electrodes in the pressure range of 10-50 mTorr, and RF power of 200 and 300 W. V(sub p), n(sub e) and n(sub i), which peak in the center of the plasma, increase with decrease of pressure. T(sub e) also increases with pressure but peaks toward the electrode edge. Both V(sub p) and T(sub e) remain nearly independent of RF power, whereas n(sub e) and n(sub i) increase with power. In all conditions the EEDFs exhibit non-Maxwellian shape and are more like Druyvesteyn form at higher energies. They exhibit a broad lip in the energy range 0-10 eV suggesting an electron loss mechanism, which could be due to via resonance electron attachment processes producing negative ions in this rich electronegative gas mixture. This behavior is more prominent towards the electrode edge.

  5. Langmuir Probe Measurements of Inductively Coupled Plasmas in CF4/Ar/O2 Mixtures

    NASA Technical Reports Server (NTRS)

    Rao, M. V. V. S.; Cruden, Brett; Sharma, Surendra; Meyyappan, Meyya

    2001-01-01

    Inductively coupled plasmas of CF4:Ar:O2, which have been of importance to material processing, were studied in the GEC cell at 80:10:10, 60:20:20, and 40:30:30 mixture ratios. Radial distributions of plasma potential (V(sub p)), electron and ion number densities (n(sub e) and n(sub i), electron temperature (T(sub e)), and electron energy distribution functions (EEDFs) were measured in the mid-plane of plasma across the electrodes in the pressure range of 10-50 mTorr, and RF (radio frequency) power of 200 and 300 W. V(sub p), n(sub e) and n(sub i), which peak in the center of the plasma, increase with decrease of pressure. T(sub e) also increases with pressure but peaks toward the electrode edge. Both V(sub p) and T(sub e) remain nearly independent of RF power, whereas n(sub e) and n(sub i) increase with power. In all conditions the EEDFs exhibit non-Maxwellian shape and are more like Druyvesteyn form at higher energies. They exhibit a broad dip in the energy range 0-10 eV suggesting an electron loss mechanism, which could be due to via resonance electron attachment processes producing negative ions in this rich electronegative gas mixture. This behavior is more prominent towards the electrode edge.

  6. Probing the transition between seismically coupled and decoupled segments along an ancient subduction interface

    NASA Astrophysics Data System (ADS)

    Angiboust, Samuel; Kirsch, Josephine; Oncken, Onno; Glodny, Johannes; Monié, Patrick; Rybacki, Erik

    2015-06-01

    The transition zone at the downdip end of seismic coupling along subduction interfaces is often the site of megathrust earthquake nucleation and concentrated postseismic afterslip, as well as the focus site of episodic tremor and slip features. Exhumed remnants of the former Alpine subduction zone found in the Swiss Alps allow analyzing fluid and deformation processes near the transition zone region (30-40 km paleodepth). The Dent Blanche Thrust (DBT) is a lower blueschist-facies shear zone interpreted as a fossilized subduction interface where granitic mylonites overlie a metamorphosed accretionary wedge. We report field observations from the DBT region where multiple, several tens of meters thick foliated cataclastic networks are interlayered within the basal DBT mylonites. Petrological results and microstructural observations indicate that the various cataclasis events took place at near-peak metamorphic conditions (400-500°C, 1.1-1.3 GPa) during subduction of the Tethyan seafloor in Eocene times (42-48 Ma). Some of these networks exhibit mutual crosscutting relationships between mylonites, foliated cataclasites, and vein systems indicating mutual overprinting between brittle deformation and ductile creep. Whole-rock chemical compositions, in situ 40Ar-39Ar age data of recrystallized phengite, and Sr isotopic signatures reveal that DBT rocks also underwent multiple hydrofracturing and metasomatic events via the infiltration of fluids mainly derived from the oceanic metasediments underneath the DBT. From the rock fabrics, we infer strain rate fluctuations of several orders of magnitude beyond subduction strain rates (˜10-12 s-1) accompanied by fluctuation of supralithostatic and quasi-lithostatic fluid pressures (1 ≥ λ > 0.95). DBT brittle-plastic deformation switches highlight the diversity of deformation processes and fluid-rock interactions in the transition zone region of the subduction interface.

  7. Probing the transition between seismically coupled and decoupled segments along an ancient subduction interface

    NASA Astrophysics Data System (ADS)

    Angiboust, Samuel; Kirsch, Josephine; Oncken, Onno; Glodny, Johannes; Monié, Patrick; Rybacki, Erik

    2015-04-01

    Although of paramount importance for understanding the nature of mechanical coupling in subduction zones, the portions downdip of the locked segments of subduction interfaces remain poorly understood. These deep transition zones often are sites of megathrust earthquake nucleation and concentrated postseismic afterslip, as well as the focus sites of episodic tremor and slip features, recently discovered at several plate boundaries. The extensive, exhumed remnants of the former Alpine subduction zone found in the Swiss Alps allow analyzing fluid and deformation processes at the original depths of 30-40 km, typical for the depth range of such transition zones. We identify the shear zone at the base of the Dent Blanche complex (Dent Blanche Thrust, DBT) as a lower blueschist-facies, fossilized subduction interface where granitic mylonites overlie a metamorphosed ophiolite. We report field observations from the DBT region where a complex, discontinuous network of meter- to tens of meters-thick foliated cataclasites is interlayered with the basal DBT mylonites. Petrological results indicate that cataclasis took place at near peak metamorphic conditions (450-500°C, c. 1.2 GPa) during subduction of the Tethyan seafloor in Eocene times (42-48 Ma). Despite some tectonic reactivation during exhumation, these networks exhibit mutual cross-cutting relationships between mylonites, foliated cataclasites and vein systems indicating multiple switching between brittle deformation and ductile creep. Whole-rock chemical compositions, in situ 40Ar-39Ar age data of newly formed phengite, and strontium isotopic signatures reveal that these rocks also underwent multiple hydrofracturing events via infiltration of fluids mainly derived from the ophiolitic metasediments underneath the DBT. From the rock fabrics we infer strain rate fluctuations of several orders of magnitude beyond subduction strain rates (c. 10-12s-1) accompanied by fluctuation of near-lithostatic fluid pressures (1>λ>0

  8. Water protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions

    SciTech Connect

    Mamontov, Eugene; Chu, Xiang-Qiang

    2012-01-01

    Both the structure and dynamics of biomolecules are known to be essential for their biological function. In the dehydrated state, the function of biomolecules, such as proteins, is severely impeded, so hydration is required for bioactivity. The dynamics of the hydrated biomolecules and their hydration water are related - but how closely? The problem involves several layers of complexity. Even for water in the bulk state, the contribution from various dynamic components to the overall dynamics is not fully understood. In biological systems, the effects of confinement on the hydration water further complicate the picture. Even if the various components of the hydration water dynamics are properly understood, which of them are coupled to the protein dynamics, and how? The studies of protein dynamics over the wide temperature range, from physiological to low temperatures, provide some answers to these question. At low temperatures, both the protein and its hydration water behave as solids, with only vibrational degrees of freedom. As the temperature is increased, non-vibrational dynamic components start contributing to the measurable dynamics and eventually become dominant at physiological temperatures. Thus, the temperature dependence of the dynamics of protein and its hydration water may allow probing various dynamic components separately. In order to suppress the water freezing, the low-temperature studies of protein rely on either low-hydrated samples (essentially, hydrated protein powders), or cryo-protective solutions. Both approaches introduce the hydration environments not characteristic of the protein environments in living systems, which are typically aqueous protein solutions of various concentrations. In this paper, we discuss the coupling between the dynamic components of the protein and its hydration water by critical examining of the existing literature, and then propose that proteins can be studied in an aqueous solution that is remarkably similar in

  9. STM probe on the surface electronic states of spin-orbit coupled materials

    NASA Astrophysics Data System (ADS)

    Zhou, Wenwen

    Spin-orbit coupling (SOC) is the interaction of an electron's intrinsic angular momentum (spin) with its orbital momentum. The strength of this interaction is proportional to Z4 where Z is the atomic number, so generally it is stronger in atoms with higher atomic number, such as bismuth (Z=83) and iridium (Z=77). In materials composed of such heavy elements, the prominent SOC can be sufficient to modify the band structure of the system and lead to distinct phase of matter. In recent years, SOC has been demonstrated to play a critical role in determining the unusual properties of a variety of compounds. SOC associated materials with exotic electronic states have also provided a fertile platform for studying emergent phenomena as well as new physics. As a consequence, the research on these interesting materials with any insight into understanding the microscopic origin of their unique properties and complex phases is of great importance. In this context, we implement scanning tunneling microscopy (STM) and spectroscopy (STS) to explore the surface states (SS) of the two major categories of SOC involved materials, Bi-based topological insulators (TI) and Ir-based transition metal oxides (TMO). As a powerful tool in surface science which has achieved great success in wide variety of material fields, STM/STS is ideal to study the local density of states of the subject material with nanometer length scales and is able to offer detailed information about the surface electronic structure. In the first part of this thesis, we report on the electronic band structures of three-dimensional TIs Bi2Te3 and Bi2Se 3. Topological insulators are distinct quantum states of matter that have been intensely studied nowadays. Although they behave like ordinary insulators in showing fully gapped bulk bands, they host a topologically protected surface state consisting of two-dimensional massless Dirac fermions which exhibits metallic behavior. Indeed, this unique gapless surface state is a

  10. An improved thin-layer chromatography/mass spectrometry coupling using a surface sampling probe electrospray ion trap system

    SciTech Connect

    Ford, Michael J; Van Berkel, Gary J

    2004-01-01

    A combined surface sampling probe/electrospray emitter coupled with an ion trap mass spectrometer was used for the direct read out of unmodified reversed-phase C18 thin-layer chromatography (TLC) plates. The operation of the surface sampling electrospray ionization interface in positive and negative ionization modes was demonstrated through the direct analysis of TLC plates on which a commercial test mix comprised of four dye compounds viz., rhodamine B, fluorescein, naphthol blue black, and fast green FCF, and an extract of the caffeine-containing plant Ilex vomitoria, were spotted and developed. Acquisition of full-scan mass spectra and automated collection of MS/MS product ion spectra while scanning a development lane along the surface of a TLC plate demonstrated the advantages of using an ion trap in this combination. Details of the sampling system, benefits of analyzing a developed lane in both positive ion and negative ion modes, levels of detection while surface scanning, surface scan speed effects, and the utility of three-dimensional data display, are also discussed.

  11. Trace analysis of energetic materials via direct analyte-probed nanoextraction coupled to direct analysis in real time mass spectrometry.

    PubMed

    Clemons, Kristina; Dake, Jeffrey; Sisco, Edward; Verbeck, Guido F

    2013-09-10

    Direct analysis in real time mass spectrometry (DART-MS) has proven to be a useful forensic tool for the trace analysis of energetic materials. While other techniques for detecting trace amounts of explosives involve extraction, derivatization, solvent exchange, or sample clean-up, DART-MS requires none of these. Typical DART-MS analyses directly from a solid sample or from a swab have been quite successful; however, these methods may not always be an optimal sampling technique in a forensic setting. For example, if the sample were only located in an area which included a latent fingerprint of interest, direct DART-MS analysis or the use of a swab would almost certainly destroy the print. To avoid ruining such potentially invaluable evidence, another method has been developed which will leave the fingerprint virtually untouched. Direct analyte-probed nanoextraction coupled to nanospray ionization-mass spectrometry (DAPNe-NSI-MS) has demonstrated excellent sensitivity and repeatability in forensic analyses of trace amounts of illicit drugs from various types of surfaces. This technique employs a nanomanipulator in conjunction with bright-field microscopy to extract single particles from a surface of interest and has provided a limit of detection of 300 attograms for caffeine. Combining DAPNe with DART-MS provides another level of flexibility in forensic analysis, and has proven to be a sufficient detection method for trinitrotoluene (TNT), RDX, and 1-methylaminoanthraquinone (MAAQ).

  12. A jet emission model to probe the dynamics of accretion and ejection coupling in black hole X-ray binaries

    NASA Astrophysics Data System (ADS)

    Malzac, Julien

    2016-07-01

    Compact jets are probably the most common form of jets in X-ray binaries and Active Galactic Nuclei. They seem to be present in all sources in the so-called hard X-ray spectral state. They are characterised by a nearly flat Spectral Energy Distribution (SED) extending from the radio to the infrared bands. This emission is usually interpreted as partially self absorbed synchrotron emission from relativistic leptons accelerated in the jet. The observed flat spectral shape requires energy dissipation and acceleration of particules over a wide range of distances along the jet. This distributed energy dissipation is likely to be powered by internal shocks caused by fluctuations of the outflow velocity. I will discuss such an internal shock model in the context of black hole binaries. I will show that internal shocks can produce the observed SEDs and also predict a strong, wavelength dependent, variability that resembles the observed one. The assumed velocity fluctuations of the jet must originate in the accretion flow. The model thus predicts a strong connection between the observable properties of the jet in the radio to IR bands, and the variability of the accretion flow as observed in X-rays. If the model is correct, this offers a unique possibility to probe the dynamics of the coupled accretion and ejection processes leading to the formation of compact jets.

  13. Light propagation from fluorescent probes in biological tissues by coupled time-dependent parabolic simplified spherical harmonics equations

    PubMed Central

    Domínguez, Jorge Bouza; Bérubé-Lauzière, Yves

    2011-01-01

    We introduce a system of coupled time-dependent parabolic simplified spherical harmonic equations to model the propagation of both excitation and fluorescence light in biological tissues. We resort to a finite element approach to obtain the time-dependent profile of the excitation and the fluorescence light fields in the medium. We present results for cases involving two geometries in three-dimensions: a homogeneous cylinder with an embedded fluorescent inclusion and a realistically-shaped rodent with an embedded inclusion alike an organ filled with a fluorescent probe. For the cylindrical geometry, we show the differences in the time-dependent fluorescence response for a point-like, a spherical, and a spherically Gaussian distributed fluorescent inclusion. From our results, we conclude that the model is able to describe the time-dependent excitation and fluorescent light transfer in small geometries with high absorption coefficients and in nondiffusive domains, as may be found in small animal diffuse optical tomography (DOT) and fluorescence DOT imaging. PMID:21483606

  14. Langmuir Probe Measurements of Inductively Coupled CHF3/Ar and Ar/CHF3/O2 Plasmas

    NASA Technical Reports Server (NTRS)

    Sharma, S. P.; Rao, M. V. V. S.; Meyyappan, M.

    2000-01-01

    Plasma parameters, such as, electron number density (ne), electron temperature (Te), y electron energy distribution function (EEDF), mean electron energy (Ee), ion number density (ni), and plasma potential (Vp), have been measured by using Langmuir probe in low-pressure (10-50 mTorr) inductively coupled CHF3/Ar and CHF3/Ar/O2 plasmas generated in the GEC cell. The measurements were made at the center of the plasma, keeping the lower electrode grounded, for various CHF3/Ar and Ar/CHF3/O2 mixtures operating at 10-50 mTorr pressures and two input RF power levels, 200 and 300 W. EEDF data show a strong Druyvesteyn distribution with relatively lower number of low energy electrons as compared to a Maxwell distribution and a large electron population with energies higher than the plasma potential. The results further show that at low CHF3 concentrations (less than 50%) the electron number density remains nearly constant with increase in pressure. At higher CHF3 concentrations, however, it decreases with increase in pressure. Plasma potential and electron temperature increase with decrease in pressure and with increase in CHF3 concentration. An analysis of the above observations and mechanisms will be presented.

  15. Estimation of intermolecular interactions in polymer networks

    SciTech Connect

    Subrananian, P.R.; Galiatsatos, V.

    1993-12-31

    Strain-birefringence measurements have been used to estimate intermolecular interactions in polymer networks. The intensity of the interaction has been quantified through a theoretical scheme recently proposed by Erman. The results show that these interactions diminish with decreasing molecular weight between cross-links and decreasing cross-link functionality.

  16. Effect of intermolecular hydrogen bonding and proton transfer on fluorescence of salicylic acid

    NASA Astrophysics Data System (ADS)

    Denisov, G. S.; Golubev, N. S.; Schreiber, V. M.; Shajakhmedov, Sh. S.; Shurukhina, A. V.

    1997-12-01

    Effects of intermolecular interactions, in particular the influence of intermolecular hydrogen bonds formed by salicylic acid (SA) as a proton donor with proton acceptors of different strength, on fluorescence spectra of SA in non-aqueous solutions have been investigated. Infrared spectra of studied systems have been analyzed in order to elucidate the ground state structure of the complexes formed. It has been found that at the room temperature in dilute solutions in non-polar or slightly polar aprotic solvents, where the SA molecule is not involved in intermolecular hydrogen bonding, the position of the main (blue) fluorescence component is determined by the excited state intramolecular proton transfer (ESIPT) in the lowest singlet excited state S 1. With increasing proton acceptor ability of the environment, when formation of weak or middle strength intermolecular H-bonds is possible, the emission band shifts gradually to lower frequency, the quantum yield falls and poorly resolved doublet structure becomes more pronounced, especially in the solvents containing heavy bromine atoms. As a possible reason for these effects, coupling between the S 1 and closely lying triplet term is considered. With the strongest proton acceptors like aliphatic amines, intermolecular proton transfer with ionic pair formation in the ground state and double (intra- and intermolecular) proton transfer in the excited state take place, resulting in a blue shift of the emission band. Similar emission is typical for the SA anion in aqueous solutions. The p Ka value of SA in S 1 state has been found to be 3.1. Such a small value can be explained taking into account the ESIPT reaction following the excitation. The SA complex with pyridine exhibits emission spectrum containing both molecular-like and anion-like bands with relative intensities strongly dependent on the temperature and solvent properties. The most probable origin of this dual emission is the molecular-ionic tautomerism caused by

  17. Intermolecular electron transfer from intramolecular excitation and coherent acoustic phonon generation in a hydrogen-bonded charge-transfer solid.

    PubMed

    Rury, Aaron S; Sorenson, Shayne; Dawlaty, Jahan M

    2016-03-14

    Organic materials that produce coherent lattice phonon excitations in response to external stimuli may provide next generation solutions in a wide range of applications. However, for these materials to lead to functional devices in technology, a full understanding of the possible driving forces of coherent lattice phonon generation must be attained. To facilitate the achievement of this goal, we have undertaken an optical spectroscopic study of an organic charge-transfer material formed from the ubiquitous reduction-oxidation pair hydroquinone and p-benzoquinone. Upon pumping this material, known as quinhydrone, on its intermolecular charge transfer resonance as well as an intramolecular resonance of p-benzoquinone, we find sub-cm(-1) oscillations whose dispersion with probe energy resembles that of a coherent acoustic phonon that we argue is coherently excited following changes in the electron density of quinhydrone. Using the dynamical information from these ultrafast pump-probe measurements, we find that the fastest process we can resolve does not change whether we pump quinhydrone at either energy. Electron-phonon coupling from both ultrafast coherent vibrational and steady-state resonance Raman spectroscopies allows us to determine that intramolecular electronic excitation of p-benzoquinone also drives the electron transfer process in quinhydrone. These results demonstrate the wide range of electronic excitations of the parent of molecules found in many functional organic materials that can drive coherent lattice phonon excitations useful for applications in electronics, photonics, and information technology.

  18. Intermolecular electron transfer from intramolecular excitation and coherent acoustic phonon generation in a hydrogen-bonded charge-transfer solid.

    PubMed

    Rury, Aaron S; Sorenson, Shayne; Dawlaty, Jahan M

    2016-03-14

    Organic materials that produce coherent lattice phonon excitations in response to external stimuli may provide next generation solutions in a wide range of applications. However, for these materials to lead to functional devices in technology, a full understanding of the possible driving forces of coherent lattice phonon generation must be attained. To facilitate the achievement of this goal, we have undertaken an optical spectroscopic study of an organic charge-transfer material formed from the ubiquitous reduction-oxidation pair hydroquinone and p-benzoquinone. Upon pumping this material, known as quinhydrone, on its intermolecular charge transfer resonance as well as an intramolecular resonance of p-benzoquinone, we find sub-cm(-1) oscillations whose dispersion with probe energy resembles that of a coherent acoustic phonon that we argue is coherently excited following changes in the electron density of quinhydrone. Using the dynamical information from these ultrafast pump-probe measurements, we find that the fastest process we can resolve does not change whether we pump quinhydrone at either energy. Electron-phonon coupling from both ultrafast coherent vibrational and steady-state resonance Raman spectroscopies allows us to determine that intramolecular electronic excitation of p-benzoquinone also drives the electron transfer process in quinhydrone. These results demonstrate the wide range of electronic excitations of the parent of molecules found in many functional organic materials that can drive coherent lattice phonon excitations useful for applications in electronics, photonics, and information technology. PMID:26979698

  19. Magnetic order and interfacial coupling in oxide thin films and heterostructures probed with soft x-ray dichroism

    SciTech Connect

    Arenholz, Elke; van der Laan, G.

    2009-02-01

    The combination of novel magnetic properties induced by reduced dimensionality and strong magnetic interactions across interfaces leads to intriguing new properties in magnetic hetero- and nanostructures not observed in the constituent materials in bulk form. It is the careful optimization of the characteristics of the individual layers as well as the magnetic coupling across the interface that allows us to control the magnetic properties and tailor them for devices, e.g., in information storage and processing technology. Soft x-ray magnetic spectroscopies can make unique contributions to improving our understanding of complex magnetic nanostructures since these techniques provide elemental, valence- and site-symmetry specific information with high sensitivity and tunable probing depth. X-ray magnetic circular dichroism (XMCD) is sensitive to (unidirectional) ferromagnetic order, while x-ray magnetic linear dichroism (XMLD) can also detect (uniaxial) antiferromagnetic order. A crystalline electric field with cubic symmetry induces only a weak angular dependence in XMCD spectra [1] but can cause a very pronounced anisotropy in XMLD spectra [2]. Furthermore, non-magnetic sites with a distorted local cubic symmetry can give rise to an x-ray linear dichroism (XLD). In this presentation, we discuss how to distinguish between the individual contributions to soft x-ray dichroism spectra in order to extract the wealth of information about magnetic thin films, interfaces and hetero- and nanostructures contained in the data [3, 4, 5] We determined the magnetic structure of La{sub 0.7}Sr{sub 0.3}MnO{sub 3} (LSMO)/La{sub 0.7}Sr{sub 0.3}FeO{sub 3} (LSFO) superlattices with 6 unit cell thick sublayers using soft x-ray magnetic dichroism [5]. Circular dichroism was employed to study the characteristics of the ferromagnetic LSMO layer indicating a reduced magnetic ordering temperature of 200 K compared to the bulk value of 360 K. Linear dichroism is used to analyze the

  20. Probing C P -violating h t ¯t coupling in e+e-→h γ

    NASA Astrophysics Data System (ADS)

    Li, Gang; Wang, Hao-Ran; Zhu, Shou-hua

    2016-03-01

    We investigate the possibility of probing the C P -violating h t ¯t coupling in the process e+e-→h γ at the future high luminosity e+e- colliders. Our numerical results show that the cross section for this process can be significantly increased for the allowed C P phase ξ and center of mass energy. For example, the cross section is about 10 times that in the standard model (SM) for √{s }=350 GeV and ξ =3 π /5 (see text for ξ definition). The simulation for the signal process e+e-→h γ →b b ¯ γ and its backgrounds shows that the signal significance can reach about 5 σ and more than 2.1 σ for √{s }=350 GeV and 500 GeV, respectively, with the integrated luminosity L =3 ab-1 and ξ ∈[π /2 ,3 π /5 ]. For L =10 ab-1 , the signal significance can be greater than 5 σ for √{s }=350 GeV and about 4 σ for √{s }=500 GeV with the C P phase ξ ∈[π /2 ,3 π /5 ]. Besides the cross section enhancement, the C P -violating h t ¯t coupling will induce a forward-backward asymmetry AF B which is absent in the SM and is a clear signal of new C P violation. Compared with the AF B in the Higgs decay h →l+l-γ , the AF B can be greatly enhanced in the production process. For example, AF B can reach -0.55 for ξ =π /4 and √{s }=500 GeV . Because of the large backgrounds, the significance of the expected AF B can be observed only at 1.68 σ with L =10 ab-1 and √{s }=500 GeV . It is essential to trigger the single photon in the final state to separate the bottom jets arising from scalar or vector bosons, in order to isolate the signal from the backgrounds more efficiently.

  1. Optical emission spectroscopy and Langmuir probe diagnostics of CH{sub 3}F/O{sub 2} inductively coupled plasmas

    SciTech Connect

    Karakas, Erdinc; Donnelly, Vincent M.; Economou, Demetre J.

    2013-06-07

    A CH{sub 3}F:O{sub 2} (50%:50%) inductively coupled discharge, sustained in a compact plasma reactor, was investigated as a function of power (20-400 W) and pressure (9-30 mTorr), using optical emission spectroscopy and Langmuir probe measurements. The electron density increased linearly with power but only weakly with pressure. The effective electron temperature was nearly independent of power and pressure. The gas temperature, obtained from the rotational structure of N{sub 2} (C {yields} B) optical emission, increased from 400 to 900 K as a function of inductive mode power between 75 and 400 W at 10 mTorr. For constant feed gas flow, the absolute H, F, and O atom densities, estimated by optical emission rare gas actinometry, increased linearly with power. The absolute number density ratios H/Ar, F/Ar, and O/Ar, increased, decreased, and remained constant, respectively, with pressure. The H-atom density was estimated to be 5.4 Multiplication-Sign 10{sup 13} cm{sup -3} at 400 W and 10 mTorr (gas temperature = 900 K), implying a high degree of dissociation of the CH{sub 3}F feedstock gas. The F and O atom number densities were much lower (8.3 Multiplication-Sign 10{sup 12} cm{sup -3} and 5.9 Multiplication-Sign 10{sup 12} cm{sup -3}, respectively) for the same conditions, suggesting that most of the fluorine and oxygen is contained in reaction products HF, CO, CO{sub 2}, H{sub 2}O, and OH. The relative number densities of HF, CO, and CO{sub 2} were observed to first rapidly increase with power, and then reach a plateau or decay slightly at higher power. Reaction mechanisms were proposed to explain the observed behavior of the number density of F and HF vs. power and pressure.

  2. Optical emission spectroscopy and Langmuir probe diagnostics of CH3F/O2 inductively coupled plasmas

    NASA Astrophysics Data System (ADS)

    Karakas, Erdinc; Donnelly, Vincent M.; Economou, Demetre J.

    2013-06-01

    A CH3F:O2 (50%:50%) inductively coupled discharge, sustained in a compact plasma reactor, was investigated as a function of power (20-400 W) and pressure (9-30 mTorr), using optical emission spectroscopy and Langmuir probe measurements. The electron density increased linearly with power but only weakly with pressure. The effective electron temperature was nearly independent of power and pressure. The gas temperature, obtained from the rotational structure of N2 (C → B) optical emission, increased from 400 to 900 K as a function of inductive mode power between 75 and 400 W at 10 mTorr. For constant feed gas flow, the absolute H, F, and O atom densities, estimated by optical emission rare gas actinometry, increased linearly with power. The absolute number density ratios H/Ar, F/Ar, and O/Ar, increased, decreased, and remained constant, respectively, with pressure. The H-atom density was estimated to be 5.4 × 1013 cm-3 at 400 W and 10 mTorr (gas temperature = 900 K), implying a high degree of dissociation of the CH3F feedstock gas. The F and O atom number densities were much lower (8.3 × 1012 cm-3 and 5.9 × 1012 cm-3, respectively) for the same conditions, suggesting that most of the fluorine and oxygen is contained in reaction products HF, CO, CO2, H2O, and OH. The relative number densities of HF, CO, and CO2 were observed to first rapidly increase with power, and then reach a plateau or decay slightly at higher power. Reaction mechanisms were proposed to explain the observed behavior of the number density of F and HF vs. power and pressure.

  3. Optical emission diagnostics with electric probe measurements of inductively coupled Ar/O{sub 2}/Ar-O{sub 2} plasmas

    SciTech Connect

    Chung, T. H.; Kang, Hae Ra; Bae, Min Keun

    2012-11-15

    Physical properties of low-pressure inductively coupled argon, oxygen, and Ar-O{sub 2} mixture plasmas are investigated using optical emission spectroscopy (OES) combined with an rf-compensated Langmuir probe measurement. In each gas discharge, the electron density and the electron temperature were obtained by using the probe. The electron temperature was also obtained by OES models and compared with that measured by the probe. The electron temperature was observed to decrease with increasing power and pressure and also observed to decrease with increasing Ar content. Argon metastable densities were calculated based on an optical transition model. In Ar-O{sub 2} discharges, the dissociation fraction of O{sub 2} molecules was estimated using optical emission actinometry. The dissociation fraction was observed to increase with increasing power and Ar content.

  4. Design of molecular beacons: 3' couple quenchers improve fluorogenic properties of a probe in real-time PCR assay.

    PubMed

    Ryazantsev, Dmitry Y; Kvach, Maksim V; Tsybulsky, Dmitry A; Prokhorenko, Igor A; Stepanova, Irina A; Martynenko, Yury V; Gontarev, Sergey V; Shmanai, Vadim V; Zavriev, Sergey K; Korshun, Vladimir A

    2014-06-01

    Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5'-terminus of the probe) or a pair of BHQ1 quenchers on 3'-terminus (with (BHQ1)2 or BHQ1-BHQ1 composition) is reported. These probes were used for the first time in a real-time PCR assay and showed considerable improvements in fluorogenic properties (the total fluorescence increase or signal-to-background ratio) in assay conditions vs. conventional one-FAM-one-BHQ1 molecular beacon probes as well as vs. hydrolyzable one-FAM-one-BHQ1 TaqMan probes. At the same time, such multiple modifications of the probe do not influence its Cq (a fractional PCR cycle used for quantification). The probe MB14 containing a BHQ1-BHQ1 pair showed a PCR fluorescence/background value of 9.6 which is more than two times higher than that of a regular probe MB2 (4.6). This study demonstrates prospects for the design of highly fluorogenic molecular beacon probes suitable for quantitative real-time PCR and for other potential applications (e.g. intracellular RNA detection and SNP/mutation analysis).

  5. Intermolecular electrostatic energies using density fitting.

    PubMed

    Cisneros, G Andrés; Piquemal, Jean-Philip; Darden, Thomas A

    2005-07-22

    A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+-H2O, Cu+-H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies.

  6. A simple strategy of probe DNA immobilization by diazotization-coupling on self-assembled 4-aminothiophenol for DNA electrochemical biosensor.

    PubMed

    Li, Feng; Chen, Wei; Dong, Pingjun; Zhang, Shusheng

    2009-03-15

    A novel and simple strategy for fabricating of DNA electrochemical biosensor was developed based on covalent coupling of probe NH(2)-ssDNA (S(1)) on Au electrode that had been functionalized by diazotization of assembled 4-aminothiophenol (4-ATP) monolayer. The thiol group of 4-ATP allowed the stable assembly of 4-ATP monolayer. The following diazotization reaction was directly performed to prepare functional diazo-ATP film for covalent coupling of probe S(1). Remarkably, it was noting that the diazo-ATP provided a surface with high conductibility for electron transfer. The complementary ssDNA was determined by using differential pulse voltammetry. The linear range of the developed biosensor was from 1.57 x 10(-9) to 4.52 x 10(-7)M with a detection limit of 3.26 x 10(-10)M. The fabricated biosensor possessed good selectivity and could be regenerated. The covalent immobilization of probe S(1) by simple diazotization-coupling on self-assembled 4-ATP monolayer could serve as a versatile platform for DNA immobilization and biosensors fabricating. PMID:19124235

  7. Intermolecular dimerization with pillared layered clay templates.

    SciTech Connect

    Wiederrecht, G. P.; Sandi, G.; Carrado, K. A.; Seifert, S.; Chemistry

    2001-11-19

    Solutions of pyrene in the presence of a pillared, layered montmorillonite clay produce hybrid organic-inorganic materials with substantial molecular loading in the gallery regions between the clay layers. The results are in sharp contrast to other aromatics, such as benzene, naphthalene, or perylene, which show minimal incorporation of the molecules into the gallery regions of the clay. We present evidence that the unusual affinity for pyrene to form intermolecular dimers is the reason for the high loading. Pyrene monomers are easily introduced to the layers. Through steric hindrance, subsequent intermolecular dimer formation is allowed, and they are captured by the pillared, layered structure. CW and time-resolved emission spectra strongly indicate the presence of face-to-face intermolecular dimers (excimers) within the clay galleries. The combination of the ease of high molecular loading into an inorganic, high aspect ratio template and the collective optical properties of the organic layer may be useful as a new means to create hybrid structures.

  8. An isotopic mass effect on the intermolecular potential

    SciTech Connect

    Herman, Michael F.; Currier, Robert Patrick; Clegg, Samuel M.

    2015-09-28

    The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born–Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this paper, the intermolecular dipole–dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born–Oppenheimer surface. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  9. An assay for intermolecular exchange of alpha crystallin

    NASA Technical Reports Server (NTRS)

    Gopalakrishnan, S.; Takemoto, L.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    An affinity column of alpha crystallin linked to cyanogen bromide-activated Sepharose was developed to study the exchange of alpha subunits. Alpha crystallin bound to the Sepharose-alpha complex was dissociated with 8 mol/l urea, followed by quantitation using high-performance reverse-phase liquid chromatography. The time course of binding at 37 degrees C showed a hyperbolic binding pattern reaching equilibrium between 6-18 hr. Under these conditions, binding of beta and gamma crystallins to the same matrix was less than 10% of the alpha values, as was binding of alpha to glycine-coupled Sepharose. This assay was used to demonstrate changes in the subunit exchange of alpha crystallins present in high molecular weight versus lower molecular weight aggregates of the human lens. These results show that this binding procedure was a specific reproducible assay that might be used to study intermolecular interactions of the alpha crystallins.

  10. Cathodoluminescence, laser ablasion inductively coupled plasma mass spectrometry, electron probe microanalysis and electron paramagnetic resonance analyses of natural sphalerite

    USGS Publications Warehouse

    Karakus, M.; Hagni, R.D.; Koenig, A.; Ciftc, E.

    2008-01-01

    Natural sphalerite associated with copper, silver, lead-zinc, tin and tungsten deposits from various world-famous mineral deposits have been studied by cathodoluminescence (CL), laser ablasion inductively coupled plasma mass spectrometry (LA-ICP-MS), electron probe microanalysis (EPMA) and electron paramagnetic resonance (EPR) to determine the relationship between trace element type and content and the CL properties of sphalerite. In general, sphalerite produces a spectrum of CL colour under electron bombardment that includes deep blue, turquoise, lime green, yellow-orange, orange-red and dull dark red depending on the type and concentration of trace quantities of activator ions. Sphalerite from most deposits shows a bright yellow-orange CL colour with ??max centred at 585 nm due to Mn2+ ion, and the intensity of CL is strongly dependent primarily on Fe2+ concentration. The blue emission band with ??max centred at 470-490 nm correlates with Ga and Ag at the Tsumeb, Horn Silver, Balmat and Kankoy mines. Colloform sphalerite from older well-known European lead-zinc deposits and late Cretaceous Kuroko-type VMS deposits of Turkey shows intense yellowish CL colour and their CL spectra are characterised by extremely broad emission bands ranging from 450 to 750 nm. These samples are characterised by low Mn (<10 ppm) and Ag (<1 ppm), and they are enriched in Tl (1-30 ppm) and Pb (80-1500 ppm). Strong green CL is produced by sphalerite from the Balmat-Edwards district. Amber, lime-green and red-orange sphalerite produced weak orange-red CL at room temperatures, with several emission bands centred at 490, 580, 630, 680, 745, with ??max at 630 nm being the strongest. These emission bands are well correlated with trace quantities of Sn, In, Cu and Mn activators. Sphalerite from the famous Ogdensburg and Franklin mines exhibited brilliant deep blue and orange CL colours and the blue CL may be related to Se. Cathodoluminescence behaviour of sphalerite serves to characterise ore

  11. COUPLING

    DOEpatents

    Frisch, E.; Johnson, C.G.

    1962-05-15

    A detachable coupling arrangement is described which provides for varying the length of the handle of a tool used in relatively narrow channels. The arrangement consists of mating the key and keyhole formations in the cooperating handle sections. (AEC)

  12. Computational studies on intermolecular interactions in solvation

    NASA Astrophysics Data System (ADS)

    Song, Weiping

    This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It

  13. Sensitive Glycoprotein Sandwich Assays by the Synergistic Effect of In Situ Generation of Raman Probes and Plasmonic Coupling of Ag Core-Au Satellite Nanostructures.

    PubMed

    Bi, Xiaoshuang; Li, Xueyuan; Chen, Dong; Du, Xuezhong

    2016-05-01

    Sensitive surface-enhanced Raman scattering (SERS) assays of glycoproteins have been proposed using p-aminothiophenol (PATP)-embedded Ag core-Au satellite nanostructures modified with p-mercaptophenylboronic acid (PMBA) and the self-assembled monolayer of PMBA on a smooth gold-coated wafer. The apparent Raman probe PATP on the surfaces of the Ag cores underwent a photodimerization to generate 4,4'-dimercaptoazobenzene (DMAB) in situ upon excitation of laser, and the in situ generated DMAB acted as the actual Raman probe with considerably strong SERS signals, which was further enhanced by the plasmonic coupling of the Ag core-Au satellite nanostructures due to the synergistic effect. The sandwich assays of glycoproteins showed high sensitivity and excellent selectivity against nonglycoproteins. The Ag core-Au satellite SERS nanostructures can be used for highly sensitive SERS assays of other analytes.

  14. Quantitative determination of the lateral density and intermolecular correlation between proteins anchored on the membrane surfaces using grazing incidence small-angle X-ray scattering and grazing incidence X-ray fluorescence

    NASA Astrophysics Data System (ADS)

    Abuillan, Wasim; Vorobiev, Alexei; Hartel, Andreas; Jones, Nicola G.; Engstler, Markus; Tanaka, Motomu

    2012-11-01

    As a physical model of the surface of cells coated with densely packed, non-crystalline proteins coupled to lipid anchors, we functionalized the surface of phospholipid membranes by coupling of neutravidin to biotinylated lipid anchors. After the characterization of fine structures perpendicular to the plane of membrane using specular X-ray reflectivity, the same membrane was characterized by grazing incidence small angle X-ray scattering (GISAXS). Within the framework of distorted wave Born approximation and two-dimensional Percus-Yevick function, we can analyze the form and structure factors of the non-crystalline, membrane-anchored proteins for the first time. As a new experimental technique to quantify the surface density of proteins on the membrane surface, we utilized grazing incidence X-ray fluorescence (GIXF). Here, the mean intermolecular distance between proteins from the sulfur peak intensities can be calculated by applying Abelé's matrix formalism. The characteristic correlation distance between non-crystalline neutravidin obtained by the GISAXS analysis agrees well with the intermolecular distance calculated by GIXF, suggesting a large potential of the combination of GISAXS and GIXF in probing the lateral density and correlation of non-crystalline proteins displayed on the membrane surface.

  15. The diversity of physical forces and mechanisms in intermolecular interactions.

    PubMed

    Berezovsky, Igor N

    2011-06-01

    Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein interactions, viral protein with high intrinsic disorder and hyperthermostable protein complexes. Intermolecular interactions provide folding upon binding as a part of function in the viral case, while they secure and stabilize specific native interfaces as a prerequisite for function in hyperthermostable complexes. We propose a generalized concept of protein stability and interactions, which includes intermolecular interactions comprising distinct combinations of stabilizing forces depending on the types of interacting partners.

  16. Spin-lattice coupling in uranium dioxide probed by magnetostriction measurements at high magnetic fields (P08358-E001-PF)

    SciTech Connect

    Gofryk, K.; Jaime, M.

    2014-12-01

    Our preliminary magnetostriction measurements have already shown a strong interplay of lattice dynamic and magnetism in both antiferromagnetic and paramagnetic states, and give unambiguous evidence of strong spin- phonon coupling in uranium dioxide. Further studies are planned to address the puzzling behavior of UO2 in magnetic and paramagnetic states and details of the spin-phonon coupling.

  17. Hybridization-sensitive on-off DNA probe: application of the exciton coupling effect to effective fluorescence quenching.

    PubMed

    Ikeda, Shuji; Okamoto, Akimitsu

    2008-06-01

    The design of dyes that emit fluorescence only when they recognize the target molecule, that is, chemistry for the effective quenching of free dyes, must play a significant role in the development of the next generation of functional fluorescent dyes. On the basis of this concept, we designed a doubly fluorescence-labeled nucleoside. Two thiazole orange dyes were covalently linked to a single nucleotide in a DNA probe. An absorption band at approximately 480 nm appeared strongly when the probe was in a single-stranded state, whereas an absorption band at approximately 510 nm became predominant when the probe was hybridized with the complementary strand. The shift in the absorption bands shows the existence of an excitonic interaction caused by the formation of an H aggregate between dyes, and as a result, emission from the probe before hybridization was suppressed. Dissociation of aggregates by hybridization with the complementary strand resulted in the disruption of the excitonic interaction and strong emission from the hybrid. This clear change in fluorescence intensity that is dependent on hybridization is useful for visible gene analysis.

  18. The origins of the directionality of noncovalent intermolecular interactions.

    PubMed

    Wang, Changwei; Guan, Liangyu; Danovich, David; Shaik, Sason; Mo, Yirong

    2016-01-01

    The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. PMID:26010349

  19. The origins of the directionality of noncovalent intermolecular interactions.

    PubMed

    Wang, Changwei; Guan, Liangyu; Danovich, David; Shaik, Sason; Mo, Yirong

    2016-01-01

    The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds.

  20. Theoretical and numerical evaluation of polarimeter using counter-circularly-polarized-probing-laser under the coupling between Faraday and Cotton-Mouton effect

    NASA Astrophysics Data System (ADS)

    Imazawa, Ryota; Kawano, Yasunori; Itami, Kiyoshi

    2016-04-01

    This study evaluated an effect of an coupling between the Faraday and Cotton-Mouton effect to a measurement signal of the Dodel-Kunz method which uses counter-circular-polarized probing-laser for measuring the Faraday effect. When the coupling is small (the Faraday effect is dominant and the characteristic eigenmodes are approximately circularly polarized), the measurement signal can be algebraically expressed and it is shown that the finite effect of the coupling is still significant. When the Faraday effect is not dominant, a numerical calculation is necessary. The numerical calculation under an ITER-like condition (Bt = 5.3 T, Ip = 15 MA, a = 2 m, ne = 1020 m-3 and λ = 119 μm) showed that difference between the pure Faraday rotation and the measurement signal of the Dodel-Kunz method was an order of one degree, which exceeds allowable error of ITER poloidal polarimeter. In conclusion, similar to other polarimeter techniques, the Dodel-Kunz method is not free from the coupling between the Faraday and Cotton-Mouton effect.

  1. Some mathematical models of intermolecular autophosphorylation.

    PubMed

    Doherty, Kevin; Meere, Martin; Piiroinen, Petri T

    2015-04-01

    Intermolecular autophosphorylation refers to the process whereby a molecule of an enzyme phosphorylates another molecule of the same enzyme. The enzyme thereby catalyses its own phosphorylation. In the present paper, we develop two generic models of intermolecular autophosphorylation that also include dephosphorylation by a phosphatase of constant concentration. The first of these, a solely time-dependent model, is written as one ordinary differential equation that relies upon mass-action and Michaelis-Menten kinetics. Beginning with the enzyme in its dephosphorylated state, it predicts a lag before the enzyme becomes significantly phosphorylated, for suitable parameter values. It also predicts that there exists a threshold concentration for the phosphorylation of enzyme and that for suitable parameter values, a continuous or discontinuous switch in the phosphorylation of enzyme are possible. The model developed here has the advantage that it is relatively easy to analyse compared with most existing models for autophosphorylation and can qualitatively describe many different systems. We also extend our time-dependent model of autophosphorylation to include a spatial dependence, as well as localised binding reactions. This spatio-temporal model consists of a system of partial differential equations that describe a soluble autophosphorylating enzyme in a spherical geometry. We use the spatio-temporal model to describe the phosphorylation of an enzyme throughout the cell due to an increase in local concentration by binding. Using physically realistic values for model parameters, our results provide a proof-of-concept of the process of activation by local concentration and suggest that, in the presence of a phosphatase, this activation can be irreversible.

  2. Study of ablation and implosion stages in wire arrays using coupled ultraviolet and X-ray probing diagnostics

    NASA Astrophysics Data System (ADS)

    Anderson, A. A.; Ivanov, V. V.; Astanovitskiy, A. L.; Papp, D.; Wiewior, P. P.; Chalyy, O.

    2015-11-01

    Star and cylindrical wire arrays were studied using laser probing and X-ray radiography at the 1-MA Zebra pulse power generator at the University of Nevada, Reno. The Leopard laser provided backlighting, producing a laser plasma from a Si target which emitted an X-ray probing pulse at the wavelength of 6.65 Å. A spherically bent quartz crystal imaged the backlit wires onto X-ray film. Laser probing diagnostics at the wavelength of 266 nm included a 3-channel polarimeter for Faraday rotation diagnostic and two-frame laser interferometry with two shearing interferometers to study the evolution of the plasma electron density at the ablation and implosion stages. Dynamics of the plasma density profile in Al wire arrays at the ablation stage were directly studied with interferometry, and expansion of wire cores was measured with X-ray radiography. The magnetic field in the imploding plasma was measured with the Faraday rotation diagnostic, and current was reconstructed.

  3. Study of ablation and implosion stages in wire arrays using coupled ultraviolet and X-ray probing diagnostics

    SciTech Connect

    Anderson, A. A.; Ivanov, V. V.; Astanovitskiy, A. L.; Wiewior, P. P.; Chalyy, O.; Papp, D.

    2015-11-15

    Star and cylindrical wire arrays were studied using laser probing and X-ray radiography at the 1-MA Zebra pulse power generator at the University of Nevada, Reno. The Leopard laser provided backlighting, producing a laser plasma from a Si target which emitted an X-ray probing pulse at the wavelength of 6.65 Å. A spherically bent quartz crystal imaged the backlit wires onto X-ray film. Laser probing diagnostics at the wavelength of 266 nm included a 3-channel polarimeter for Faraday rotation diagnostic and two-frame laser interferometry with two shearing interferometers to study the evolution of the plasma electron density at the ablation and implosion stages. Dynamics of the plasma density profile in Al wire arrays at the ablation stage were directly studied with interferometry, and expansion of wire cores was measured with X-ray radiography. The magnetic field in the imploding plasma was measured with the Faraday rotation diagnostic, and current was reconstructed.

  4. Coupling an electrospray source and a solids probe/chemical ionization source to a selected ion flow tube apparatus

    SciTech Connect

    Melko, Joshua J.; Ard, Shaun G.; Shuman, Nicholas S.; Viggiano, Albert A.; Pedder, Randall E.; Taormina, Christopher R.

    2015-08-15

    A new ion source region has been constructed and attached to a variable temperature selected ion flow tube. The source features the capabilities of electron impact, chemical ionization, a solids probe, and electrospray ionization. The performance of the instrument is demonstrated through a series of reactions from ions created in each of the new source regions. The chemical ionization source is able to create H{sub 3}O{sup +}, but not as efficiently as similar sources with larger apertures. The ability of this source to support a solids probe, however, greatly expands our capabilities. A variety of rhenium cations and dications are created from the solids probe in sufficient abundance to study in the flow tube. The reaction of Re{sup +} with O{sub 2} proceeds with a rate constant that agrees with the literature measurements, while the reaction of Re{sub 2}{sup 2+} is found to charge transfer with O{sub 2} at about 60% of the collision rate; we have also performed calculations that support the charge transfer pathway. The electrospray source is used to create Ba{sup +}, which is reacted with N{sub 2}O to create BaO{sup +}, and we find a rate constant that agrees with the literature.

  5. Coupling an electrospray source and a solids probe/chemical ionization source to a selected ion flow tube apparatus.

    PubMed

    Melko, Joshua J; Ard, Shaun G; Shuman, Nicholas S; Pedder, Randall E; Taormina, Christopher R; Viggiano, Albert A

    2015-08-01

    A new ion source region has been constructed and attached to a variable temperature selected ion flow tube. The source features the capabilities of electron impact, chemical ionization, a solids probe, and electrospray ionization. The performance of the instrument is demonstrated through a series of reactions from ions created in each of the new source regions. The chemical ionization source is able to create H3O(+), but not as efficiently as similar sources with larger apertures. The ability of this source to support a solids probe, however, greatly expands our capabilities. A variety of rhenium cations and dications are created from the solids probe in sufficient abundance to study in the flow tube. The reaction of Re(+) with O2 proceeds with a rate constant that agrees with the literature measurements, while the reaction of Re2(2+) is found to charge transfer with O2 at about 60% of the collision rate; we have also performed calculations that support the charge transfer pathway. The electrospray source is used to create Ba(+), which is reacted with N2O to create BaO(+), and we find a rate constant that agrees with the literature. PMID:26329209

  6. Coupling an electrospray source and a solids probe/chemical ionization source to a selected ion flow tube apparatus

    NASA Astrophysics Data System (ADS)

    Melko, Joshua J.; Ard, Shaun G.; Shuman, Nicholas S.; Pedder, Randall E.; Taormina, Christopher R.; Viggiano, Albert A.

    2015-08-01

    A new ion source region has been constructed and attached to a variable temperature selected ion flow tube. The source features the capabilities of electron impact, chemical ionization, a solids probe, and electrospray ionization. The performance of the instrument is demonstrated through a series of reactions from ions created in each of the new source regions. The chemical ionization source is able to create H3O+, but not as efficiently as similar sources with larger apertures. The ability of this source to support a solids probe, however, greatly expands our capabilities. A variety of rhenium cations and dications are created from the solids probe in sufficient abundance to study in the flow tube. The reaction of Re+ with O2 proceeds with a rate constant that agrees with the literature measurements, while the reaction of Re22+ is found to charge transfer with O2 at about 60% of the collision rate; we have also performed calculations that support the charge transfer pathway. The electrospray source is used to create Ba+, which is reacted with N2O to create BaO+, and we find a rate constant that agrees with the literature.

  7. An isotopic mass effect on the intermolecular potential

    DOE PAGES

    Herman, Michael F.; Currier, Robert Patrick; Clegg, Samuel M.

    2015-09-28

    The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born–Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this paper, the intermolecular dipole–dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born–Oppenheimer surface. Finally, the analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologuemore » thermodynamics.« less

  8. Probing the flexibility of internal rotation in silylated phenols with the NMR scalar spin-spin coupling constants.

    PubMed

    Sychrovský, Vladimír; Benda, Ladislav; Prokop, Alexandr; Blechta, Vratislav; Schraml, Jan; Spirko, Vladimír

    2008-06-12

    The rotation of a trimethylsiloxy (TMSO) group in three silylated phenols (with three different ortho substituents -H, -CH3, and -C(CH3)3) was studied with the NMR (n)J(Si,C), n = 2, 3, 4, 5, scalar spin-spin coupling between the (29)Si nucleus of the TMSO group and the (13)C nuclei of the phenyl ring. The internal rotation potential calculated with the B3LYP and MP2 calculation methods including the effect of a solvent environment (gas phase, chloroform, and water) was used for the calculation of the dynamical averages of the scalar coupling constants in the framework of the rigid-bender formalism. Solvent effects, the quality of the rotational potential, and the applicability of the classical molecular dynamic to the problem is discussed. Quantum effects have a sizable impact on scalar couplings, particularly for the internal rotational states well localized within the wells of the potential surfaces for the TMSO group. The overall difference between the experimental and theoretical scalar couplings calculated for the global energy-minima structures (static model) decreases substantially for both model potentials (B3LYP, MP2) when the molecular motion of the TMSO group is taken into account. The calculated data indicate that the inclusion of molecular motion is necessary for the accurate calculation of the scalar coupling constants and their reliable structural interpretation for any system which possesses a large-amplitude motion. PMID:18491850

  9. Infrared probe of spin-phonon coupling in antiferromagnetic honeycomb lattice compound Li2MnO3

    NASA Astrophysics Data System (ADS)

    Song, Seungjae; Lee, Sanghyun; Jeon, Seyoung; Park, Je-Geun; Moon, S. J.

    2015-12-01

    We investigated temperature-dependent infrared-active phonon modes of honeycomb Li2MnO3 which shows an antiferromagnetic transition at T N  =  36 K. In the far-infrared frequency region, we observed fourteen phonon modes. We obtained the temperature dependence of each phonon mode from the analysis of optical conductivity spectra by using the Lorentz and the Fano-type oscillator models. We found that the resonance frequencies of nine phonon modes showed an anomalous behavior near T N that should be attributed to the spin-phonon coupling. We calculated the magnitude of the spin-phonon coupling constant from the shift in the resonance frequencies of the phonon modes below T N. Our results suggest that Li2MnO3 is weakly frustrated and that spin-phonon coupling plays a role in antiferromagnetic ordering.

  10. X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

    SciTech Connect

    Mou, Q.; Benmore, C. J.; Yarger, J. L.

    2015-06-01

    XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

  11. Generalization of Ryan's theorem: Probing tidal coupling with gravitational waves from nearly circular, nearly equatorial, extreme-mass-ratio inspirals

    SciTech Connect

    Li Chao; Lovelace, Geoffrey

    2008-03-15

    Extreme-mass-ratio inspirals (EMRIs) and intermediate-mass-ratio inspirals (IMRIs) - binaries in which a stellar-mass object spirals into a massive black hole or other massive, compact body - are important sources of gravitational waves for LISA and LIGO, respectively. Thorne has speculated that the waves from EMRIs and IMRIs encode, in principle, all the details of (i) the central body's spacetime geometry (metric), (ii) the tidal coupling (energy and angular momentum exchange) between the central body and orbiting object, and (iii) the evolving orbital elements. Fintan Ryan has given a first partial proof that this speculation is correct: Restricting himself to nearly circular, nearly equatorial orbits and ignoring tidal coupling, Ryan proved that the central body's metric is encoded in the waves. In this paper we generalize Ryan's theorem. Retaining Ryan's restriction to nearly circular and nearly equatorial orbits, and dropping the assumption of no tidal coupling, we prove that Thorne's conjecture is nearly fully correct: the waves encode not only the central body's metric but also the evolving orbital elements and (in a sense slightly different from Thorne's conjecture) the evolving tidal coupling.

  12. Quantitative analysis of cell surface membrane proteins using membrane-impermeable chemical probe coupled with 18O labeling

    PubMed Central

    Zhang, Haizhen; Brown, Roslyn N.; Qian, Wei-Jun; Monroe, Matthew E.; Purvine, Samuel O.; Moore, Ronald J.; Gritsenko, Marina A.; Shi, Liang; Romine, Margaret F; Fredrickson, James K.; Paša-Tolić, Ljiljana; Smith, Richard D.; Lipton, Mary S.

    2010-01-01

    We report a mass spectrometry-based strategy for quantitative analysis of cell surface membrane proteome changes. The strategy includes enrichment of surface membrane proteins using a membrane-impermeable chemical probe followed by stable isotope 18O labeling and LC-MS analysis. We applied this strategy for enriching membrane proteins expressed by Shewanella oneidensis MR-1, a gram-negative bacterium with known metal-reduction capability via extracellular electron transfer between outer membrane proteins and extracellular electron receptors. LC/MS/MS analysis resulted in the identification of about 400 proteins with 79% of them being predicted to be membrane localized. Quantitative aspects of the membrane enrichment were shown by peptide level 16O and 18O labeling of proteins from wild-type and mutant cells (generated from deletion of a type II secretion protein, GspD) prior to LC-MS analysis. Using a chemical probe labeled pure protein as an internal standard for normalization, the quantitative data revealed reduced abundances in ΔgspD mutant cells of many outer membrane proteins including the outer membrane c-cype cytochromes OmcA and MtrC, in agreement with previously investigation demonstrating that these proteins are substrates of the type II secretion system. PMID:20380418

  13. Radio frequency-compensated Langmuir probe with auxiliary double probes

    SciTech Connect

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-15

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas.

  14. Radio frequency-compensated Langmuir probe with auxiliary double probes.

    PubMed

    Oh, Se-Jin; Oh, Seung-Ju; Chung, Chin-Wook

    2010-09-01

    A radio frequency (rf) compensation design using auxiliary double probes connected in parallel with a main measurement probe was developed for Langmuir probe diagnostics. This probe structure can reduce the sheath impedance of the main probe. In our probe design, the sheath capacitance of the probe can be increased and its sheath resistance can be decreased with increasing dc bias differential voltage between the auxiliary double probes. The I-V characteristic curve and electron energy distribution functions measured by our probe system had sufficient rf compensation performance in inductively coupled plasmas.

  15. The Effect of Electrode Coupling on Single Molecule Device Characteristics: An X-Ray Spectroscopy and Scanning Probe Microscopy Study

    NASA Astrophysics Data System (ADS)

    Batra, Arunabh

    This thesis studies electronic properties of molecular devices in the limiting cases of strong and weak electrode-molecule coupling. In these two limits, we use the complementary techniques of X-Ray spectroscopy and Scanning Tunneling Microscopy (STM) to understand the mechanisms for electrode-molecule bond formation, the energy level realignment due to metal-molecule bonds, the effect of coupling strength on single-molecule conductance in low-bias measurements, and the effect of coupling on transport under high-bias. We also introduce molecular designs with inherent asymmetries, and develop an analytical method to determine the effect of these features on high-bias conductance. This understanding of the role of electrode-molecule coupling in high-bias regimes enables us to develop a series of functional electronic devices whose properties can be predictably tuned through chemical design. First, we explore the weak electrode-molecule coupling regime by studing the interaction of two types of paracyclophane derivates that are coupled 'through-space' to underlying gold substrates. The two paracyclophane derivatives differ in the strength of their intramolecular through-space coupling. X-Ray photoemission spectroscopy (XPS) and Near-Edge X-ray Absorbance Fine Structure (NEXAFS) spectroscopy allows us to determine the orientation of both molecules; Resonant Photoemission Spectroscopy (RPES) then allows us to measure charge transfer time from molecule to metal for both molecules. This study provides a quantititative measure of charge transfer time as a function of through-space coupling strength. Next we use this understanding in STM based single-molecule current-voltage measurements of a series of molecules that couple through-space to one electrode, and through-bond to the other. We find that in the high-bias regime, these molecules respond differently depending on the direction of the applied field. This asymmetric response to electric field direction results in

  16. Intermolecular domain docking in the hairpin ribozyme

    PubMed Central

    Sumita, Minako; White, Neil A.; Julien, Kristine R.; Hoogstraten, Charles G.

    2013-01-01

    The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a “double conformational capture” model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding. PMID:23324606

  17. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    NASA Astrophysics Data System (ADS)

    Gruodis, A.; Galikova, N.; Šarka, K.; Saulė, R.; Batiuškaitė, D.; Saulis, G.

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Most patients are inoperable and hepatoma cells are resistant to conventional chemotherapies. Thus, the development of novel therapies for HCC treatment is of paramount importance. Amongst different alimentary factors, vitamin C and vitamin K3 In the present work, it has been shown that the treatment of mouse hepatoma MH-22A cells by vitamin C and vitamin K3 at the ratio of 100:1 greatly enhanced their cytotoxicity. When cells were subjected to vitamin C at 200 μM or to vitamin K3 at 2 μM separately, their viability reduced by only about 10%. However, when vitamins C and K3 were combined at the same concentrations, they killed more than 90% of cells. To elucidate the mechanism of the synergistic cytotoxicity of the C&K3 mixture, theoretical quantum-chemical analysis of the dynamics of intermolecular electron transfer (IET) processes within the complexes containing C (five forms) and K3 (one form) has been carried out. Optimization of the ground state complex geometry has been provided by means of GAUSSIAN03 package. Simulation of the IET has been carried out using NUVOLA package, in the framework of molecular orbitals (MO). The rate of IET has been calculated using Fermi Golden rule. The results of simulations allow us to create the preliminary model of the reaction pathway.

  18. Propagation studies of metastable intermolecular composites (MIC).

    SciTech Connect

    Son, S. F.; Busse, J. R.; Asay, B. W.; Peterson, P. D.; Mang, J. T.; Bockmon, B.; Pantoya, M.

    2002-01-01

    Thermite materials are attractive energetic materials because the reactions are highly exothermic, have high energy densities, and high temperatures of combustion. However, the application of thermite materials has been limited because of the relative slow release of energy compared to other energetic materials. Engineered nano-scale composite energetic materials, such as Al/MoO{sub 3}, show promise for additional energetic material applications because they can react very rapidly. The composite material studied in this work consists of tailored, ultra-fine grain (30-200 nm diameter) aluminum particles that dramatically increase energy release rates of these thermite materials. These reactant clusters of fuel and oxidizer particles are in nearly atomic scale proximity to each other but are constrained from reaction until triggered. Despite the growing importance of nano-scale energetic materials, even the most basic combustion characteristics of these materials have not been thoroughly studied. This paper reports initial studies of the ignition and combustion of metastable intermolecular composites (MIC) materials. The goals were lo obtain an improved understanding of flame propagation mechanisms and combustion behaviors associated with nano-structured energetic materials. Information on issues such as reaction rate and behavior as a function of composition (mixture ratio), initial static charge, and particle size are essential and will allow scientists to design applications incorporating the benefits of these compounds. The materials have been characterized, specifically focusing on particle size, shape, distribution and morphology.

  19. Human Leukocyte Antigen Typing Using a Knowledge Base Coupled with a High-Throughput Oligonucleotide Probe Array Analysis

    PubMed Central

    Zhang, Guang Lan; Keskin, Derin B.; Lin, Hsin-Nan; Lin, Hong Huang; DeLuca, David S.; Leppanen, Scott; Milford, Edgar L.; Reinherz, Ellis L.; Brusic, Vladimir

    2014-01-01

    Human leukocyte antigens (HLA) are important biomarkers because multiple diseases, drug toxicity, and vaccine responses reveal strong HLA associations. Current clinical HLA typing is an elimination process requiring serial testing. We present an alternative in situ synthesized DNA-based microarray method that contains hundreds of thousands of probes representing a complete overlapping set covering 1,610 clinically relevant HLA class I alleles accompanied by computational tools for assigning HLA type to 4-digit resolution. Our proof-of-concept experiment included 21 blood samples, 18 cell lines, and multiple controls. The method is accurate, robust, and amenable to automation. Typing errors were restricted to homozygous samples or those with very closely related alleles from the same locus, but readily resolved by targeted DNA sequencing validation of flagged samples. High-throughput HLA typing technologies that are effective, yet inexpensive, can be used to analyze the world’s populations, benefiting both global public health and personalized health care. PMID:25505899

  20. Reduced coupling of water molecules near the surface of reverse micelles.

    PubMed

    Bakulin, Artem A; Pshenichnikov, Maxim S

    2011-11-21

    We report on vibrational dynamics of water near the surface of AOT reverse micelles studied by narrow-band excitation, mid-IR pump-probe spectroscopy. Evidence of OH-stretch frequency splitting into the symmetric and asymmetric modes is clearly observed for the interfacial H(2)O molecules. The polarization memory of interfacial waters is preserved over an exceptionally extended >10 ps timescale which is a factor of 100 longer than in bulk water. These observations point towards negligibly small intermolecular vibrational coupling between the water molecules as well as strongly reduced water rotational mobility within the interfacial water layer. PMID:21959913

  1. Feasibility study of a swept frequency electromagnetic probe (SWEEP) using inductive coupling for the determination of subsurface conductivity of the earth and water prospecting in arid regions

    NASA Technical Reports Server (NTRS)

    Latorraca, G. A.; Bannister, L. H.

    1974-01-01

    Techniques developed for electromagnetic probing of the lunar interior, and techniques developed for the generation of high power audio frequencies were combined to make practical a magnetic inductive coupling system for the rapid measurement of ground conductivity profiles which are helpful when prospecting for the presence and quality of subsurface water. A system which involves the measurement of the direction, intensity, and time phase of the magnetic field observed near the surface of the earth at a distance from a horizontal coil energized so as to create a field that penetrates the earth was designed and studied to deduce the conductivity and stratification of the subsurface. Theoretical studies and a rudimentary experiment in an arid region showed that the approach is conceptually valid and that this geophysical prospecting technique can be developed for the economical exploration of subterranean water resources.

  2. Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells

    PubMed Central

    Guo, Jia; Hanawalt, Philip C.; Spivak, Graciela

    2013-01-01

    Oxidized bases in DNA have been implicated in cancer, aging and neurodegenerative disease. We have developed an approach combining single-cell gel electrophoresis (comet) with fluorescence in situ hybridization (FISH) that enables the comparative quantification of low, physiologically relevant levels of DNA lesions in the respective strands of defined nucleotide sequences and in the genome overall. We have synthesized single-stranded probes targeting the termini of DNA segments of interest using a polymerase chain reaction-based method. These probes facilitate detection of damage at the single-molecule level, as the lesions are converted to DNA strand breaks by lesion-specific endonucleases or glycosylases. To validate our method, we have documented transcription-coupled repair of cyclobutane pyrimidine dimers in the ataxia telangiectasia-mutated (ATM) gene in human fibroblasts irradiated with 254 nm ultraviolet at 0.1 J/m2, a dose ∼100-fold lower than those typically used. The high specificity and sensitivity of our approach revealed that 7,8-dihydro-8-oxoguanine (8-oxoG) at an incidence of approximately three lesions per megabase is preferentially repaired in the transcribed strand of the ATM gene. We have also demonstrated that the hOGG1, XPA, CSB and UVSSA proteins, as well as actively elongating RNA polymerase II, are required for this process, suggesting cross-talk between DNA repair pathways. PMID:23775797

  3. Comet-FISH with strand-specific probes reveals transcription-coupled repair of 8-oxoGuanine in human cells.

    PubMed

    Guo, Jia; Hanawalt, Philip C; Spivak, Graciela

    2013-09-01

    Oxidized bases in DNA have been implicated in cancer, aging and neurodegenerative disease. We have developed an approach combining single-cell gel electrophoresis (comet) with fluorescence in situ hybridization (FISH) that enables the comparative quantification of low, physiologically relevant levels of DNA lesions in the respective strands of defined nucleotide sequences and in the genome overall. We have synthesized single-stranded probes targeting the termini of DNA segments of interest using a polymerase chain reaction-based method. These probes facilitate detection of damage at the single-molecule level, as the lesions are converted to DNA strand breaks by lesion-specific endonucleases or glycosylases. To validate our method, we have documented transcription-coupled repair of cyclobutane pyrimidine dimers in the ataxia telangiectasia-mutated (ATM) gene in human fibroblasts irradiated with 254 nm ultraviolet at 0.1 J/m2, a dose ∼100-fold lower than those typically used. The high specificity and sensitivity of our approach revealed that 7,8-dihydro-8-oxoguanine (8-oxoG) at an incidence of approximately three lesions per megabase is preferentially repaired in the transcribed strand of the ATM gene. We have also demonstrated that the hOGG1, XPA, CSB and UVSSA proteins, as well as actively elongating RNA polymerase II, are required for this process, suggesting cross-talk between DNA repair pathways. PMID:23775797

  4. System for effecting underwater coupling of optical fiber cables characterized by a novel V-probe cable capture mechanism

    NASA Astrophysics Data System (ADS)

    Hillenbrand, Christopher F.; Barron, Thomas D.; Nugent, David M.

    1995-03-01

    A submarine trails one fiber optic cable and an undersea vehicle is controlled by this first cable. A missile/torpedo trails a second cable that is to be coupled to the first cable. The second cable has a segment suspended vertically underwater between a buoyant pod and a sea anchor type buoy. The undersea vehicle, or Autonomous Undersea Vehicle, (AUV) hunts for the pod by conventional homing means. A forked cable pickup device in the nose of the AUV captures the suspended cable segment directing it into a slot so a male socket in the underside of the pod mates with a female socket in the slot.

  5. The Torque of the Planet: NASA Researcher Uses NCCS Computers to Probe Atmosphere-Land-Ocean Coupling

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The study of Earth science is like a giant puzzle, says Braulio Sanchez. "The more you know about the individual pieces, the easier it is to fit them together." A researcher with Goddard's Space Geodesy Branch, Sanchez has been using NCCS supercomputer and mass storage resources to show how the angular momenta of the atmosphere, the oceans, and the solid Earth are dynamically coupled. Sanchez has calculated the magnitude of atmospheric torque on the planet and has determined some of the possible effects that torque has on Earth's rotation.

  6. Temperature-induced electronsbnd phonon coupling behaviour of AgGaS2 probed by Brillouin spectroscopy

    NASA Astrophysics Data System (ADS)

    Kavitha, C.; Narayana, Chandrabhas

    2014-10-01

    Low-temperature Brillouin scattering studies on Chalcopyrite AgGaS2 have been carried out between the temperatures ranges 20sbnd 300 K. We observe the Brillouin modes for AgGaS2 as follows: for crossed polarization (VH) the two modes are around 5.4 and 18 GHz, labelled as RSW1 (Rayleigh surface mode), LA (longitudinal) modes and for parallel polarization (HH), we see the modes are around 4.5 and 11 GHz, labelled as RSW2, TA (transverse acoustic). According to this acoustic phonon mode behaviour with temperature, we do see phase transition at 80 K for AgGaS2. The phase change observed at 80 K is attributed to a strong electronsbnd phonon coupling between the acoustic modes, which modulates the acoustic mode frequency 10sbnd 15%. The strong electronsbnd phonon coupling between acoustic modes (LA and TA), which is seen from the anomalous behaviour below 80 K, shows the electronic transition to be of the type direct to indirect band gap. The sound velocity and elastic constants have been calculated using Brillouin modes, which are in good agreement with previous reports.

  7. Intermolecular Vibrations of Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, Michael Roy Casselman

    Hydrophobic amino acids interact with their chemical environment through a combination of electrostatic, hydrogen bonding, dipole, induced dipole, and dispersion forces. These interactions all have their own characteristic energy scale and distance dependence. The low-frequency (0.1-5 THz, 5-150 cm-1) vibrational modes of amino acids in the solid state are a direct indicator of the interactions between the molecules, which include interactions between an amino acid functional group and its surroundings. This information is central to understanding the dynamics and morphology of proteins. The alpha-carbon is a chiral center for all of the hydrophobic amino acids, meaning that they exist in two forms, traditionally referred to as L- and D-enantiomers. This nomenclature indicates which direction the molecule rotates plane-polarized visible light (levorotory and dextrorotory). Chiral a-amino acids in proteins are exclusively the L-variety In the solid state, the crystal lattice of the pure L-enantiomer is the mirror image of the D-enantiomer crystal lattice. These solids are energetically identical. Enantiomers also have identical spectroscopic properties except when the measurement is polarization sensitive. A mixture of equal amounts D- and L-amino acid enantiomers can crystallize into a racemic (DL-) structure that is different from that of the pure enantiomers. Whether a solution of both enantiomers will crystallize into a racemic form or spontaneously resolve into a mixture of separate D- and L-crystals largely depends on the interactions between molecules available in the various possible configurations. This is an active area of research. Low-frequency vibrations with intermolecular character are very sensitive to changes in lattice geometry, and consequently the vibrational spectra of racemic crystals are usually quite distinct from the spectra of the crystals of the corresponding pure enantiomers in the far-infrared (far-IR). THz time-domain spectroscopy (THz

  8. Interatomic (Intermolecular) Decay Processes in Clusters: Current Status and Outlook

    SciTech Connect

    Averbukh, V.; Cederbaum, L. S.

    2007-11-29

    Since their theoretical prediction a decade ago, interatomic (intermolecular) Coulombic decay (ICD) and related processes have been in the focus of intensive theoretical and experimental research. The spectacular progress in this direction has been stimulated both by the fundamental importance of the new electronic decay phenomena and by the exciting possibility of their practical application, for example in spectroscopy. We review the current status of the research of interatomic (intermolecular) decay phenomena in clusters and discuss some perspectives of this new field.

  9. Frontier orbital symmetry control of intermolecular electron transfer

    SciTech Connect

    Stevens, B.

    1990-11-01

    Research continued on the study of intermolecular electron transfer. This report discusses the following topics: fluorescence quenching by electron transfer and the modification of quenching dynamics by solvent properties and net free energy change; transient absorption measurements following selective excitation of 1:1 EDA complex isomers; selective quenching of dual fluorescence from linked EDA systems; electron-transfer sensitized cycloreversion of rubrene endoperoxide; and vibronic modification of adiabatic requirements for intermolecular electron transfer. (CBS)

  10. Mass Spectrometric and Langmuir Probe Measurements in Inductively Coupled Plasmas in Ar, CHF3/Ar and CHF3/Ar/O2 Mixtures

    NASA Technical Reports Server (NTRS)

    Kim, J. S.; Rao, M. V. V. S.; Cappelli, M. A.; Sharma, S. P.; Meyyappan, M.; Arnold, Jim (Technical Monitor)

    2000-01-01

    Absolute fluxes and energy distributions of ions in inductively coupled plasmas of Ar, CHF3/Ar, and CHF3/Ar/O2 have been measured. These plasmas were generated in a Gaseous Electronics Conference (GEC) cell modified for inductive coupling at pressures 10-50 mTorr and 100-300 W of 13.56 MHz radio frequency (RF) power in various feedgas mixtures. In pure Ar plasmas, the Ar(+) flux increases linearly with pressure as well as RF-power. Total ion flux in CHF3 mixtures decreases with increase in pressure and also CHF3 concentration. Relative ion fluxes observed in the present studies are analyzed with the help of available cross sections for electron impact ionization and charge-exchange ion-molecule reactions. Measurements of plasma potential, electron and ion number densities, electron energy distribution function, and mean electron energy have also been made in the center of the plasma with a RF compensated Langmuir probe. Plasma potential values are compared with the mean ion energies determined from the measured ion energy distributions and are consistent. Electron temperature, plasma potential, and mean ion energy vary inversely with pressure, but increase with CHF3 content in the mixture.

  11. Probing mechanical principles of focal contacts in cell–matrix adhesion with a coupled stochastic–elastic modelling framework

    PubMed Central

    Gao, Huajian; Qian, Jin; Chen, Bin

    2011-01-01

    Cell–matrix adhesion depends on the collective behaviours of clusters of receptor–ligand bonds called focal contacts between cell and extracellular matrix. While the behaviour of a single molecular bond is governed by statistical mechanics at the molecular scale, continuum mechanics should be valid at a larger scale. This paper presents an overview of a series of recent theoretical studies aimed at probing the basic mechanical principles of focal contacts in cell–matrix adhesion via stochastic–elastic models in which stochastic descriptions of molecular bonds and elastic descriptions of interfacial traction–separation are unified in a single modelling framework. The intention here is to illustrate these principles using simple analytical and numerical models. The aim of the discussions is to provide possible clues to the following questions: why does the size of focal adhesions (FAs) fall into a narrow range around the micrometre scale? How can cells sense and respond to substrates of varied stiffness via FAs? How do the magnitude and orientation of mechanical forces affect the binding dynamics of FAs? The effects of cluster size, cell–matrix elastic modulus, loading direction and cytoskeletal pretension on the lifetime of FA clusters have been investigated by theoretical arguments as well as Monte Carlo numerical simulations, with results showing that intermediate adhesion size, stiff substrate, cytoskeleton stiffening, low-angle pulling and moderate cytoskeletal pretension are factors that contribute to stable FAs. From a mechanistic point of view, these results provide possible explanations for a wide range of experimental observations and suggest multiple mechanisms by which cells can actively control adhesion and de-adhesion via cytoskeletal contractile machinery in response to mechanical properties of their surroundings. PMID:21632610

  12. Multiple DNA Extractions Coupled with Stable-Isotope Probing of Anthracene-Degrading Bacteria in Contaminated Soil▿†

    PubMed Central

    Jones, Maiysha D.; Singleton, David R.; Sun, Wei; Aitken, Michael D.

    2011-01-01

    In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the 13C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-13C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from 13C-enriched DNA and were designated “anthracene group 1.” Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP. PMID:21398486

  13. Probing the role of interlayer coupling and coulomb interactions on electronic structure in few-layer MoSe₂ nanostructures.

    PubMed

    Bradley, Aaron J; Ugeda, Miguel M; da Jornada, Felipe H; Qiu, Diana Y; Ruan, Wei; Zhang, Yi; Wickenburg, Sebastian; Riss, Alexander; Lu, Jiong; Mo, Sung-Kwan; Hussain, Zahid; Shen, Zhi-Xun; Louie, Steven G; Crommie, Michael F

    2015-04-01

    Despite the weak nature of interlayer forces in transition metal dichalcogenide (TMD) materials, their properties are highly dependent on the number of layers in the few-layer two-dimensional (2D) limit. Here, we present a combined scanning tunneling microscopy/spectroscopy and GW theoretical study of the electronic structure of high quality single- and few-layer MoSe2 grown on bilayer graphene. We find that the electronic (quasiparticle) bandgap, a fundamental parameter for transport and optical phenomena, decreases by nearly one electronvolt when going from one layer to three due to interlayer coupling and screening effects. Our results paint a clear picture of the evolution of the electronic wave function hybridization in the valleys of both the valence and conduction bands as the number of layers is changed. This demonstrates the importance of layer number and electron-electron interactions on van der Waals heterostructures and helps to clarify how their electronic properties might be tuned in future 2D nanodevices.

  14. Using Fixed-Node Diffusion Monte Carlo to Probe Rotation-Vibration Coupling in Highly Fluxional Asymmetric Top Molecules

    NASA Astrophysics Data System (ADS)

    Petit, Andrew S.; Wellen, Bethany A.; McCoy, Anne B.

    2012-06-01

    Our group has developed a fixed-node Diffusion Monte Carlo (DMC) methodology that can be used to describe rotationally excited states of highly fluxional symmetric top molecules. This technique has been thoroughly benchmarked using rotationally excited states of H_3^+, H_3O^+, and NH_3 with J≤12. Here, we report a recently developed extension of this methodology to asymmetric top molecules which undergo large amplitude, zero-point vibrational motion. The nodal surfaces used in the fixed-node DMC calculations are obtained from rigid-rotor wave functions calculated using the system's ground state vibrationally averaged rotational constants. The algorithms used to evaluate node crossing and re-crossing are generalized to account for the pronounced curvature exhibited by the nodal surfaces of asymmetric top molecules with κ ≈ 0 due to the strong mixing of two or more symmetric top basis functions. Finally, the insight that can be obtained from these calculations into the nature and strength of the vibration-rotation coupling present in highly fluxional asymmetric top molecules will be briefly discussed and further elaborated on in the following talk. A. S. Petit and A. B. McCoy, J. Phys. Chem. A 113, 12706 (2009). A. S. Petit, B. A. Wellen, and A. B. McCoy, J. Chem. Phys. 136, 074101 (2012).

  15. Analysis of cytochrome P450 metabolites of arachidonic acid by stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry.

    PubMed

    Zhu, Quan-Fei; Hao, Yan-Hong; Liu, Ming-Zhou; Yue, Jiang; Ni, Jian; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-09-01

    Cytochrome P450 metabolites of arachidonic acid (AA) belong to eicosanoids and are potent lipid mediators of inflammation. It is well-known that eicosanoids play an important role in numerous pathophysiological processes. Therefore, quantitative analysis of cytochrome P450 metabolites of AA, including hydroxyeicosatetraenoic acids (HETEs), epoxyeicosatreinoic acids (EETs), and dihydroxyeicosatrienoic acids (DHETs) can provide crucial information to uncover underlying mechanisms of cytochrome P450 metabolites of AA related diseases. Herein, we developed a highly sensitive method to identify and quantify HETEs, EETs, and DHETs in lipid extracts of biological samples based on stable isotope probe labeling coupled with ultra high-performance liquid chromatography/mass spectrometry. To this end, a pair of stable isotope probes, 2-dimethylaminoethylamine (DMED) and d4-2-dimethylaminoethylamine (d4-DMED), were utilized to facilely label eicosanoids. The heavy labeled eicosanoid standards were prepared and used as internal standards for quantification to minimize the matrix and ion suppression effects in mass spectrometry analysis. In addition, the detection sensitivities of DMED labeled eicosanoids improved by 3-104 folds in standard solution and 5-138 folds in serum matrix compared with unlabeled analytes. Moreover, a good separation of eicosanoids isomers was achieved upon DMED labeling. The established method provided substantial sensitivity (limit of quantification at sub-picogram), high specificity, and broad linear dynamics range (3 orders of magnitude). We further quantified cytochrome P450 metabolites of AA in rat liver, heart, brain tissues and human serum using the developed method. The results showed that 19 eicosanoids could be distinctly detected and the contents of 11-, 15-, 16-, 20-HETE, 5,6-EET, and 14,15-EET in type 2 diabetes mellitus patients and 5-, 11-, 12-, 15-, 16-, 20-HETE, 8,9-EET, and 5,6-DHET in myeloid leukemia patients had significant changes

  16. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    SciTech Connect

    González, M.; Lemus-Santana, A.A.; Rodríguez-Hernández, J.; Aguirre-Velez, C.I.; Knobel, M.; Reguera, E.

    2013-08-15

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.

  17. Pd0-mediated rapid cross-coupling reactions, the rapid C-[11C]methylations, revolutionarily advancing the syntheses of short-lived PET molecular probes.

    PubMed

    Suzuki, Masaaki; Doi, Hisashi; Koyama, Hiroko; Zhang, Zhouen; Hosoya, Takamitsu; Onoe, Hirotaka; Watanabe, Yasuyoshi

    2014-06-01

    Positron emission tomography is a noninvasive method for monitoring drug (or diagnostic) behavior and its localization on the target molecules in the living systems, including the human body, using a short-lived positron-emitting radionuclide. New methodologies for introducing representative short-lived radionuclides, (11)C and (18)F, into the carbon frameworks of biologically active organic compounds have been established by developing rapid C-[(11)C]methylations and C-[(18)F]fluoromethylations using rapid Pd(0)-mediated cross-coupling reactions between [(11)C]methyl iodide (sp(3)-hybridized carbon) and an excess amount of organotributylstannane or organoboronic acid ester having sp(2) (phenyl, heteroaromatic, or alkenyl), sp(alkynyl), or sp(3) (benzyl and cinnamyl)-hybridized carbons; and [(18)F]fluoromethyl halide (iodide or bromide) and an organoboronic acid ester, respectively. These rapid reactions provide a firm foundation for an efficient and general synthesis of short-lived (11)C- or (18)F-labeled PET molecular probes to promote in vivo molecular imaging studies.

  18. Synergy between measurements of gravitational waves and the triple-Higgs coupling in probing the first-order electroweak phase transition

    NASA Astrophysics Data System (ADS)

    Hashino, Katsuya; Kakizaki, Mitsuru; Kanemura, Shinya; Matsui, Toshinori

    2016-07-01

    Probing the Higgs potential and new physics behind the electroweak symmetry breaking is one of the most important issues of particle physics. In particular, the nature of the electroweak phase transition is essential for understanding the physics of the early Universe, such that the strongly first-order phase transition is required for a successful scenario of electroweak baryogenesis. The strongly first-order phase transition is expected to be tested by precisely measuring the triple Higgs boson coupling at future colliders like the International Linear Collider. It can also be explored via the spectrum of stochastic gravitational waves to be measured at future space-based interferometers such as eLISA and DECIGO. We discuss the complementarity of both the methods in testing the strongly first-order phase transition of the electroweak symmetry in models with additional isospin singlet scalar fields with and without classical scale invariance. We find that they are synergetic in identifying specific models of electroweak symmetry breaking in more detail.

  19. Cavity Photons as a Probe for Charge Relaxation Resistance and Photon Emission in a Quantum Dot Coupled to Normal and Superconducting Continua

    NASA Astrophysics Data System (ADS)

    Bruhat, L. E.; Viennot, J. J.; Dartiailh, M. C.; Desjardins, M. M.; Kontos, T.; Cottet, A.

    2016-04-01

    Microwave cavities have been widely used to investigate the behavior of closed few-level systems. Here, we show that they also represent a powerful probe for the dynamics of charge transfer between a discrete electronic level and fermionic continua. We have combined experiment and theory for a carbon nanotube quantum dot coupled to normal metal and superconducting contacts. In equilibrium conditions, where our device behaves as an effective quantum dot-normal metal junction, we approach a universal photon dissipation regime governed by a quantum charge relaxation effect. We observe how photon dissipation is modified when the dot admittance turns from capacitive to inductive. When the fermionic reservoirs are voltage biased, the dot can even cause photon emission due to inelastic tunneling to/from a Bardeen-Cooper-Schrieffer peak in the density of states of the superconducting contact. We can model these numerous effects quantitatively in terms of the charge susceptibility of the quantum dot circuit. This validates an approach that could be used to study a wide class of mesoscopic QED devices.

  20. Intermolecular exciton-exciton annihilation in phospholipid vesicles doped with [Ru(bpy)2dppz]2+

    NASA Astrophysics Data System (ADS)

    De la Cadena, Alejandro; Pascher, Torbjörn; Davydova, Dar'ya; Akimov, Denis; Herrmann, Felix; Presselt, Martin; Wächtler, Maria; Dietzek, Benjamin

    2016-01-01

    The ultrafast photophysics of [Ru(bpy)2dppz]2+ (dppz = dipyrido[3,2-a:2‧,3‧-c]-phenazine) embedded into the walls of phospholipid vesicles has been studied by femtosecond time-resolved pump-probe spectroscopy. While [Ru(bpy)2dppz]2+ has been studied intensively with respect to its intramolecular charge transfer processes, which are associated with the well known light-switch effect, this study focuses on intermolecular energy transfer processes taking place upon dense packing of the complexes into a phospholipid membrane composed of dipalmitoyl-L-α-phosphatidylglycerol, which can be thought of as a simplistic model of a cellular membrane. The data indicate additional quenching of excited [Ru(bpy)2dppz]2+ upon increasing the pump-pulse intensity. Hence, the observed photophysics, which is assigned to the presence of intermolecular exciton-exciton annihilation at high pump-intensities, might be related to the ultrafast photophysics of [Ru(bpy)2dppz]2+ when used as a chromophore to stain cells, an effect that may be taken into account during the employment of novel cellular markers based on Ru polypyridine complexes.

  1. Insights into the Complexity of Weak Intermolecular Interactions Interfering in Host-Guest Systems.

    PubMed

    Zhang, Dawei; Chatelet, Bastien; Serrano, Eloisa; Perraud, Olivier; Dutasta, Jean-Pierre; Robert, Vincent; Martinez, Alexandre

    2015-10-01

    The recognition properties of heteroditopic hemicryptophane hosts towards anions, cations, and neutral pairs, combining both cation-π and anion-π interaction sites, were investigated to probe the complexity of interfering weak intermolecular interactions. It is suggested from NMR experiments, and supported by CASSCF/CASPT2 calculations, that the binding constants of anions can be modulated by a factor of up to 100 by varying the fluorination sites on the electron-poor aromatic rings. Interestingly, this subtle chemical modification can also reverse the sign of cooperativity in ion-pair recognition. Wavefunction calculations highlight how short- and long-range interactions interfere in this recognition process, suggesting that a disruption of anion-π interactions can occur in the presence of a co-bound cation. Such molecules can be viewed as prototypes for examining complex processes controlled by the competition of weak interactions.

  2. Intramolecular and intermolecular vibrational energy relaxation of CH 2I 2 dissolved in supercritical fluid

    NASA Astrophysics Data System (ADS)

    Sekiguchi, K.; Shimojima, A.; Kajimoto, O.

    2002-04-01

    A pump-probe experiment was performed to examine vibrational population relaxation of diiodomethane (CH 2I 2) molecule dissolved in supercritical CO 2. Using an apparatus with femtosecond time resolution, we observed the contributions of intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) separately. IVR and VET rates were measured with varying solvent densities at a constant temperature. It is shown that the IVR rate is not density dependent while the VET rate increases with increasing density from 0.4 to 0.8 g cm-3. This observation suggests that the rate of the VET process is determined by solute-solvent collisions whereas the IVR rate is not much affected by solute-solvent interaction.

  3. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

    Crystals of naphthalene form on the surface of an acetone solution and dance about in an animated fashion illustrating surface tension, crystallization, and intermolecular forces. Additional experiments reveal the properties of the solution. Flows within the solutions can be visualized by various means. Previous demonstrations of surface motion…

  4. Learning about Intermolecular Interactions from the Cambridge Structural Database

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.

    2012-01-01

    A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the…

  5. Ionic strength and intermolecular contacts in protein crystals

    NASA Astrophysics Data System (ADS)

    Iyer, Ganesh H.; Dasgupta, Swagata; Bell, Jeffrey A.

    2000-08-01

    The ionic strengths of crystallization solutions for 206 proteins were observed to form a bimodal distribution. The data was divided into two sets at an ionic strength of 4.4 M, and knowledge-based potentials were calculated to determine contact preferences at intermolecular crystal interfaces. Consistent with previous observations over all ionic strengths, intermolecular crystal contacts tend to exclude nonpolar amino acids; lysine is the least favored polar amino acid at crystal contacts; and arginine and glutamine are the two most favored amino acid at crystal contacts. However, some aspects of intermolecular contact preferences within protein crystals are significantly dependent on ionic strength. Arginine is the most favored residue at low ionic strength, but it takes second place to glutamine at high ionic strength. Other major ionic strength-dependent differences in protein crystal contacts can be explained by the binding of cations or anions. While others have shown the importance of ion binding experimentally in selected protein crystals, these statistical results indicate that intermolecular interface formation must involve ion-mediated contacts in a large number of protein crystals.

  6. Morphology and the Strength of Intermolecular Contact in Protein Crystals

    NASA Technical Reports Server (NTRS)

    Matsuura, Yoshiki; Chernov, Alexander A.

    2002-01-01

    The strengths of intermolecular contacts (macrobonds) in four lysozyme crystals were estimated based on the strengths of individual intermolecular interatomic interaction pairs. The periodic bond chain of these macrobonds accounts for the morphology of protein crystals as shown previously. Further in this paper, the surface area of contact, polar coordinate representation of contact site, Coulombic contribution on the macrobond strength, and the surface energy of the crystal have been evaluated. Comparing location of intermolecular contacts in different polymorphic crystal modifications, we show that these contacts can form a wide variety of patches on the molecular surface. The patches are located practically everywhere on this surface except for the concave active site. The contacts frequently include water molecules, with specific intermolecular hydrogen-bonds on the background of non-specific attractive interactions. The strengths of macrobonds are also compared to those of other protein complex systems. Making use of the contact strengths and taking into account bond hydration we also estimated crystal-water interfacial energies for different crystal faces.

  7. Intermolecular atom-atom bonds in crystals - a chemical perspective.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-03-01

    Short atom-atom distances between molecules are almost always indicative of specific intermolecular bonding. These distances may be used to assess the significance of all hydrogen bonds, including the C-H⋯O and even weaker C-H⋯F varieties.

  8. Student Understanding of Intermolecular Forces: A Multimodal Study

    ERIC Educational Resources Information Center

    Cooper, Melanie M.; Williams, Leah C.; Underwood, Sonia M.

    2015-01-01

    The ability to use representations of molecular structure to predict the macroscopic properties of a substance is central to the development of a robust understanding of chemistry. Intermolecular forces (IMFs) play an important role in this process because they provide a mechanism for how and why molecules interact. In this study, we investigate…

  9. Connecting Protein Structure to Intermolecular Interactions: A Computer Modeling Laboratory

    ERIC Educational Resources Information Center

    Abualia, Mohammed; Schroeder, Lianne; Garcia, Megan; Daubenmire, Patrick L.; Wink, Donald J.; Clark, Ginevra A.

    2016-01-01

    An understanding of protein folding relies on a solid foundation of a number of critical chemical concepts, such as molecular structure, intra-/intermolecular interactions, and relating structure to function. Recent reports show that students struggle on all levels to achieve these understandings and use them in meaningful ways. Further, several…

  10. Hydrogen-hydrogen intermolecular structure of polyethylene in the melt

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Habenschuss, A.; Smith, G. D.; Borodin, O.; Tso, C.; Hsieh, E. T.; Soper, A. K.

    1999-05-01

    Three polyethylene samples, which differed in their degree of deuteration, were studied in neutron diffraction isotopic substitution (NDIS) experiments at 428 K. These results were complemented at small wavevectors by small angle neutron measurements. The intermolecular hydrogen-hydrogen (HH) structure function, hHH(Q), was obtained without recourse to intramolecular structure models, as demonstrated in a prior report. The PE experimental results are compared to computer simulation results for the alkanes C100 at 509 K and C44 at 350, 400, and 450 K. The small temperature dependence of the HH intermolecular radial distribution functions, gHH(r) for C44 indicates that the differences observed between the PE, C100, and C44 (450 K) results are, for the most part, not due to just temperature differences. It is shown that the string model, an analytic result from an integral equation theory of polymers (PRISM), can account approximately for the overall shape of the gHH(r) functions, and that this overall shape is dependent on the radius of gyration of the molecule. Further analysis shows that there are two other contributions to gHH(r), both of which are independent of chain length to first order. The first is due to chain-chain packing, and the second is due to local HH intermolecular correlations. These results are significant because they demonstrate that hHH(Q) is a useful function for studying intermolecular polymer structure, which has been shown to underpin phase behavior in polyolefin blends.

  11. Copper-catalyzed intermolecular asymmetric propargylic dearomatization of indoles.

    PubMed

    Shao, Wen; Li, He; Liu, Chuan; Liu, Chen-Jiang; You, Shu-Li

    2015-06-22

    The first copper-catalyzed intermolecular dearomatization of indoles by an asymmetric propargylic substitution reaction was developed. This method provides a highly efficient synthesis of versatile furoindoline and pyrroloindoline derivatives containing a quaternary carbon stereogenic center and a terminal alkyne moiety with up to 86 % yield and 98 % ee. PMID:25968474

  12. Evaluation of atmospheric solid analysis probe ionization coupled to ion mobility mass spectrometry for characterization of poly(ether ether ketone) polymers.

    PubMed

    Cossoul, Emilie; Hubert-Roux, Marie; Sebban, Muriel; Churlaud, Florence; Oulyadi, Hassan; Afonso, Carlos

    2015-01-26

    Recently, the interest of the coupling between atmospheric solid analysis probe (ASAP) and ion mobility-mass spectrometry has been revealed in the field of polymers. This method associates a direct ionization technique with a bi-dimensional separation method. Poly(ether ether ketones) (PEEK) belong to the family of the poly(aryl ether ketones) (PAEK) which are high performance aromatic polymers usually used in aerospace, electronics and nuclear industries. PEEK are important commercial thermoplastics with excellent chemical resistance and good mechanical properties. Because of their low solubility, few structural characterization studies of PEEK have been reported. In mass spectrometry, only MALDI-TOF analyses for polymer synthesis monitoring have been described with the use of strong acids such as sulfuric acid. This work demonstrates that ASAP is particularly efficient for analysis of PEEK in a solvent free approach with the production of intact small oligomers (n≤2). Five types of PEEK oligomers with different end-groups were evidenced. With MALDI-TOF, the same end-groups with almost the same relative abundance were obtained which support the hypothesis that the oligomers detected in ASAP are intact small oligomers and not fragments or pyrolysis products. This is particularly interesting as generally the ASAP analysis of polymers yields pyrolysis products with the loss of end-group information. The end-groups assignments have been confirmed by tandem mass spectrometry (MS/MS) experiments on the M(+) molecular ions, which allowed highlighting some specific neutral or radical losses as well as two diagnostic product ions. Thus, ASAP-IM/MS/MS proves to be a fast and efficient alternative way to characterize low solubility polymers such as PEEK. PMID:25542357

  13. Investigation of the Binding Interaction of Fatty Acids with Human G Protein-Coupled Receptor 40 Using a Site-Specific Fluorescence Probe by Flow Cytometry.

    PubMed

    Ren, Xiao-Min; Cao, Lin-Ying; Zhang, Jing; Qin, Wei-Ping; Yang, Yu; Wan, Bin; Guo, Liang-Hong

    2016-04-01

    Human G protein-coupled receptor 40 (hGPR40), with medium- and long-chain free fatty acids (FFAs) as its natural ligands, plays an important role in the enhancement of glucose-dependent insulin secretion. To date, information about the direct binding of FFAs to hGPR40 is very limited, and how carbon-chain length affects the activities of FFAs on hGPR40 is not yet understood. In this study, a fluorescein-fasiglifam analogue (F-TAK-875A) conjugate was designed and synthesized as a site-specific fluorescence probe to study the interaction of FFAs with hGPR40. hGPR40 was expressed in human embryonic kidney 293 cells and labeled with F-TAK-875A. By using flow cytometry, competitive binding of FFA and F-TAK-875A to hGPR40-expressed cells was measured. Binding affinities of 18 saturated FFAs, with carbon-chain lengths ranging from C6 to C23, were analyzed. The results showed that the binding potencies of FFAs to hGPR40 were dependent on carbon length. There was a positive correlation between length and binding potency for seven FFAs (C9-C15), with myristic acid (C15) showing the highest potency, 0.2% relative to TAK-875. For FFAs with a length of fewer than C9 or more than C15, they had very weak or no binding. Molecular docking results showed that the binding pocket of TAK-875 in hGPR40 could enclose FFAs with lengths of C15 or fewer. However, for FFAs with lengths longer than C15, part of the alkyl chain extended out of the binding pocket. This study provided insights into the structural dependence of FFAs binding to and activation of hGPR40.

  14. Long-term nitrogen fertilization of paddy soil shifts iron-reducing microbial community revealed by RNA-(13)C-acetate probing coupled with pyrosequencing.

    PubMed

    Ding, Long-Jun; Su, Jian-Qiang; Xu, Hui-Juan; Jia, Zhong-Jun; Zhu, Yong-Guan

    2015-03-01

    Iron reduction is an important biogeochemical process in paddy soils, yet little is known about the microbial coupling between nitrogen and iron reduction. Here, we investigated the shift of acetate-metabolizing iron-reducers under long-term nitrogen fertilization using (13)C-acetate-based ribosomal RNA (rRNA)-stable isotope probing (SIP) and pyrosequencing in an incubation experiment, and the shift of putative iron-reducers in original field samples were investigated by 16S rRNA gene-based pyrosequencing. During SIP incubations, in the presence of iron(III) oxyhydroxides, more iron(II) formation and less methane production were detected in nitrogen-fertilized (N) compared with non-fertilized (NF) soil. In (13)C-rRNA from microcosms amended with ferrihydrite (FER), Geobacter spp. were the important active iron-reducers in both soils, and labeled to a greater extent in N (31% of the bacterial classified sequences) than NF soils (11%). Pyrosequencing of the total 16S rRNA transcripts from microcosms at the whole community level further revealed hitherto unknown metabolisms of potential FER reduction by microorganisms including Pseudomonas and Solibacillus spp. in N soil, Dechloromonas, Clostridium, Bacillus and Solibacillus spp. in NF soil. Goethite (GOE) amendment stimulated Geobacter spp. to a lesser extent in both soils compared with FER treatment. Pseudomonas spp. in the N soil and Clostridium spp. in the NF soil may also be involved in GOE reduction. Pyrosequencing results from field samples showed that Geobacter spp. were the most abundant putative iron-reducers in both soils, and significantly stimulated by long-term nitrogen fertilization. Overall, for the first time, we demonstrate that long-term nitrogen fertilization promotes iron(III) reduction and modulates iron-reducing bacterial community in paddy soils.

  15. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes.

    PubMed

    Eichmann, Cédric; Orts, Julien; Tzitzilonis, Christos; Vögeli, Beat; Smrt, Sean; Lorieau, Justin; Riek, Roland

    2014-12-11

    The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.

  16. Dynamics of intermolecular interactions in CCl4via the isotope effect by femtosecond time-resolved spectroscopy.

    PubMed

    Konarska, Jadwiga; Gadomski, Wojciech; Ratajska-Gadomska, Bożena; Polok, Kamil; Pudłowski, Grzegorz; Kardaś, Tomasz M

    2016-06-21

    We report our study on the ultrafast dynamics of intermolecular interactions in liquid CCl4. A transient transmission time domain signal, obtained in the 40 ps delay range, exhibits beating at the difference frequency of the totally symmetric stretching vibrations of the tetrachloride isotopologues. We show that the spectra obtained as the windowed Fourier transform of different parts of the time domain signal in the range of this totally symmetric vibration, split due to the isotope effect, carry the information about the dynamics of the coherently excited, coupled molecules. We use a simple theoretical model in order to prove that the intermolecular interaction influences the relative amplitudes of the isotopologue peaks in the spectrum. Moreover, we demonstrate that the pump induced coherence in the system leads to additional strengthening of the interaction, which can be observed in the spectra obtained from the experimental time domain signal. PMID:27244535

  17. Intermolecular forces and the glass transition.

    PubMed

    Hall, Randall W; Wolynes, Peter G

    2008-01-17

    Random first-order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random first-order transition theory, is used to treat individual glassy configurations, whereas the liquid phase is treated using common liquid-state approximations. Free energies are calculated using liquid-state perturbation theory. The transition temperature, T*A, the temperature where the onset of activated behavior is predicted by mean field theory; the lower crossover temperature, T*C, where barrierless motions actually occur through fractal or stringy motions (corresponding to the phenomenological mode coupling transition temperature); and T*K, the Kauzmann temperature (corresponding to an extrapolated entropy crisis), are calculated in addition to T*g, the glass transition temperature that corresponds to laboratory cooling rates. Relationships between these quantities agree well with existing experimental and simulation data on van der Waals liquids. Both the isobaric and isochoric behavior in the supercooled regime are studied, providing results for DeltaCV and DeltaCp that can be used to calculate the fragility as a function of density and pressure, respectively. The predicted variations in the alpha-relaxation time with temperature and density conform to the empirical density-temperature scaling relations found by Casalini and Roland. We thereby demonstrate the microscopic origin of their observations. Finally, the relationship first suggested by Sastry between the spinodal temperature and the Kauzmann temperatures, as a function of density, is examined. The present microscopic calculations support the existence of an intersection of these two temperatures at sufficiently low temperatures.

  18. Dipole-dipole interactions in solution mixtures probed by two-dimensional synchronous spectroscopy based on orthogonal sample design scheme.

    PubMed

    Li, Hui-zhen; Tao, Dong-liang; Qi, Jian; Wu, Jin-guang; Xu, Yi-zhuang; Noda, Isao

    2014-04-24

    Two-dimensional (2D) synchronous spectroscopy together with a new approach called "Orthogonal Sample Design Scheme" was used to study the dipole-dipole interactions in two representative ternary chemical systems (N,N-dimethyllformamide (DMF)/CH3COOC2H5/CCl4 and C60/CH3COOC2H5/CCl4). For the first system, dipole-dipole interactions among carbonyl groups from DMF and CH3COOC2H5 are characterized by using the cross peak in 2D Fourier Transform Infrared Radiation (FT-IR) spectroscopy. For the second system, intermolecular interaction among π-π transition from C60 and vibration transition from the carbonyl band of ethyl acetate is probed by using 2D spectra. The experimental results demonstrate that "Orthogonal Sample Design Scheme" can effectively remove interfering part that is not relevant to intermolecular interaction. Additional procedures are carried out to preclude the possibilities of producing interfering cross peaks by other reasons, such as experimental errors. Dipole-dipole interactions that manifest in the form of deviation from the Beer-Lambert law generate distinct cross peaks visualized in the resultant 2D synchronous spectra of the two chemical systems. This work demonstrates that 2D synchronous spectra coupled with orthogonal sample design scheme provide us an applicable experimental approach to probing and characterizing dipole-dipole interactions in complex molecular systems. PMID:24582337

  19. Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem.

    PubMed

    Kim, Youngmi; Yang, Chaoyong James; Tan, Weihong

    2007-01-01

    Hairpin nucleic acid probes have been highly useful in many areas, especially for intracellular and in vitro nucleic acid detection. The success of these probes can be attributed to the ease with which their conformational change upon target binding can be coupled to a variety of signal transduction mechanisms. However, false-positive signals arise from the opening of the hairpin due mainly to thermal fluctuations and stem invasions. Stem invasions occur when the stem interacts with its complementary sequence and are especially problematic in complex biological samples. To address the problem of stem invasions in hairpin probes, we have created a modified molecular beacon that incorporates unnatural enantiomeric l-DNA in the stem and natural d-DNA or 2'-O-Me-modified RNA in the loop. l-DNA has the same physical characteristics as d-DNA except that l-DNA cannot form stable duplexes with d-DNA. Here we show that incorporating l-DNA into the stem region of a molecular beacon reduces intra- and intermolecular stem invasions, increases the melting temperature, improves selectivity to its target, and leads to enhanced bio-stability. Our results suggest that l-DNA is useful for designing functional nucleic acid probes especially for biological applications.

  20. Architecture based on the integration of intermolecular G-quadruplex structure with sticky-end pairing and colorimetric detection of DNA hybridization

    NASA Astrophysics Data System (ADS)

    Li, Hongbo; Wu, Zai-Sheng; Shen, Zhifa; Shen, Guoli; Yu, Ruqin

    2014-01-01

    An interesting discovery is reported in that G-rich hairpin-based recognition probes can self-assemble into a nano-architecture based on the integration of an intermolecular G-quadruplex structure with the sticky-end pairing effect in the presence of target DNAs. Moreover, GNPs modified with partly complementary DNAs can intensively aggregate by hybridization-based intercalation between intermolecular G-quadruplexes, indicating an inspiring assembly mechanism and a powerful colorimetric DNA detection. The proposed intermolecular G-quadruplex-integrated sticky-end pairing assembly (called GISA)-based colorimetric system allows a specific and quantitative assay of p53 DNA with a linear range of more than two orders of magnitude and a detection limit of 0.2 nM, suggesting a considerably improved analytical performance. And more to the point, the discrimination of single-base mismatched target DNAs can be easily conducted via visual observation. The successful development of the present colorimetric system, especially the GISA-based aggregation mechanism of GNPs is different from traditional approaches, and offers a critical insight into the dependence of the GNP aggregation on the structural properties of oligonucleotides, opening a good way to design colorimetric sensing probes and DNA nanostructure. An interesting discovery is reported in that G-rich hairpin-based recognition probes can self-assemble into a nano-architecture based on the integration of an intermolecular G-quadruplex structure with the sticky-end pairing effect in the presence of target DNAs. Moreover, GNPs modified with partly complementary DNAs can intensively aggregate by hybridization-based intercalation between intermolecular G-quadruplexes, indicating an inspiring assembly mechanism and a powerful colorimetric DNA detection. The proposed intermolecular G-quadruplex-integrated sticky-end pairing assembly (called GISA)-based colorimetric system allows a specific and quantitative assay of p53 DNA

  1. Intermolecular vibrations in hydrophobic amino acid crystals: experiments and calculations.

    PubMed

    Williams, Michael R C; Aschaffenburg, Daniel J; Ofori-Okai, Benjamin K; Schmuttenmaer, Charles A

    2013-09-12

    Intermolecular vibrations of amino acid crystals occur in the THz, or far-infrared, region of the electromagnetic spectrum. We have measured the THz and Raman spectra of DL-leucine as well as two polymorphs of DL-valine, the spectroscopic properties of which have not previously been compared. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals interactions between molecules are not accounted for in standard density functional theory. Therefore, to calculate the vibrational modes, we used a recently developed approach that includes these nonlocal electron correlation forces. We discuss methods for comparing results from different theoretical models using metrics other than calculated vibrational frequency and intensity, and we also report a new approach enabling concise comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements.

  2. Intramolecular versus intermolecular disulfide bonds in prion proteins.

    PubMed

    Welker, Ervin; Raymond, Lynne D; Scheraga, Harold A; Caughey, Byron

    2002-09-01

    Prion protein (PrP) is the major component of the partially protease-resistant aggregate that accumulates in mammals with transmissible spongiform encephalopathies. The two cysteines of the scrapie form, PrP(Sc), were found to be in their oxidized (i.e. disulfide) form (Turk, E., Teplow, D. B., Hood, L. E., and Prusiner, S. B. (1988) Eur. J. Biochem. 176, 21-30); however, uncertainty remains as to whether the disulfide bonds are intra- or intermolecular. It is demonstrated here that the monomers of PrP(Sc) are not linked by intermolecular disulfide bonds. Furthermore, evidence is provided that PrP(Sc) can induce the conversion of the oxidized, disulfide-intact form of the monomeric cellular prion protein to its protease-resistant form without the temporary breakage and subsequent re-formation of the disulfide bonds in cell-free reactions.

  3. Separation of intra- and intermolecular contributions to the PELDOR signal

    NASA Astrophysics Data System (ADS)

    Schöps, Philipp; Plackmeyer, Jörn; Marko, Andriy

    2016-08-01

    Pulsed Electron-electron Double Resonance (PELDOR) is commonly used to measure distances between native paramagnetic centers or spin labels attached to complex biological macromolecules. In PELDOR the energies of electron magnetic dipolar interactions are measured by analyzing the oscillation frequencies of the recorded time resolved signal. Since PELDOR is an ensemble method, the detected signal contains contributions from intramolecular, as well as intermolecular electron spin interactions. The intramolecular part of the signal contains the information about the structure of the studied molecules, thus it is very important to accurately separate intra- and intermolecular contributions to the total signal. This separation can become ambiguous, when the length of the PELDOR signal is not much longer than twice the oscillation period of the signal. In this work we suggest a modulation depth scaling method, which can use short PELDOR signals in order to extract the intermolecular contribution. Using synthetic data we demonstrate the advantages of the new approach and analyze its stability with regard to signal noise. The method was also successfully tested on experimental data of three systems measured at Q-Band frequencies, two model compounds in deuterated and protonated solvents and one biological sample, namely BetP. The application of the new method with an assigned value of the signal modulation depth enables us to determine the interspin distances in all cases. This is especially interesting for the model compound with an interspin distance of 5.2 nm in the protonated solvent and the biological sample, since an accurate separation of the intra- and intermolecular PELDOR signal contributions would be difficult with the standard approach in those cases.

  4. Covalent intermolecular interaction of the nitric oxide dimer (NO)2

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Zheng, Gui-Li; Lv, Gang; Geng, Yi-Zhao; Ji, Qing

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  5. Morphology development in polymer blends exhibiting strong intermolecular interactions

    SciTech Connect

    Weiss, R.A.; Feng, Y.; Han, C.C.; Karim, A.

    1996-12-31

    He et al. measured the spinodal decomposition (SD) kinetics of a blend of poly(butyl methacrylate) with a polystyrene modified with 1.5 mol% of a hydroxy-containing comonomer that exhibited intermolecular hydrogen bonding, who studied blends. For small excursions into the spinodal region, multiple structures developed in the blend, which suggested that multiple mechanisms may be involved in the phase separation process. For most cases, however, the kinetics of phase separation followed Cahn-Hilliard theory in the early stage of spinodal decomposition and a self-similar mechanism in the later stages, similar to non-associating polymer blends such as PS/PVME. The failure to observe an effect of a specific intermolecular interaction on SD kinetics may be a consequence of the low concentration of hydroxyl groups on the polystyrene, ca. five per chain, and the weakening of the hydrogen bond at the elevated temperatures used to study phase separation where the crosslink effect of hydrogen bonding may not be significant. At elevated temperatures, the association-dissociation equilibrium shifts towards non-associated hydroxyl and ester groups. An objective of the present study was to use a polymer blend having a relatively higher degree of intermolecular association at the phase separation temperature and to investigate how physical crosslinks affect the phase separation kinetics accompanying spinodal decomposition.

  6. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

    A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed. PMID:25353178

  7. Reliable prediction of three-body intermolecular interactions using dispersion-corrected second-order Møller-Plesset perturbation theory

    SciTech Connect

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-28

    Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.

  8. Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins.

    PubMed

    Sorci, Mirco; Dassa, Bareket; Liu, Hongwei; Anand, Gaurav; Dutta, Amit K; Pietrokovski, Shmuel; Belfort, Marlene; Belfort, Georges

    2013-06-18

    In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 μm/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair.

  9. Rubrene: The Interplay between Intramolecular and Intermolecular Interactions Determines the Planarization of Its Tetracene Core in the Solid State.

    PubMed

    Sutton, Christopher; Marshall, Michael S; Sherrill, C David; Risko, Chad; Brédas, Jean-Luc

    2015-07-15

    Rubrene is one of the most studied molecular semiconductors; its chemical structure consists of a tetracene backbone with four phenyl rings appended to the two central fused rings. Derivatization of these phenyl rings can lead to two very different solid-state molecular conformations and packings: One in which the tetracene core is planar and there exists substantive overlap among neighboring π-conjugated backbones; and another where the tetracene core is twisted and the overlap of neighboring π-conjugated backbones is completely disrupted. State-of-the-art electronic structure calculations show for all isolated rubrene derivatives that the twisted conformation is more favorable (by -1.7 to -4.1 kcal mol(-1)), which is a consequence of energetically unfavorable exchange-repulsion interactions among the phenyl side groups. Calculations based on available crystallographic structures reveal that planar conformations of the tetracene core in the solid state result from intermolecular interactions that can be tuned through well-chosen functionalization of the phenyl side groups and lead to improved intermolecular electronic couplings. Understanding the interplay of these intramolecular and intermolecular interactions provides insight into how to chemically modify rubrene and similar molecular semiconductors to improve the intrinsic materials electronic properties. PMID:26075966

  10. Intermolecular chiral recognition probed by enantiodifferential excited-state quenching kinetics.

    PubMed

    Stockman, T G; Klevickis, C A; Grisham, C M; Richardson, F S

    1996-01-01

    Time-resolved chiroptical luminescence (TR-CL) measurements are used to study the kinetics of chirality-dependent excited-state quenching processes in aqueous solution. Experiments are carried out on samples that contain a racemic mixture of chiral luminophore molecules (L) in solution with a small, optically active concentration of chiral quencher molecules (Q). The luminophores are excited with a pulse of unpolarized light to create an initially racemic excited-state population of lambda L* and delta L* enantiomers, and TR-CL measurements are then used to monitor the differential decay kinetics of the lambda L* and delta L* subpopulations. Observed differences between the lambda L* and delta L* decay kinetics reflect differential rate processes and efficiencies for lambda L*-Q versus delta L*-Q quenching actions, and they are diagnostic of chiral discriminatory interactions between the luminophore and quencher molecules. In this study, the luminophores are either Eu(dpa)3(3-) or Tb(dpa)3(3-) coordination complexes (where dpa denotes a dipicolinate dianion ligand), and the quenchers are diastereomeric structures of Cr(H2O)4(ATP), Rh(H2O)4(ATP) and Rh(H2O)3(ATP) (where ATP identical to adenosine triphosphate). The Ln(dpa)3(3-) (Ln identical to En3+ or Tb3+) complexes have three-bladed propeller-like structures of D3 symmetry, and in aqueous solution they exist as a racemic mixture of left-handed (lambda) and right-handed (delta) configurational isomers (enantiomers). The results show that the chiral quencher molecules can distinguish between the lambda and delta enantiomeric structures of the luminophores in their excited-state quenching actions. The degree and sense of enantiomeric preference in these quenching actions are governed by the electronic and stereochemical properties of the quencher molecules. Twenty-one different luminophore-quencher systems are examined in this study, and they exhibit interestingly diverse enantiodifferential quenching kinetics. The results reflect the extraordinary sensitivity of chiral recognition and discrimination processes to relatively small, and sometimes subtle, changes in molecular electronic and stereochemical structure.

  11. Computing free energy hypersurfaces for anisotropic intermolecular associations.

    PubMed

    Strümpfer, Johan; Naidoo, Kevin J

    2010-01-30

    We previously used an adaptive reaction coordinate force biasing method for calculating the free energy of conformation (Naidoo and Brady, J Am Chem Soc 1999, 121, 2244) and chemical reactions (Rajamani et al., J Comput Chem 2003, 24, 1775) amongst others. Here, we describe a generalized version able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces method. To illustrate it, we describe how we calculate a multidimensional intermolecular orientational free energy, which can be used to investigate complex systems such as protein conformation and liquids. This multidimensional intermolecular free energy W(r, theta(1), theta(2), phi) provides a measure of orientationally dependent interactions that are appropriate for applications in systems that inherently have molecular anisotropic features. It is a highly informative free energy volume, which can be used to parameterize key terms such as the Gay-Berne intermolecular potential in coarse grain simulations. To demonstrate the value of the information gained from the W(r, theta(1), theta(2), phi) hypersurfaces we calculated them for TIP3P, TIP4P, and TIP5P dimer water models in vacuum. A comparison with a commonly used one-dimensional distance free energy profile is made to illustrate the significant increase in configurational information. The W(r) plots show little difference between the three models while the W(r, theta(1), theta(2), phi) hypersurfaces reveal the underlying energetic reasons why these potentials reproduce tetrahedrality in the condensed phase so differently from each.

  12. Photon Antibunching in Complex Intermolecular Fluorescence Quenching Kinetics.

    PubMed

    Sharma, Arjun; Enderlein, Jörg; Kumbhakar, Manoj

    2016-08-18

    We present a novel fluorescence spectroscopic method, which combines fluorescence antibunching, time-correlated single-photon counting (TCSPC), and steady-state emission spectroscopy, to study chemical reactions at the single molecule level. We exemplify our method on investigating intermolecular fluorescence quenching of Rhodamine110 by aniline. We demonstrate that the combination of measurements of fluorescence antibunching, fluorescence lifetime, and fluorescence steady state intensity, captures the full picture of the complex quenching kinetics, which involves static and dynamics quenching, and which cannot be seen by steady-state or lifetime measurements alone. PMID:27468007

  13. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  14. Resonance Raman spectra of organic molecules absorbed on inorganic semiconducting surfaces: Contribution from both localized intramolecular excitation and intermolecular charge transfer excitation

    SciTech Connect

    Ye, ChuanXiang; Zhao, Yi E-mail: liangwz@xmu.edu.cn; Liang, WanZhen E-mail: liangwz@xmu.edu.cn

    2015-10-21

    The time-dependent correlation function approach for the calculations of absorption and resonance Raman spectra (RRS) of organic molecules absorbed on semiconductor surfaces [Y. Zhao and W. Z. Liang, J. Chem. Phys. 135, 044108 (2011)] is extended to include the contribution of the intermolecular charge transfer (CT) excitation from the absorbers to the semiconducting nanoparticles. The results demonstrate that the bidirectionally interfacial CT significantly modifies the spectral line shapes. Although the intermolecular CT excitation makes the absorption spectra red shift slightly, it essentially changes the relative intensities of mode-specific RRS and causes the oscillation behavior of surface enhanced Raman spectra with respect to interfacial electronic couplings. Furthermore, the constructive and destructive interferences of RRS from the localized molecular excitation and CT excitation are observed with respect to the electronic coupling and the bottom position of conductor band. The interferences are determined by both excitation pathways and bidirectionally interfacial CT.

  15. Spectrophotometric probe

    DOEpatents

    Prather, William S.; O'Rourke, Patrick E.

    1994-01-01

    A support structure bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe.

  16. Spectrophotometric probe

    DOEpatents

    Prather, W.S.; O'Rourke, P.E.

    1994-08-02

    A support structure is described bearing at least one probe for making spectrophotometric measurements of a fluid using a source of light and a spectrophotometer. The probe includes a housing with two optical fibers and a planoconvex lens. A sleeve bearing a mirror surrounds the housing. The lens is separated from the mirror by a fixed distance, defining an interior space for receiving a volume of the fluid sample. A plurality of throughholes extending through the sleeve communicate between the sample volume and the exterior of the probe, all but one hole bearing a screen. A protective jacket surrounds the probe. A hollow conduit bearing a tube is formed in the wall of the probe for venting any air in the interior space when fluid enters. The probe is held at an acute angle so the optic fibers carrying the light to and from the probe are not bent severely on emergence from the probe. 3 figs.

  17. Characterization of intermolecular structure of β(2)-microglobulin core fragments in amyloid fibrils by vacuum-ultraviolet circular dichroism spectroscopy and circular dichroism theory.

    PubMed

    Matsuo, Koichi; Hiramatsu, Hirotsugu; Gekko, Kunihiko; Namatame, Hirofumi; Taniguchi, Masaki; Woody, Robert W

    2014-03-20

    Intermolecular structures are important factors for understanding the conformational properties of amyloid fibrils. In this study, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy and circular dichroism (CD) theory were used for characterizing the intermolecular structures of β2-microglobulin (β2m) core fragments in the amyloid fibrils. The VUVCD spectra of β2m20-41, β2m21-31, and β2m21-29 fragments in the amyloid fibrils exhibited characteristic features, but they were affected not only by the backbone conformations but also by the aromatic side-chain conformations. To estimate the contributions of aromatic side-chains to the spectra, the theoretical spectra were calculated from the simulated structures of β2m21-29 amyloid fibrils with various types of β-sheet stacking (parallel or antiparallel) using CD theory. We found that the experimental spectrum of β2m21-29 fibrils is largely affected by aromatic-backbone couplings, which are induced by the interaction between transitions within the aromatic and backbone chromophores, and these couplings are sensitive to the type of stacking among the β-sheets of the fibrils. Further theoretical analyses of simulated structures incorporating mutated aromatic residues suggested that the β2m21-29 fibrils are composed of amyloid accumulations in which the parallel β-sheets stack in an antiparallel manner and that the characteristic Phe-Tyr interactions among the β-sheet stacks affect the aromatic-backbone coupling. These findings indicate that the coupling components, which depend on the characteristic intermolecular structures, induce the spectral differences among three fragments in the amyloid fibrils. These advanced spectral analyses using CD theory provide a useful method for characterizing the intermolecular structures of protein and peptide fragment complexes.

  18. Intermolecular Hybridization Creating Nanopore Orbital in a Supramolecular Hydrocarbon Sheet.

    PubMed

    Zhang, Yi-Qi; Björk, Jonas; Barth, Johannes V; Klappenberger, Florian

    2016-07-13

    Molecular orbital engineering is a key ingredient for the design of organic devices. Intermolecular hybridization promises efficient charge carrier transport but usually requires dense packing for significant wave function overlap. Here we use scanning tunneling spectroscopy to spatially resolve the electronic structure of a surface-confined nanoporous supramolecular sheet of a prototypical hydrocarbon compound featuring terminal alkyne (-CCH) groups. Surprisingly, localized nanopore orbitals are observed, with their electron density centered in the cavities surrounded by the functional moieties. Density functional theory calculations reveal that these new electronic states originate from the intermolecular hybridization of six in-plane π-orbitals of the carbon-carbon triple bonds, exhibiting significant electronic splitting and an energy downshift of approximately 1 eV. Importantly, these nanopore states are distinct from previously reported interfacial states. We unravel the underlying connection between the formation of nanopore orbital and geometric arrangements of functional groups, thus demonstrating the generality of applying related orbital engineering concepts in various types of porous organic structures.

  19. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  20. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-01-01

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations. PMID:26306198

  1. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGES

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

  2. Quantitative analysis of intermolecular interactions in orthorhombic rubrene.

    PubMed

    Hathwar, Venkatesha R; Sist, Mattia; Jørgensen, Mads R V; Mamakhel, Aref H; Wang, Xiaoping; Hoffmann, Christina M; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-09-01

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H-H interactions. The electron density features of H-H bonding, and the interaction energy of molecular dimers connected by H-H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations. PMID:26306198

  3. Difference between ²JC2H3 and ²JC3H2 spin-spin couplings in heterocyclic five- and six-membered rings as a probe for studying σ-ring currents: a quantum chemical analysis.

    PubMed

    Contreras, Rubén H; dos Santos, Francisco P; Ducati, Lucas C; Tormena, Cláudio F

    2010-12-01

    Adequate analyses of canonical molecular orbitals (CMOs) can provide rather detailed information on the importance of different σ-Fermi contact (FC) coupling pathways (FC term transmitted through the σ-skeleton). Knowledge of the spatial distribution of CMOs is obtained by expanding them in terms of natural bond orbitals (NBOs). Their relative importance for transmitting the σ-FC contribution to a given spin-spin coupling constants (SSCCs) is estimated by resorting to the expression of the FC term given by the polarisation propagator formalism. In this way, it is possible to classify the effects affecting such couplings in two different ways: delocalisation interactions taking place in the neighbourhood of the coupling nuclei and 'round the ring' effects. The latter, associated with σ-ring currents, are observed to yield significant differences between the FC terms of (2)J(C2H3) and (2)J(C3H2) SSCCs which, consequently, are taken as probes to gauge the differences in σ-ring currents for the five-membered rings (furan, thiophene, selenophene and pyrrol) and also for the six-membered rings (benzene, pyridine, protonated pyridine and N-oxide pyridine) used in the present study.

  4. Swan probe: A nanoliter-scale and high-throughput sampling interface for coupling electrospray ionization mass spectrometry with microfluidic droplet array and multiwell plate.

    PubMed

    Jin, Di-Qiong; Zhu, Ying; Fang, Qun

    2014-11-01

    Mass spectrometry provides a versatile detection method for high-throughput drug screening because it permits the use of native biological substrates and the direct quantification of unlabeled reaction products. This paper describes the design and application of a Swan-shaped probe for high-throughput and nanoliter-scale analysis of biological samples in both a microfluidic droplet array and a multiwell plate with electrospray ionization mass spectrometry (ESI-MS). The Swan probe is fabricated using a single capillary with quite low cost, and it consists of a U-shaped section with a micrometer-sized hole for sampling and a tapered tip for sample electrospray ionization. Continuous sample introduction was carried out under both sampling modes of push-pull and spontaneous injection by sequentially dipping the probe in the sample solutions and then removing them. High-throughput and reliable ESI-MS analysis was achieved in analyzing 256 droplets within 90 min with a peak height RSD of 12.6% (n = 256). To validate its potential in drug discovery, the present system was applied in the screening of inhibitors of acetylcholinesterase (AchE) and the measurement of the IC50 values of identified inhibitors. PMID:25302930

  5. On the effect of a radiation field in modifying the intermolecular interaction between two chiral molecules

    SciTech Connect

    Salam, A.

    2006-01-07

    The change in the mutual energy of interaction between a pair of chiral molecules coupled via the exchange of a single virtual photon and in the presence of an electromagnetic field is calculated using nonrelativistic quantum electrodynamics. The particular viewpoint adopted is one that has an intuitive physical appeal and resembles a classical treatment. It involves the coupling of electric and magnetic dipole moments induced at each center by the incident radiation field to the resonant dipole-dipole interaction tensor. The energy shift is evaluated for fixed as well as random orientations of the molecular pair with respect to the direction of propagation of the field. A complete polarization analysis is carried out for the former situation by examining the effect of incident radiation that is linearly or circularly polarized and traveling in a direction that is parallel or perpendicular to the intermolecular distance vector. After tumble averaging, all polarization dependence of the energy shift vanishes. In both cases the interaction energy is directly proportional to the irradiance of the applied field, and is discriminatory, changing sign when one optically active species is replaced by its enantiomer. The asymptotic behavior of the energy shift at the limits of large and small separations is also studied.

  6. Keto-enol tautomerization and intermolecular proton transfer in photoionized cyclopentanone dimer in the gas phase

    SciTech Connect

    Ghosh, Arup K.; Chatterjee, Piyali; Chakraborty, Tapas

    2014-07-28

    Time-of-flight mass spectra of cyclopentanone and its clusters cooled in a supersonic jet expansion have been measured following 4-, 3-, and 2-photon ionizations by the 2nd, 3rd, and 4th harmonic wavelengths, respectively, of a Q-switched Nd:YAG laser. The mass spectra reveal signatures of energetically favored keto to enol tautomerization of the molecular ion leading to intermolecular proton transfer, and this observation is found sharply dependent on the ionization wavelengths used. Electronic structure calculation predicts that in spite of the energetic preference, keto-enol conversion barrier of isolated molecular ion is high. However, the barrier is significantly reduced in a CH⋯O hydrogen-bonded dimer of the molecule. The transition states associated with tautomeric conversion of both cyclopentanone monomer and dimer cations have been identified by means of intrinsic reaction co-ordinate calculation. In a supersonic jet expansion, although a weakly bound dimer is readily generated, the corresponding cation and also the protonated counterpart are observed only for ionization by 532 nm. For other two ionization wavelengths, these species do not register in the mass spectra, where the competing reaction channels via α-cleavage of the ring become dominant. In contrast to the report of a recent study, we notice that the intact molecular ion largely survives fragmentations when ionized from the 2-photon resonant 3p Rydberg state as intermediate using nanosecond laser pulses, and the corresponding resonant 3-photon ionization spectrum has been recorded probing the intact molecular ion.

  7. Biaxial Dielectrophoresis Force Spectroscopy: A Stoichiometric Approach for Examining Intermolecular Weak Binding Interactions.

    PubMed

    Park, In Soo; Kwak, Tae Joon; Lee, Gyudo; Son, Myeonggu; Choi, Jeong Woo; Choi, Seungyeop; Nam, Kihwan; Lee, Sei-Young; Chang, Woo-Jin; Eom, Kilho; Yoon, Dae Sung; Lee, Sangyoup; Bashir, Rashid; Lee, Sang Woo

    2016-04-26

    The direct quantification of weak intermolecular binding interactions is very important for many applications in biology and medicine. Techniques that can be used to investigate such interactions under a controlled environment, while varying different parameters such as loading rate, pulling direction, rupture event measurements, and the use of different functionalized probes, are still lacking. Herein, we demonstrate a biaxial dielectrophoresis force spectroscopy (BDFS) method that can be used to investigate weak unbinding events in a high-throughput manner under controlled environments and by varying the pulling direction (i.e., transverse and/or vertical axes) as well as the loading rate. With the BDFS system, we can quantitatively analyze binding interactions related to hydrogen bonding or ionic attractions between functionalized microbeads and a surface within a microfluidic device. Our BDFS system allowed for the characterization of the number of bonds involved in an interaction, bond affinity, kinetic rates, and energy barrier heights and widths from different regimes of the energy landscape. PMID:27007455

  8. Probing the top-Higgs coupling through the secondary lepton distributions in the associated production of the top-quark pair and Higgs boson at the LHC

    NASA Astrophysics Data System (ADS)

    Kołodziej, Karol; Słapik, Aleksandra

    2015-10-01

    We complement the analysis of the anomalous top-Higgs coupling effects on the secondary lepton distributions in the associated production of the top-quark pair and Higgs boson in proton-proton collisions at the LHC of the former work by one of the present authors by taking into account the quark-antiquark production mechanism. We also present simple arguments which explain why the effects of the scalar and pseudoscalar anomalous couplings on the unpolarized cross section of the process are completely insensitive to the sign of either of them.

  9. Copper nanocluster coupling europium as an off-to-on fluorescence probe for the determination of phosphate ion in water samples.

    PubMed

    Cao, Haiyan; Chen, Zhaohui; Huang, Yuming

    2015-10-01

    This paper reports an "off-to-on" fluorescence (FL) probe for sensitively and selectively detecting phosphate ions (Pi's). Fabrication of the probe was based on the competition between Pi's and tannic acid-stabilized copper nanoclusters (TA-Cu NCs) for Eu(3+) binding. The addition of Eu(3+) ions to TA-Cu NCs triggered the aggregation of TA-Cu NCs, which quenched the FL of TA-Cu NCs. After Pi addition, the aggregated TA-Cu NCs solubilized into the aqueous solution to facilitate the Pi-triggered dispersion of TA-Cu NCs. This phenomenon was due to the stronger binding ability between Pi's and Eu(3+) than that between TA and Eu(3+), leading to FL recovery of Cu NCs. The degree of redispersion of TA-Cu NCs was directly related to Pi concentration. Thus, Pi concentration can be quantitatively determined by the change in FL of the TA-Cu NCs dispersion. Under the optimized conditions, the change in FL presented a linear relationship with Pi concentration from 0.07 μmol L(-1) to 80 μmol L(-1). The limit of detection for Pi was 9.6×10(-3) μmol L(-1) at a signal-to-noise ratio of 3. For Pi determination in real samples, only 1 mL water sample was needed. The proposed probe was highly sensitive, free from the interference of other common species in aqueous media, and particularly useful for the fast and simple diagnosis of water-eutrophication extent.

  10. Search for W' boson resonances decaying to a top and a bottom quark and probing anomalous Wtb couplings with 1 fb{sup -1} of D0 Data

    SciTech Connect

    Badaud, Frederique

    2008-11-23

    With the first evidence for single top quark production in the D0 detector at the Fermilab Tevatron pp-bar collider, the single top quark cross section is measured, limits on the masses of heavy W' boson resonances are set and anomalous Wtb couplings are studied.

  11. Thermodynamic curvature for attractive and repulsive intermolecular forces.

    PubMed

    May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George

    2013-09-01

    The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential.

  12. Atomic force microscopy measurements of intermolecular binding forces.

    PubMed

    Misevic, Gradimir N; Karamanos, Yannis; Misevic, Nikola J

    2009-01-01

    Atomic force microscopy (AFM) measurements of intermolecular binding strength between a single pair of complementary cell adhesion molecules in physiological solutions provided the first quantitative evidence for their cohesive function. This novel AFM-based nanobiotechnology opens a molecular mechanic approach for studying structure- to function-related properties of any type of individual biological macromolecules. The presented example of Porifera cell adhesion glyconectin proteoglycans showed that homotypic carbohydrate to carbohydrate interactions between two primordial proteoglycans can hold the weight of 1,600 cells. Thus, glyconectin type carbohydrates, as the most peripheral cell surface molecules of sponges (today's simplest living Metazoa), are proposed to be the primary cell adhesive molecules essential for the evolution of the multicellularity.

  13. Van der Waals Interactions in Density Functional Theory: Intermolecular Complexes

    NASA Astrophysics Data System (ADS)

    Kannemann, Felix; Becke, Axel

    2010-03-01

    Conventional density functional theory (GGA and hybrid functionals) fails to account for dispersion interactions and is therefore not applicable to systems where van der Waals interactions play a dominant role, such as intermolecular complexes and biomolecules. The exchange-hole dipole moment (XDM) dispersion model of Becke and Johnson [A. D. Becke and E. R. Johnson, J. Chem. Phys. 127, 154108 (2007)] corrects for this deficiency. We have previously shown that the XDM dispersion model can be combined with standard GGA functionals (PW86 for exchange and PBE for correlation) to give accurate binding energy curves for rare-gas diatomics [F. O. Kannemann and A. D. Becke, J. Chem. Theory Comput. 5, 719 (2009)]. Here we present further tests of the GGA-XDM method using benchmark sets including hydrogen bonding, electrostatic, dispersion and stacking interactions, and systems ranging from rare-gas diatomics to biomolecular complexes.

  14. Intermolecular-charge-transfer-induced fluorescence quenching in protic solvent

    NASA Astrophysics Data System (ADS)

    Lin, Tao; Liu, Xiaojun; Lou, Zhidong; Hou, Yanbing; Teng, Feng

    2016-11-01

    The fluorescence quenching of fluorenone in protic solvent has been extensively investigated, and the intermolecular hydrogen bond was found to play a crucial role. Unfortunately, the mechanism at atomic level is still not clear. In the present work, we theoretically put forward the charge transfer along the hydrogen bond in the excited states. The vertical excitation energies of the fluorenone-methanol complex as well as the potential energy profiles and surfaces of the vertical excited states and charge transfer states were calculated by using the ab initio electronic-structure methods. The photochemical reactions occurring in the diverse charge transfer states were compared and their decisiveness to the fluorescence quenching was discussed in the paper.

  15. Dissecting Anion Effects in Gold(I)-Catalyzed Intermolecular Cycloadditions

    PubMed Central

    Homs, Anna; Obradors, Carla; Lebœuf, David; Echavarren, Antonio M

    2014-01-01

    From a series of gold complexes of the type [t-BuXPhosAu(MeCN)]X (X=anion), the best results in intermolecular gold(I)-catalyzed reactions are obtained with the complex with the bulky and soft anion BAr4F− [BAr4F−=3,5-bis(trifluoromethyl)phenylborate] improving the original protocols by 10–30% yield. A kinetic study on the [2+2] cycloaddition reaction of alkynes with alkenes is consistent with an scenario in which the rate-determining step is the ligand exchange to generate the (η2-phenylacetylene)gold(I) complex. We have studied in detail the subtle differences that can be attributed to the anion in this formation, which result in a substantial decrease in the formation of unproductive σ,π-(alkyne)digold(I) complexes by destabilizing the conjugated acid formed. PMID:26190958

  16. Transetherification on Polyols by Intra- and Intermolecular Nucleophilic Substitutions

    PubMed Central

    Muraoka, Takahiro; Adachi, Kota; Chowdhury, Rainy; Kinbara, Kazushi

    2014-01-01

    Transetherification on polyols involving intra- and intermolecular nucleophilic substitutions is reported. Di- or trialkoxide formation of propane-1,3-diol or 2-(hydroxymethyl)propane-1,3-diol derivatives by NaH triggers the reaction via oxetanes formation, where the order to add NaH and a polyol significantly influences the yields of products. It was demonstrated that the protective group on the pentaerythritol skeleton is apparently transferred to the hydrophilic and hydrophobic chain molecules bearing a leaving group in one-step, and a protective group conversion from tosyl to benzyl was successful using a benzyl-appending triol to afford a desired product in 67% yield. PMID:24663293

  17. Multiplex quantitative foodborne pathogen detection using high resolution CE-SSCP coupled stuffer-free multiplex ligation-dependent probe amplification.

    PubMed

    Chung, Boram; Shin, Gi Won; Na, Jeongkyeong; Oh, Mi-Hwa; Jung, Gyoo Yeol

    2012-05-01

    Sensitive multiplex detection methods for foodborne pathogens are important in controlling food safety, and detection of genetic markers is accepted to be one of the best tools for sensitive detection. Although CE technology offers great potential in terms of sensitive multiplex detection, the necessary amplification is confined to markers sharing common primers such as the 16S rRNA gene. For precise and sensitive detection, pathogen-specific genes are optimal markers. Although multiplex ligation-dependent probe amplification (MLPA) is appropriate for amplification of specific markers, the requirement for stuffers, to ensure length-dependent separation on CE, is a major obstacle in detection of foodborne pathogens. In the present study, we developed stuffer-free MLPA using high-resolution CE-SSCP to sensitively detect ten foodborne pathogens. The probe set for MLPA prior to CE-SSCP analysis was designed for species-specific detection. After careful optimization of each MLPA step, to ensure that CE-SSCP analysis was informative, we found that all ten pathogens could be reliably identified; the limits of detection were 0.5-5 pg of genomic DNA, and more than 100-fold increase could be quantitatively determined. Thus, MLPA-CE-SSCP is a sensitive and reliable technique for pathogen detection.

  18. Evaluation of intermolecular forces in a circulating system.

    PubMed

    Guo, Qiuquan; Liu, Mei; Yang, Jun

    2011-11-01

    Intercellular interactions, which are mediated by a variety of complex intercellular molecules through the processes of formation and dissociation of molecular bonds, play a critical role in regulating cellular functions in biological systems. Various approaches are applied to evaluate intercellular or molecular bonding forces. To quantify the intermolecular interaction forces, flow chamber has become a meaningful technique as it can ultimately mimic the cellular microenvironment in vivo under physiological flow conditions. Hydrodynamic forces are usually used to predict the intercellular forces down to the single molecular level. However, results show that only using hydrodynamic force will overestimate up to 30% of the receptor-ligand strength when the non-specific forces such as Derjaguin-Landau-Verway-Overbeek (DLVO) forces become un-neglected. Due to the nature of high ion concentration in the physiological condition, electrostatic force is largely screened which will cause DLVO force unbalanced. In this study, we propose to take account of the DLVO force, including van der Waals (VDW) force and electrostatic force, to predict the intermolecular forces of a cell doublet and cell-substrate model in a circulating system. Results also show that the DLVO force has a nonlinear effect as the cell-cell or cell-substrate distance changes. In addition, we used the framework of high accuracy hydrodynamic theories proved in colloidal systems. It is concluded that DLVO force could not be ignored in quantitative studies of molecular interaction forces in circulating system. More accurate prediction of intercellular forces needs to take account of both hydrodynamic force and DLVO force.

  19. Intermolecular potential functions from spectroscopic properties of weakly bound complexes

    SciTech Connect

    Muenter, J.S.

    1992-01-01

    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  20. Intermolecular Interactions in the Mechanism of Skeletal Muscle Sarcoplasmic Reticulum Ca2+-ATPase (SERCA1): Evidence for a Tri-protomer*

    PubMed Central

    Mahaney, James E.; Thomas, David D.; Farrance, Iain K.; Froehlich, Jeffrey P.

    2013-01-01

    Native membrane sarcoplasmic reticulum (SR) Ca2+-ATPase isolated from skeletal muscle (SERCA1) exhibits oligomeric kinetic behavior (Mahaney, J.E., Thomas, D.D., and Froehlich, J.P. (2004) Biochemistry 43:4400–4416). In the present study we used quenched-flow mixing, electron paramagnetic resonance (EPR) and chemical cross-linking to probe for intermolecular interactions at physiological (0.1M) and high (0.4 M) KCl. Exposure SR membranes to water- and lipid-soluble cross-linking reagents revealed a mixture of SERCA1 oligomeric species consisting mainly of dimers and trimers. Titration of iodoacetamide spin labeled-SERCA1 with AMPPCP in the presence of 10 µM Ca2+ and 0.1 M KCl revealed high (KD = 45 µM) and low affinity (KD = 315 µM) nucleotide binding sites in a 2:1 ratio, respectively. Raising the [KCl] to 0.4 M increased the fraction of weak binding sites and lowered the KD of the high affinity component (20 µM). Phosphorylation by 10 µM ATP at 21°C and 0.1 M KCl produced an early burst of Pi production without a corresponding decline in the steady state phosphoenzyme (EP) level. The steady state EP level was twice as large as the Pi burst and received equal contributions from E1P and E2P. Chasing the phosphoenzyme at 0.4 M KCl and 2°C with ADP revealed a biphasic time course of E1P formation with a slow phase that matched the kinetics of the transient EPR signal from the spin-labeled Ca2+-ATPase. The absence of a fast component in the EPR signal excludes E1P as its source. Instead, it arises from the slow, KCl-dependent transformation at the start of the cycle which controls the formation of downstream intermediates with an increased mole fraction of rotationally restricted probes. We modeled this behavior with a SERCA1 trimer in which the formation of E1P/E2/E2P from E1ATP/E2P/E1P results from concerted transformations in the subunits coupling phosphorylation (E1ATP → E1P + ADP) to dephosphorylation (E2P → E2 + Pi) and the conversion of E1P to E2P

  1. Problem-Based Learning in 9th Grade Chemistry Class: "Intermolecular Forces"

    ERIC Educational Resources Information Center

    Tarhan, Leman; Ayar-Kayali, Hulya; Urek, Raziye Ozturk; Acar, Burcin

    2008-01-01

    This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students' understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student's alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight…

  2. Synergy between twisted conformation and effective intermolecular interactions: strategy for efficient mechanochromic luminogens with high contrast.

    PubMed

    Yuan, Wang Zhang; Tan, Yeqiang; Gong, Yongyang; Lu, Ping; Lam, Jacky W Y; Shen, Xiao Yuan; Feng, Cunfang; Sung, Herman H-Y; Lu, Yawei; Williams, Ian D; Sun, Jing Zhi; Zhang, Yongming; Tang, Ben Zhong

    2013-05-28

    A strategy towards efficient mechanochromic luminogens with high contrast is developed. The twisted propeller-like conformations and effective intermolecular interactions not only endow the luminogens with AIE characteristics and high efficiency in the crystalline state, but also render them to undergo conformational planarization and disruption in intermolecular interactions upon mechanical stimuli, resulting in remarkable changes in emission wavelength and efficiency.

  3. Meeting the Challenge of Intermolecular Gold(I)-Catalyzed Cycloadditions of Alkynes and Allenes

    PubMed Central

    Muratore, Michael E; Homs, Anna; Obradors, Carla; Echavarren, Antonio M

    2014-01-01

    The development of gold(I)-catalyzed intermolecular carbo- and hetero-cycloadditions of alkynes and allenes has been more challenging than their intramolecular counterparts. Here we review, with a mechanistic perspective, the most fundamental intermolecular cycloadditions of alkynes and allenes with alkenes. PMID:25048645

  4. Liquid chromatography-inductively coupled plasma-based metallomic approaches to probe health-relevant interactions between xenobiotics and mammalian organisms.

    PubMed

    Gómez-Ariza, José Luis; Jahromi, Elham Zeini; González-Fernández, Macarena; García-Barrera, Tamara; Gailer, Jürgen

    2011-06-01

    In mammals, the transport of essential elements from the gastrointestinal tract to organs is orchestrated by biochemical mechanisms which have evolved over millions of years. The subsequent organ-based assembly of sufficient amounts of metalloproteins is a prerequisite to maintain mammalian health and well-being. The chronic exposure of various human populations to environmentally abundant toxic metals/metalloid compounds and/or the deliberate administration of medicinal drugs, however, can adversely affect these processes which may eventually result in disease. A better understanding of the perturbation of these processes has the potential to advance human health, but their visualization poses a major problem. Nonetheless, liquid chromatography-inductively coupled plasma-based 'metallomics' methods, however, can provide much needed insight. Size-exclusion chromatography-inductively coupled plasma atomic emission spectrometry, for example, can be used to visualize changes that toxic metals/medicinal drugs exert at the metalloprotein level when they are added to plasma in vitro. In addition, size-exclusion chromatography-inductively coupled plasma mass spectrometry can be employed to analyze organs from toxic metal/medicinal drug-exposed organisms for metalloproteins to gain insight into the biochemical changes that are associated with their acute or chronic toxicity. The execution of such studies-from the selection of an appropriate model organism to the generation of accurate analytical data-is littered with potential pitfalls that may result in artifacts. Drawing on recent lessons that were learned by two research groups, this tutorial review is intended to provide relevant information with regard to the experimental design and the practical application of these aforementioned metallomics tools in applied health research.

  5. Dynamics, NMR parameters and hyperfine coupling constants of the Fe3O4(1 0 0)-water interface: Implications for MRI probes

    NASA Astrophysics Data System (ADS)

    Gonçalves, Mateus A.; Peixoto, Fernando C.; da Cunha, Elaine F. F.; Ramalho, Teodorico C.

    2014-08-01

    Magnetite is an iron oxide widely used as contrast agent in MRI, receiving considerable interest from nanoscience and nanotechnology. In this work, the face 1 0 0 of the magnetite structure was studied with water in order to obtain 1H hyperfine coupling constants (HFCCs). Molecular dynamics (MD) calculations were performed using the ReaxFF program and for statistical inefficiency, structures were selected for HFCC and NMR calculations. From our theoretical findings, the magnetite in solution considerably increases the 1H HFCC of water molecules. From our results, it is essential to incorporate the dynamics and solvent effects into NMR calculations of relaxation parameters.

  6. Unparalleled Ease of Access to a Library of Biheteroaryl Fluorophores via Oxidative Cross-Coupling Reactions: Discovery of Photostable NIR Probe for Mitochondria.

    PubMed

    Cheng, Yangyang; Li, Gaocan; Liu, Yang; Shi, Yang; Gao, Ge; Wu, Di; Lan, Jingbo; You, Jingsong

    2016-04-13

    The development of straightforward accesses to organic functional materials through C-H activation is a revolutionary trend in organic synthesis. In this article, we propose a concise strategy to construct a large library of donor-acceptor-type biheteroaryl fluorophores via the palladium-catalyzed oxidative C-H/C-H cross-coupling of electron-deficient 2H-indazoles with electron-rich heteroarenes. The directly coupled biheteroaryl fluorophores, named Indazo-Fluors, exhibit continuously tunable full-color emissions with quantum yields up to 93% and large Stokes shifts up to 8705 cm(-1) in CH2Cl2. By further fine-tuning of the substituent on the core skeleton, Indazo-Fluor 3l (FW = 274; λem = 725 nm) is obtained as the lowest molecular weight near-infrared (NIR) fluorophore with emission wavelength over 720 nm in the solid state. The NIR dye 5h specifically lights up mitochondria in living cells with bright red luminescence. Typically, commercially available mitochondria trackers suffer from poor photostability. Indazo-Fluor 5h exhibits superior photostability and very low cytotoxicity, which would be a prominent reagent for in vivo mitochondria imaging. PMID:26854564

  7. Diagnostics of capacitively-coupled hydrocarbon plasmas for deposition of diamond-like carbon films using quadrupole mass spectrometry and Langmuir probe

    NASA Astrophysics Data System (ADS)

    Oda, Akinori; Fukai, Shun; Kousaka, Hiroyuki; Ohta, Takayuki

    2015-09-01

    Diamond-like carbon (DLC) films are the hydrogenated amorphous carbon films, which contains a mixture of sp2- and sp3-bonded carbon. The DLC films have been widely used for various applications, such as automotive, semiconductors, medical devices, since have excellent material properties in lower friction, higher chemical stability, higher hardness, higher wear resistance. Until now, numerous investigations on the DLC films using plasma assisted chemical vapor deposition have been done. For precise control of coating technique of DLC films, it is enormously important to clarify the fundamental properties in hydrocarbon plasmas, as a source of hydrocarbon ions and radicals. In this paper, the fundamental properties in a low pressure radio-frequency hydrocarbon (Ar/CH4 (1 %) gas mixture) plasmas have been diagnosed using a quadrupole mass spectrometer (HIDEN ANARYTICAL Ltd., EQP-300) and Langmuir probe system (HIDEN ANARYTICAL Ltd., ESPion). This work was partly supported by KAKENHI (No.26420247), and a ``Grant for Advanced Industrial Technology Development (No.11B06004d)'' in 2011 from the New Energy and Industrial Technology Development Organization (NEDO) of Japan.

  8. Experimental probes of axions

    SciTech Connect

    Chou, Aaron S.; /Fermilab

    2009-10-01

    Experimental searches for axions or axion-like particles rely on semiclassical phenomena resulting from the postulated coupling of the axion to two photons. Sensitive probes of the extremely small coupling constant can be made by exploiting familiar, coherent electromagnetic laboratory techniques, including resonant enhancement of transitions using microwave and optical cavities, Bragg scattering, and coherent photon-axion oscillations. The axion beam may either be astrophysical in origin as in the case of dark matter axion searches and solar axion searches, or created in the laboratory from laser interactions with magnetic fields. This note is meant to be a sampling of recent experimental results.

  9. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    SciTech Connect

    Osiry, H.; Cano, A.; Lemus-Santana, A.A.; Rodríguez, A.; Carbonio, R.E.; Reguera, E.

    2015-10-15

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  10. Intermolecular forces between low generation PAMAM dendrimer condensed DNA helices: role of cation architecture.

    PubMed

    An, Min; Parkin, Sean R; DeRouchey, Jason E

    2014-01-28

    In recent years, dendriplexes, complexes of cationic dendrimers with DNA, have become attractive DNA delivery vehicles due to their well-defined chemistries. To better understand the nature of the forces condensing dendriplexes, we studied low generation poly(amidoamine) (PAMAM) dendrimer-DNA complexes and compared them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we have investigated the effect of molecular chain architecture on DNA-DNA intermolecular forces that determine the net attraction and equilibrium interhelical distance within these polycation condensed DNA arrays. In order to compact DNA, linear cations are believed to bind in DNA grooves and to interact with the phosphate backbone of apposing helices. We have previously shown a length dependent attraction resulting in higher packaging densities with increasing charge for linear cations. Hyperbranched polycations, such as polycationic dendrimers, presumably would not be able to bind to DNA and correlate their charges in the same manner as linear cations. We show that attractive and repulsive force amplitudes in PAMAM-DNA assemblies display significantly different trends than comparably charged linear arginines resulting in lower DNA packaging densities with increasing PAMAM generation. The salt and pH dependencies of packaging in PAMAM dendrimer-DNA and linear arginine-DNA complexes were also investigated. Significant differences in the force curve behaviour and salt and pH sensitivities suggest that different binding modes may be present in DNA condensed by dendrimers when compared to linear polycations.

  11. Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system

    SciTech Connect

    Hormain, Laureline; Monnerville, Maurice Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-04-14

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

  12. Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential

    SciTech Connect

    Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D.

    2013-11-21

    We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.

  13. Intercalation of organic molecules in 2D copper (II) nitroprusside: Intermolecular interactions and magnetic properties

    NASA Astrophysics Data System (ADS)

    Osiry, H.; Cano, A.; Lemus-Santana, A. A.; Rodríguez, A.; Carbonio, R. E.; Reguera, E.

    2015-10-01

    This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π-π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting.

  14. High pressure luminescence probes in polymers

    SciTech Connect

    Drickamer, H.G.

    1980-01-01

    High pressure luminescence has proved to be a very powerful tool for characterizing crystalline solids and liquids. Two problems involving glassy polymers are analyzed. In the first problem the excited states of azulene and its derivatives are used to probe intermolecular interactions in PMMA and PS. In the second problem the change in emission intensity with pressure from two excimer states of polyvinylcarbazole as a pure polymer and in dilute solution in polystyrene (PS), polymethylmethacrylate (PMMA) and polyisoliutylene (PIB) is studied. The relative emission from the two states depends strongly on the possibility for motion of polymer segments. The observations are related to the proximity to the glass transition.

  15. Vibrational dynamics of aqueous hydroxide solutions probed using broadband 2DIR spectroscopy

    SciTech Connect

    Mandal, Aritra; Tokmakoff, Andrei

    2015-11-21

    We employed ultrafast transient absorption and broadband 2DIR spectroscopy to study the vibrational dynamics of aqueous hydroxide solutions by exciting the O–H stretch vibrations of the strongly hydrogen-bonded hydroxide solvation shell water and probing the continuum absorption of the solvated ion between 1500 and 3800 cm{sup −1}. We observe rapid vibrational relaxation processes on 150–250 fs time scales across the entire probed spectral region as well as slower vibrational dynamics on 1–2 ps time scales. Furthermore, the O–H stretch excitation loses its frequency memory in 180 fs, and vibrational energy exchange between bulk-like water vibrations and hydroxide-associated water vibrations occurs in ∼200 fs. The fast dynamics in this system originate in strong nonlinear coupling between intra- and intermolecular vibrations and are explained in terms of non-adiabatic vibrational relaxation. These measurements indicate that the vibrational dynamics of the aqueous hydroxide complex are faster than the time scales reported for long-range transport of protons in aqueous hydroxide solutions.

  16. Intermolecular Photocatalyzed Heck-like Coupling of Unactivated Alkyl Bromides by a Dinuclear Gold Complex.

    PubMed

    Xie, Jin; Li, Jian; Weingand, Vanessa; Rudolph, Matthias; Hashmi, A Stephen K

    2016-08-26

    A practical protocol for a photocatalyzed alkyl-Heck-like reaction of unactivated alkyl bromides and different alkenes promoted by dinuclear gold photoredox catalysis in the presence of an inorganic base is reported. Primary, secondary, and tertiary unactivated alkyl bromides with β-hydrogen can be applied. Esters, aldehydes, ketones, nitriles, alcohols, heterocycles, alkynes, alkenes, ethers, and halogen moieties are all well tolerated. In addition to 1,1-diarylalkenes, silylenolethers and enamides can also be applied, which further increases the synthetic potential of the reaction. The mild reaction conditions, broad substrate scope, and an excellent functional-group tolerance deliver an ideal tool for synthetic chemists that can even be used for challenging late-stage modifications of complex natural products.

  17. Resonant Auger decay driving intermolecular Coulombic decay in molecular dimers

    NASA Astrophysics Data System (ADS)

    Trinter, F.; Schöffler, M. S.; Kim, H.-K.; Sturm, F. P.; Cole, K.; Neumann, N.; Vredenborg, A.; Williams, J.; Bocharova, I.; Guillemin, R.; Simon, M.; Belkacem, A.; Landers, A. L.; Weber, Th.; Schmidt-Böcking, H.; Dörner, R.; Jahnke, T.

    2014-01-01

    In 1997, it was predicted that an electronically excited atom or molecule placed in a loosely bound chemical system (such as a hydrogen-bonded or van-der-Waals-bonded cluster) could efficiently decay by transferring its excess energy to a neighbouring species that would then emit a low-energy electron. This intermolecular Coulombic decay (ICD) process has since been shown to be a common phenomenon, raising questions about its role in DNA damage induced by ionizing radiation, in which low-energy electrons are known to play an important part. It was recently suggested that ICD can be triggered efficiently and site-selectively by resonantly core-exciting a target atom, which then transforms through Auger decay into an ionic species with sufficiently high excitation energy to permit ICD to occur. Here we show experimentally that resonant Auger decay can indeed trigger ICD in dimers of both molecular nitrogen and carbon monoxide. By using ion and electron momentum spectroscopy to measure simultaneously the charged species created in the resonant-Auger-driven ICD cascade, we find that ICD occurs in less time than the 20femtoseconds it would take for individual molecules to undergo dissociation. Our experimental confirmation of this process and its efficiency may trigger renewed efforts to develop resonant X-ray excitation schemes for more localized and targeted cancer radiation therapy.

  18. Quantitative tomographic imaging of intermolecular FRET in small animals

    PubMed Central

    Venugopal, Vivek; Chen, Jin; Barroso, Margarida; Intes, Xavier

    2012-01-01

    Forster resonance energy transfer (FRET) is a nonradiative transfer of energy between two fluorescent molecules (a donor and an acceptor) in nanometer range proximity. FRET imaging methods have been applied to proteomic studies and drug discovery applications based on intermolecular FRET efficiency measurements and stoichiometric measurements of FRET interaction as quantitative parameters of interest. Importantly, FRET provides information about biomolecular interactions at a molecular level, well beyond the diffraction limits of standard microscopy techniques. The application of FRET to small animal imaging will allow biomedical researchers to investigate physiological processes occurring at nanometer range in vivo as well as in situ. In this work a new method for the quantitative reconstruction of FRET measurements in small animals, incorporating a full-field tomographic acquisition system with a Monte Carlo based hierarchical reconstruction scheme, is described and validated in murine models. Our main objective is to estimate the relative concentration of two forms of donor species, i.e., a donor molecule involved in FRETing to an acceptor close by and a nonFRETing donor molecule. PMID:23243567

  19. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces.

    PubMed

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M; Otero, Roberto; Gallego, José M; Ballester, Pablo; Galan-Mascaros, José R; Ecija, David

    2016-01-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure.

  20. When do we need attractive-repulsive intermolecular potentials?

    SciTech Connect

    Venkattraman, Ayyaswamy

    2014-12-09

    The role of attractive-repulsive interactions in direct simulation Monte Carlo (DSMC) simulations is studied by comparing with traditional purely repulsive interactions. The larger collision cross section of the long-range LJ potential is shown to result in a higher collision frequency and hence a lower mean free path, by at least a factor of two, for given conditions. This results in a faster relaxation to equilibrium as is shown by comparing the fourth and sixth moments of the molecular velocity distribution obtained using 0-D DSMC simulations. A 1-D Fourier-Couette flow with a large temperature and velocity difference between the walls is used to show that matching transport properties will result in identical solutions using both LJPA and VSS models in the near-continuum regime. However, flows in the transitional regime with Knudsen number, Kn ∼ 0.5 show a dependence on the intermolecular potential in spite of matching the viscosity coefficient due to differences in the collision frequency. Attractive-repulsive potentials should be used when both transport coefficients and collision frequencies should be matched.

  1. Carbon dioxide-methanol intermolecular complexes in interstellar grain mantles

    NASA Astrophysics Data System (ADS)

    Dartois, E.; Demyk, K.; d'Hendecourt, L.; Ehrenfreund, P.

    1999-11-01

    We present new laboratory data to interpret the Infrared Space Observatory (ISO) spectra of protostellar objects, and particularly RAFGL7009S. Our experimental results show that solid methanol and carbon dioxide exhibit specific intermolecular interactions. We propose the formation of a Lewis acid-base complex between carbon dioxide and methanol molecules to explain specific substructure of the 15.2 mu m CO_2 bending mode observed in different objects. The various CO_2 bending mode patterns observed in many lines of sight can be interpreted as a combination of both this complex formation and the temperature evolution of the ices. The temperature induced segregation of ice mantles containing CO_2 can be monitored by the 13CO_2 stretching mode shift toward the pure CO_2 ice position. The large width observed for this mode towards interstellar sources partly results from the different temperatures sampled along the line of sight. Given the amount of methanol involved in RAFGL7009S, on the basis of ground based observations, we derive that about half of the so called ``6.85 mu m'' band and a quarter of the 4.9 mu m bands can be accounted for by the deformation modes and 2nu_8 transitions of CH_3OH. Based on observations with ISO, an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, the Netherlands and the United Kingdom) and with the participation of ISAS and NASA

  2. Polyelectrolyte brushes in mixed ionic medium studied via intermolecular forces

    NASA Astrophysics Data System (ADS)

    Farina, Robert; Laugel, Nicolas; Pincus, Philip; Tirrell, Matthew

    2011-03-01

    The vast uses and applications of polyelectrolyte brushes make them an attractive field of research especially with the growing interest in responsive materials. Polymers which respond via changes in temperature, pH, and ionic strength are increasingly being used for applications in drug delivery, chemical gating, etc. When polyelectrolyte brushes are found in either nature (e.g., surfaces of cartilage and mammalian lung interiors) or commercially (e.g., skin care products, shampoo, and surfaces of medical devices) they are always surrounded by mixed ionic medium. This makes the study of these brushes in varying ionic environments extremely relevant for both current and future potential applications. The polyelectrolyte brushes in this work are diblock co-polymers of poly-styrene sulfonate (N=420) and poly-t-butyl styrene (N=20) which tethers to a hydrophobic surface allowing for a purely thermodynamic study of the polyelectrolyte chains. Intermolecular forces between two brushes are measured using the SFA. As multi-valent concentrations are increased, the brushes collapse internally and form strong adhesion between one another after contact (properties not seen in a purely mono-valent environment).

  3. Intermolecular interactions, nucleation, and thermodynamics of crystallization of hemoglobin C.

    PubMed Central

    Vekilov, Peter G; Feeling-Taylor, Angela R; Petsev, Dimiter N; Galkin, Oleg; Nagel, Ronald L; Hirsch, Rhoda Elison

    2002-01-01

    The mutated hemoglobin HbC (beta 6 Glu-->Lys), in the oxygenated (R) liganded state, forms crystals inside red blood cells of patients with CC and SC diseases. Static and dynamic light scattering characterization of the interactions between the R-state (CO) HbC, HbA, and HbS molecules in low-ionic-strength solutions showed that electrostatics is unimportant and that the interactions are dominated by the specific binding of solutions' ions to the proteins. Microscopic observations and determinations of the nucleation statistics showed that the crystals of HbC nucleate and grow by the attachment of native molecules from the solution and that concurrent amorphous phases, spherulites, and microfibers are not building blocks for the crystal. Using a novel miniaturized light-scintillation technique, we quantified a strong retrograde solubility dependence on temperature. Thermodynamic analyses of HbC crystallization yielded a high positive enthalpy of 155 kJ mol(-1), i.e., the specific interactions favor HbC molecules in the solute state. Then, HbC crystallization is only possible because of the huge entropy gain of 610 J mol(-1) K(-1), likely stemming from the release of up to 10 water molecules per protein intermolecular contact-hydrophobic interaction. Thus, the higher crystallization propensity of R-state HbC is attributable to increased hydrophobicity resulting from the conformational changes that accompany the HbC beta 6 mutation. PMID:12124294

  4. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    PubMed Central

    Cirera, Borja; Giménez-Agulló, Nelson; Björk, Jonas; Martínez-Peña, Francisco; Martin-Jimenez, Alberto; Rodriguez-Fernandez, Jonathan; Pizarro, Ana M.; Otero, Roberto; Gallego, José M.; Ballester, Pablo; Galan-Mascaros, José R.; Ecija, David

    2016-01-01

    On-surface synthesis is a promising strategy for engineering heteroatomic covalent nanoarchitectures with prospects in electronics, optoelectronics and photovoltaics. Here we report the thermal tunability of reaction pathways of a molecular precursor in order to select intramolecular versus intermolecular reactions, yielding monomeric or polymeric phthalocyanine derivatives, respectively. Deposition of tetra-aza-porphyrin species bearing ethyl termini on Au(111) held at room temperature results in a close-packed assembly. Upon annealing from room temperature to 275 °C, the molecular precursors undergo a series of covalent reactions via their ethyl termini, giving rise to phthalocyanine tapes. However, deposition of the tetra-aza-porphyrin derivatives on Au(111) held at 300 °C results in the formation and self-assembly of monomeric phthalocyanines. A systematic scanning tunnelling microscopy study of reaction intermediates, combined with density functional calculations, suggests a [2+2] cycloaddition as responsible for the initial linkage between molecular precursors, whereas the monomeric reaction is rationalized as an electrocyclic ring closure. PMID:26964764

  5. Evolutionary meandering of intermolecular interactions along the drift barrier.

    PubMed

    Lynch, Michael; Hagner, Kyle

    2015-01-01

    Many cellular functions depend on highly specific intermolecular interactions, for example transcription factors and their DNA binding sites, microRNAs and their RNA binding sites, the interfaces between heterodimeric protein molecules, the stems in RNA molecules, and kinases and their response regulators in signal-transduction systems. Despite the need for complementarity between interacting partners, such pairwise systems seem to be capable of high levels of evolutionary divergence, even when subject to strong selection. Such behavior is a consequence of the diminishing advantages of increasing binding affinity between partners, the multiplicity of evolutionary pathways between selectively equivalent alternatives, and the stochastic nature of evolutionary processes. Because mutation pressure toward reduced affinity conflicts with selective pressure for greater interaction, situations can arise in which the expected distribution of the degree of matching between interacting partners is bimodal, even in the face of constant selection. Although biomolecules with larger numbers of interacting partners are subject to increased levels of evolutionary conservation, their more numerous partners need not converge on a single sequence motif or be increasingly constrained in more complex systems. These results suggest that most phylogenetic differences in the sequences of binding interfaces are not the result of adaptive fine tuning but a simple consequence of random genetic drift. PMID:25535374

  6. Final Project Report - Coupled Biogeochemical Process Evaluation for Conceptualizing Trichloriethylene Co-Metabolism: Co-Metabolic Enzyme Activity Probes and Modeling Co-Metabolism and Attenuation

    SciTech Connect

    Starr, Robert C; Orr, Brennon R; Lee, M Hope; Delwiche, Mark

    2010-02-26

    Trichloroethene (TCE) (also known as trichloroethylene) is a common contaminant in groundwater. TCE is regulated in drinking water at a concentration of 5 µg/L, and a small mass of TCE has the potential to contaminant large volumes of water. The physical and chemical characteristics of TCE allow it to migrate quickly in most subsurface environments, and thus large plumes of contaminated groundwater can form from a single release. The migration and persistence of TCE in groundwater can be limited by biodegradation. TCE can be biodegraded via different processes under either anaerobic or aerobic conditions. Anaerobic biodegradation is widely recognized, but aerobic degradation is less well recognized. Under aerobic conditions, TCE can be oxidized to non hazardous conditions via cometabolic pathways. This study applied enzyme activity probes to demonstrate that cometabolic degradation of TCE occurs in aerobic groundwater at several locations, used laboratory microcosm studies to determine aerobic degradation rates, and extrapolated lab-measured rates to in situ rates based on concentrations of microorganisms with active enzymes involved in cometabolic TCE degradation. Microcosms were constructed using basalt chips that were inoculated with microorganisms to groundwater at the Idaho National Laboratory Test Area North TCE plume by filling a set of Flow-Through In Situ Reactors (FTISRs) with chips and placing the FTISRs into the open interval of a well for several months. A parametric study was performed to evaluate predicted degradation rates and concentration trends using a competitive inhibition kinetic model, which accounts for competition for enzyme active sites by both a growth substrate and a cometabolic substrate. The competitive inhibition kinetic expression was programmed for use in the RT3D reactive transport package. Simulations of TCE plume evolution using both competitive inhibition kinetics and first order decay were performed.

  7. Excitonic couplings between molecular crystal pairs by a multistate approximation

    SciTech Connect

    Aragó, Juan Troisi, Alessandro

    2015-04-28

    In this paper, we present a diabatization scheme to compute the excitonic couplings between an arbitrary number of states in molecular pairs. The method is based on an algebraic procedure to find the diabatic states with a desired property as close as possible to that of some reference states. In common with other diabatization schemes, this method captures the physics of the important short-range contributions (exchange, overlap, and charge-transfer mediated terms) but it becomes particularly suitable in presence of more than two states of interest. The method is formulated to be usable with any level of electronic structure calculations and to diabatize different types of states by selecting different molecular properties. These features make the diabatization scheme presented here especially appropriate in the context of organic crystals, where several excitons localized on the same molecular pair may be found close in energy. In this paper, the method is validated on the tetracene crystal dimer, a well characterized case where the charge transfer (CT) states are closer in energy to the Frenkel excitons (FE). The test system was studied as a function of an external electric field (to explore the effect of changing the relative energy of the CT excited state) and as a function of different intermolecular distances (to probe the strength of the coupling between FE and CT states). Additionally, we illustrate how the approximation can be used to include the environment polarization effect.

  8. Optical probe

    DOEpatents

    Hencken, Kenneth; Flower, William L.

    1999-01-01

    A compact optical probe is disclosed particularly useful for analysis of emissions in industrial environments. The instant invention provides a geometry for optically-based measurements that allows all optical components (source, detector, rely optics, etc.) to be located in proximity to one another. The geometry of the probe disclosed herein provides a means for making optical measurements in environments where it is difficult and/or expensive to gain access to the vicinity of a flow stream to be measured. Significantly, the lens geometry of the optical probe allows the analysis location within a flow stream being monitored to be moved while maintaining optical alignment of all components even when the optical probe is focused on a plurality of different analysis points within the flow stream.

  9. Na + concentration dependence of intermolecular distance in 3,4,9,10-perylenetetracarboxylic dianhydride dimer

    NASA Astrophysics Data System (ADS)

    Fujii, Kazuhito

    2010-01-01

    We have discussed the Na + concentration dependence of the intermolecular distance of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) dimers in aqueous solution of NaOH. We have particularly focused on the S10-S00 transition of the PTCDA dimers which is sensitive to the intermolecular distance and we have found that the S10 state is split for the higher lying sublevel and the lower lying sublevel with the increase of the Na + concentrations. From the energy shift of the lower lying sublevel, we have estimated the intermolecular distance of the PTCDA dimer, that changes from 7.5 to 4.9 Å by the Na + concentration.

  10. Wave-wave and wave-particle interactions in the inner magnetosphere measured with Van Allen Probes: cross coupling between wave modes and its effect on radiation belt dynamics

    NASA Astrophysics Data System (ADS)

    Colpitts, C. A.; Cattell, C. A.; Broughton, M.; Engebretson, M. J.

    2015-12-01

    We will show observations of waveform bursts using the Electric Field and Waves (EFW) burst data on the Van Allen Probes satellites with intermediate frequency waves such as whistler mode, magnetosonic and lower hybrid. These observations show very strong modulation of these waves by lower frequency waves such as EMIC or ULF. We are analyzing the burst data and cross coupling between wave modes to determine how prevalent the cross coupling between wave modes is and under what conditions it occurs. To supplement the EFW data, each satellite is also equipped with a full complement of particle instruments, including the HOPE instrument measuring lower energy (1 eV - 50 keV) particles and MagEIS instruments measuring higher energy (20 keV - 5 MeV) particles. The energy and angular resolution of these detectors are sufficient to resolve the scattering and energization arising from the distinct wave modes, using the signatures in the trapped electron populations predicted by theory for the various mechanisms. Comparison of the burst waveform data with the electron data from HOPE and MagEIS, for times with and without coupling between the wave modes, will allow us to identify how the cross coupling affects electron dynamics in the radiation belts. The significance of wave-particle interactions in the formation and depletion of the radiation belts has long been established, but is still not completely understood. Specifically, pitch angle scattering from waves such as plasmaspheric hiss and electromagnetic ion cyclotron [EMIC] waves near the duskside plasmapause is known to contribute to electron loss from the radiation belts, primarily through precipitation into the atmosphere. Higher frequency waves such as whistler mode chorus and magnetosonic waves observed near the equator in the lower hybrid frequency range are widely believed to be primary means for electron energization. However, these and other competing processes often occur simultaneously, and an accurate model

  11. Keto-enol tautomerization and intermolecular proton transfer in photoionized cyclopentanone dimer in the gas phase

    NASA Astrophysics Data System (ADS)

    Ghosh, Arup K.; Chatterjee, Piyali; Chakraborty, Tapas

    2014-07-01

    Time-of-flight mass spectra of cyclopentanone and its clusters cooled in a supersonic jet expansion have been measured following 4-, 3-, and 2-photon ionizations by the 2nd, 3rd, and 4th harmonic wavelengths, respectively, of a Q-switched Nd:YAG laser. The mass spectra reveal signatures of energetically favored keto to enol tautomerization of the molecular ion leading to intermolecular proton transfer, and this observation is found sharply dependent on the ionization wavelengths used. Electronic structure calculation predicts that in spite of the energetic preference, keto-enol conversion barrier of isolated molecular ion is high. However, the barrier is significantly reduced in a CH⋯O hydrogen-bonded dimer of the molecule. The transition states associated with tautomeric conversion of both cyclopentanone monomer and dimer cations have been identified by means of intrinsic reaction co-ordinate calculation. In a supersonic jet expansion, although a weakly bound dimer is readily generated, the corresponding cation and also the protonated counterpart are observed only for ionization by 532 nm. For other two ionization wavelengths, these species do not register in the mass spectra, where the competing reaction channels via α-cleavage of the ring become dominant. In contrast to the report of a recent study, we notice that the intact molecular ion largely survives fragmentations when ionized from the 2-photon resonant 3p Rydberg state as intermediate using nanosecond laser pulses, and the corresponding resonant 3-photon ionization spectrum has been recorded probing the intact molecular ion.

  12. Complexities of bloom dynamics in the toxic dinoflagellate Alexandrium fundyense revealed through DNA measurements by imaging flow cytometry coupled with species-specific rRNA probes

    NASA Astrophysics Data System (ADS)

    Brosnahan, Michael L.; Farzan, Shahla; Keafer, Bruce A.; Sosik, Heidi M.; Olson, Robert J.; Anderson, Donald M.

    2014-05-01

    Measurements of the DNA content of different protist populations can shed light on a variety of processes, including cell division, sex, prey ingestion, and parasite invasion. Here, we modified an Imaging FlowCytobot (IFCB), a custom-built flow cytometer that records images of microplankton, to measure the DNA content of large dinoflagellates and other high-DNA content species. The IFCB was also configured to measure fluorescence from Cy3-labeled rRNA probes, aiding the identification of Alexandrium fundyense (syn. A. tamarense Group I), a photosynthetic dinoflagellate that causes paralytic shellfish poisoning (PSP). The modified IFCB was used to analyze samples from the development, peak and termination phases of an inshore A. fundyense bloom (Salt Pond, Eastham, MA, USA), and from a rare A. fundyense ‘red tide’ that occurred in the western Gulf of Maine, offshore of Portsmouth, NH (USA). Diploid or G2 phase (‘2C’) A. fundyense cells were frequently enriched at the near-surface, suggesting an important role for aggregation at the air-sea interface during sexual events. Also, our analysis showed that large proportions of A. fundyense cells in both the Salt Pond and red tide blooms were planozygotes during bloom decline, highlighting the importance of sexual fusion to bloom termination. At Salt Pond, bloom decline also coincided with a dramatic rise in infections by the parasite genus Amoebophrya. The samples that were most heavily infected contained many large cells with higher DNA-associated fluorescence than 2C vegetative cells, but these cells' nuclei were also frequently consumed by Amoebophrya trophonts. Neither large cell size nor increased DNA-associated fluorescence could be replicated by infecting an A. fundyense culture of vegetative cells. Therefore, we attribute these characteristics of the large Salt Pond cells to planozygote maturation rather than Amoebophrya infection, though an interaction between infection and planozygote maturation may

  13. La-doping effect on spin-orbit coupled Sr2IrO4 probed by x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, Jie; Sun, Xuanyong; Liu, Shengli; Li, Bin; Wang, Haiyun; Dong, Peng; Wang, Yu; Xu, Wei

    2016-09-01

    Sr2IrO4 was predicted to be an unconventional superconductor upon carrier doping since it highly resembles the high-temperature cuprates. Here, to understand carrier doping effect on spin-orbit coupled Mott insulator Sr2IrO4, the electronic structure and local structure distortion for Sr2 - x La x IrO4 system have been investigated by x-ray absorption spectroscopy. By comparing the intensity of white-line features at the Ir L 2,3 absorption edges, we observe remarkably large branching ratios in La-doped compounds, greater than that of the parent material Sr2IrO4, suggesting a strong spin-orbit interaction for Sr2IrO4-based system. Moreover, extended x-ray absorption fine structure spectra demonstrate more regular IrO6 octahedra, i.e. the weakened crystal electric field versus La-doping. By theoretical calculations, the synergistic effect of regular IrO6 octahedra and electron doping is established, which accounts for the transition from a Mott insulator to a conductive state in Sr2 - x La x IrO4-based system.

  14. La-doping effect on spin–orbit coupled Sr2IrO4 probed by x-ray absorption spectroscopy

    NASA Astrophysics Data System (ADS)

    Cheng, Jie; Sun, Xuanyong; Liu, Shengli; Li, Bin; Wang, Haiyun; Dong, Peng; Wang, Yu; Xu, Wei

    2016-09-01

    Sr2IrO4 was predicted to be an unconventional superconductor upon carrier doping since it highly resembles the high-temperature cuprates. Here, to understand carrier doping effect on spin–orbit coupled Mott insulator Sr2IrO4, the electronic structure and local structure distortion for Sr2 ‑ x La x IrO4 system have been investigated by x-ray absorption spectroscopy. By comparing the intensity of white-line features at the Ir L 2,3 absorption edges, we observe remarkably large branching ratios in La-doped compounds, greater than that of the parent material Sr2IrO4, suggesting a strong spin-orbit interaction for Sr2IrO4-based system. Moreover, extended x-ray absorption fine structure spectra demonstrate more regular IrO6 octahedra, i.e. the weakened crystal electric field versus La-doping. By theoretical calculations, the synergistic effect of regular IrO6 octahedra and electron doping is established, which accounts for the transition from a Mott insulator to a conductive state in Sr2 ‑ x La x IrO4-based system.

  15. Probing the Role of Interlayer Coupling and Coulomb Interactions on Electronic Structure in Few-Layer MoSe2Nanostructures

    NASA Astrophysics Data System (ADS)

    Bradley, Aaron J.; M. Ugeda, Miguel; da Jornada, Felipe H.; Qiu, Diana Y.; Ruan, Wei; Zhang, Yi; Wickenburg, Sebastian; Riss, Alexander; Lu, Jiong; Mo, Sung-Kwan; Hussain, Zahid; Shen, Zhi-Xun; Louie, Steven G.; Crommie, Michael F.

    2015-04-01

    Despite the weak nature of interlayer forces in transition metal dichalcogenide (TMD) materials, their properties are highly dependent on the number of layers in the few-layer two-dimensional (2D) limit. Here, we present a combined scanning tunneling microscopy/spectroscopy and GW theoretical study of the electronic structure of high quality single- and few-layer MoSe2 grown on bilayer graphene. We find that the electronic (quasiparticle) bandgap, a fundamental parameter for transport and optical phenomena, decreases by nearly one electronvolt when going from one layer to three due to interlayer coupling and screening effects. Our results paint a clear picture of the evolution of the electronic wave function hybridization in the valleys of both the valence and conduction bands as the number of layers is changed. This demonstrates the importance of layer number and electron-electron interactions on van der Waals heterostructures, and helps to clarify how their electronic properties might be tuned in future 2D nanodevices.

  16. Probing the Role of Interlayer Coupling and Coulomb Interactions on Electronic Structure in Few-Layer MoSe 2 Nanostructures

    DOE PAGES

    Bradley, Aaron J.; M. Ugeda, Miguel; da Jornada, Felipe H.; Qiu, Diana Y.; Ruan, Wei; Zhang, Yi; Wickenburg, Sebastian; Riss, Alexander; Lu, Jiong; Mo, Sung-Kwan; et al

    2015-03-16

    Despite the weak nature of interlayer forces in transition metal dichalcogenide (TMD) materials, their properties are highly dependent on the number of layers in the few-layer two-dimensional (2D) limit. Here, we present a combined scanning tunneling microscopy/spectroscopy and GW theoretical study of the electronic structure of high quality single- and few-layer MoSe2 grown on bilayer graphene. We find that the electronic (quasiparticle) bandgap, a fundamental parameter for transport and optical phenomena, decreases by nearly one electronvolt when going from one layer to three due to interlayer coupling and screening effects. Our results paint a clear picture of the evolution ofmore » the electronic wave function hybridization in the valleys of both the valence and conduction bands as the number of layers is changed. This demonstrates the importance of layer number and electron-electron interactions on van der Waals heterostructures and helps to clarify how their electronic properties might be tuned in future 2D nanodevices.« less

  17. Biomarkers probed in saliva by surface plasmon resonance imaging coupled to matrix-assisted laser desorption/ionization mass spectrometry in array format.

    PubMed

    Musso, Johana; Buchmann, William; Gonnet, Florence; Jarroux, Nathalie; Bellon, Sophie; Frydman, Chiraz; Brunet, Didier-Luc; Daniel, Regis

    2015-02-01

    Detection of protein biomarkers is of major interest in proteomics. This work reports the analysis of protein biomarkers directly from a biological fluid, human saliva, by surface plasmon resonance imaging coupled to mass spectrometry (SPRi-MS), using a functionalized biochip in an array format enabling multiplex SPR-MS analysis. The SPR biochip presented a gold surface functionalized by a self-assembled monolayer of short poly(ethylene oxide) chains carrying an N-hydroxysuccinimide end-group for the immobilization of antibodies. The experiments were accomplished without any sample pre-purification or spiking with the targeted biomarkers. SPRi monitoring of the interactions, immune capture from the biochip surface, and finally on-chip matrix-assisted laser desorption/ionization-MS structural identification of two protein biomarkers, salivary α-amylase and lysozyme, were successively achieved directly from saliva at the femtomole level. For lysozyme, the on-chip MS identification was completed by a proteomic analysis based on an on-chip proteolysis procedure and a peptide mass fingerprint. PMID:25524230

  18. Probing the Role of Interlayer Coupling and Coulomb Interactions on Electronic Structure in Few-Layer MoSe 2 Nanostructures

    SciTech Connect

    Bradley, Aaron J.; M. Ugeda, Miguel; da Jornada, Felipe H.; Qiu, Diana Y.; Ruan, Wei; Zhang, Yi; Wickenburg, Sebastian; Riss, Alexander; Lu, Jiong; Mo, Sung-Kwan; Hussain, Zahid; Shen, Zhi-Xun; Louie, Steven G.; Crommie, Michael F.

    2015-03-16

    Despite the weak nature of interlayer forces in transition metal dichalcogenide (TMD) materials, their properties are highly dependent on the number of layers in the few-layer two-dimensional (2D) limit. Here, we present a combined scanning tunneling microscopy/spectroscopy and GW theoretical study of the electronic structure of high quality single- and few-layer MoSe2 grown on bilayer graphene. We find that the electronic (quasiparticle) bandgap, a fundamental parameter for transport and optical phenomena, decreases by nearly one electronvolt when going from one layer to three due to interlayer coupling and screening effects. Our results paint a clear picture of the evolution of the electronic wave function hybridization in the valleys of both the valence and conduction bands as the number of layers is changed. This demonstrates the importance of layer number and electron-electron interactions on van der Waals heterostructures and helps to clarify how their electronic properties might be tuned in future 2D nanodevices.

  19. Probing the Role of Interlayer Coupling and Coulomb Interactions on Electronic Structure in Few-Layer MoSe2 Nanostructures

    PubMed Central

    2015-01-01

    Despite the weak nature of interlayer forces in transition metal dichalcogenide (TMD) materials, their properties are highly dependent on the number of layers in the few-layer two-dimensional (2D) limit. Here, we present a combined scanning tunneling microscopy/spectroscopy and GW theoretical study of the electronic structure of high quality single- and few-layer MoSe2 grown on bilayer graphene. We find that the electronic (quasiparticle) bandgap, a fundamental parameter for transport and optical phenomena, decreases by nearly one electronvolt when going from one layer to three due to interlayer coupling and screening effects. Our results paint a clear picture of the evolution of the electronic wave function hybridization in the valleys of both the valence and conduction bands as the number of layers is changed. This demonstrates the importance of layer number and electron–electron interactions on van der Waals heterostructures and helps to clarify how their electronic properties might be tuned in future 2D nanodevices. PMID:25775022

  20. Infrared Chemical Nano-Imaging: Accessing Structure, Coupling, and Dynamics on Molecular Length Scales

    SciTech Connect

    Muller, Eric A.; Pollard, Benjamin; Raschke, Markus Bernd

    2015-04-02

    This Perspective highlights recent advances in infrared vibrational chemical nano-imaging. In its implementations of scattering scanning near-field optical microscopy (s-SNOM) and photothermal-induced resonance (PTIR), IR nanospectroscopy provides few-nanometer spatial resolution for the investigation of polymer, biomaterial, and related soft-matter surfaces and nanostructures. Broad-band IR s-SNOM with coherent laser and synchrotron sources allows for chemical recognition with small-ensemble sensitivity and the potential for sensitivity reaching the single-molecule limit. Probing selected vibrational marker resonances, it gives access to nanoscale chemical imaging of composition, domain morphologies, order/disorder, molecular orientation, or crystallographic phases. Local intra- and intermolecular coupling can be measured through frequency shifts of a vibrational marker in heterogeneous environments and associated inhomogeneities in vibrational dephasing. In combination with ultrafast spectroscopy, the vibrational coherent evolution of homogeneous sub-ensembles coupled to their environment can be observed. Outstanding challenges are discussed in terms of extensions to coherent and multidimensional spectroscopies, implementation in liquid and in situ environments, general sample limitations, and engineering s-SNOM scanning probes to better control the nano-localized optical excitation and to increase sensitivity.

  1. Theoretical studies for the N2-N2O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies.

    PubMed

    Zheng, Rui; Zheng, Limin; Lu, Yunpeng; Yang, Minghui

    2015-10-21

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N2-N2O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N2O monomer is near the N2 monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm(-1), which is in good agreement with the available experimental data of 22.334 cm(-1). A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers (14)N2-N2O and (15)N2-N2O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters.

  2. Theoretical studies for the N{sub 2}–N{sub 2}O van der Waals complex: The potential energy surface, intermolecular vibrations, and rotational transition frequencies

    SciTech Connect

    Zheng, Rui; Zheng, Limin; Yang, Minghui E-mail: yangmh@wipm.ac.cn; Lu, Yunpeng E-mail: yangmh@wipm.ac.cn

    2015-10-21

    Theoretical studies of the potential energy surface (PES) and bound states are performed for the N{sub 2}–N{sub 2}O van der Waals (vdW) complex. A four-dimensional intermolecular PES is constructed at the level of single and double excitation coupled-cluster method with a non-iterative perturbation treatment of triple excitations [CCSD(T)] with aug-cc-pVTZ basis set supplemented with bond functions. Two equivalent T-shaped global minima are located, in which the O atom of N{sub 2}O monomer is near the N{sub 2} monomer. The intermolecular fundamental vibrational states are assigned by inspecting the orientation of the nodal surface of the wavefunctions. The calculated frequency for intermolecular disrotation mode is 23.086 cm{sup −1}, which is in good agreement with the available experimental data of 22.334 cm{sup −1}. A negligible tunneling splitting with the value of 4.2 MHz is determined for the ground vibrational state and the tunneling splitting increases as the increment of the vibrational frequencies. Rotational levels and transition frequencies are calculated for both isotopomers {sup 14}N{sub 2}–N{sub 2}O and {sup 15}N{sub 2}–N{sub 2}O. The accuracy of the PES is validated by the good agreement between theoretical and experimental results for the transition frequencies and spectroscopic parameters.

  3. Electronic Structure Theory for Radicaloid Systems and Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Kurlancheek, Westin

    associated with unrestriction. Second, the relaxed density matrix itself fails to be N-representable, with natural orbital occupation numbers less than zero and greater than one. Therefore, it is desirable to use a method that is not dependent on the inverse of the Hessian like orbital optimized MP2 (O2). Another system which requires the use of orbital optimization is a neutral soliton on a polyacetylene chain. In this system, the Hartree-Fock reference suffers from severe spin-polarization making the wavefunction physically unreasonable unless a very sophisticated treatment of electron correlation is used to correct this problem. Originally, it was found that computationally expensive methods like CCSD(T) and CASSCF could adequately describe small model chain but not the full system. The O2 method is found to be an dramatic improvement over traditional MP2 which can be feasibly applied to polyenyl chains long enough to characterize the soliton. It is also discovered that density functionals are generally inadequate in describing the half-width of the soliton. Finally, the last chapter takes a slightly different perspective and focuses on the addition of correlation energy to a successful energy decomposition analysis based on absolutely localized molecular orbitals. It is discovered that the resulting new method can adequately describe systems with dispersive intermolecular interactions and large amounts of charge transfer. This scheme is then applied to the water dimer systems and it is found that all of the intermolecular interactions similar in size with the electrostatic interaction being the largest and the dispersive interaction being the smallest. This method is also contrasted with other EDA schemes.

  4. Probing the Carbon-phosphorus Bond Coupling in Low-temperature Phosphine PH3—Methane CH4 Interstellar Ice Analogues

    NASA Astrophysics Data System (ADS)

    Turner, Andrew M.; Abplanalp, Matthew J.; Kaiser, Ralf I.

    2016-03-01

    Phosphine, which has now been confirmed around the carbon-rich star IRC+10216, provides the first example of a phosphorus-containing single bond in interstellar or circumstellar media. While four compounds containing both phosphorus and carbon have been discovered, none contain a carbon-phosphorus single bond. Here, we show that this moiety is plausible from the reaction of phosphine with methane in electron-irradiated interstellar ice analogues. Fractional sublimation allows for detection of individual products at distinct temperatures using reflectron time-of-flight mass spectrometry (ReTOF) coupled with vacuum ultraviolet photoionization. This method produced phosphanes and methylphosphanes as large as P8H10 and CH3P8H9, which demonstrates that a phosphorus-carbon bond can readily form and that methylphosphanes sublime at 12-17 K higher temperatures than the non-organic phosphanes. Also, irradiated ices of phosphine with deuterated-methane untangle the reaction pathways through which these methylphosphanes were formed and identified radical recombination to be preferred over carbene/phosphinidene insertion reactions. In addition, these ReTOF results confirm that CH3PH2 and CH6P2 can form via insertion of carbene and phosphinidene and that the methylenediphosphine (PH2CH2PH2) isomer forms in the ices, although methylphosphine (CH3P2H3) is likely the more abundant isomer and that phosphanes and organophosphanes preferentially fragment via the loss of a phosphino group when photoionized. While the formation of methylphosphine is overall endoergic, the intermediates produced by interactions with energetic electrons proceed toward methylphosphine favorably and barrierlessly and provide plausible mechanisms toward hitherto unidentified interstellar compounds.

  5. DFT 2H quadrupolar coupling constants of ruthenium complexes: a good probe of the coordination of hydrides in conjuction with experiments.

    PubMed

    del Rosal, Iker; Gutmann, Torsten; Maron, Laurent; Jolibois, Franck; Chaudret, Bruno; Walaszek, Bernadeta; Limbach, Hans-Heinrich; Poteau, Romuald; Buntkowsky, Gerd

    2009-07-21

    Transition metal (TM) hydrides are of great interest in chemistry because of their reactivity and their potential as catalysts for hydrogenation reactions. 2H solid-state NMR can be used in order to get information about the local environment of hydrogen atoms, and more particularly the coordination mode of hydrides in such complexes. In this work we will show that it is possible to establish at the level of density functional theory (DFT) a viable methodological strategy that allows the determination of 2H NMR parameters, namely the quadrupolar coupling constant (C(Q)) respectively the quadrupolar splitting (deltanuQ) and the asymmetry parameter (etaQ). The reliability of the method (B3PW91-DFT) and basis set effects have been first evaluated for simple organic compounds (benzene and fluorene). A good correlation between experimental and theoretical values is systematically obtained if the large basis set cc-pVTZ is used for the computations. 2H NMR properties of five mononuclear ruthenium complexes (namely Cp*RuD3(PPh3), Tp*RuD(THT)2, Tp*RuD(D2)(THT) and Tp*RuD(D2)2 and RuD2(D2)2(PCy3)2) which exhibit different ligands and hydrides involved in different coordination modes (terminal-H or eta2-H2), have been calculated and compared to previous experimental data. The results obtained are in excellent agreement with experiments. Although 2H NMR spectra are not always easy to analyze, assistance by quantum chemistry calculations allows unambiguous assignment of the signals of such spectra. As far as experiments can be achieved at very low temperatures in order to avoid dynamic effects, this hybrid theoretical/experimental tool may give useful insights in the context of the characterization of ruthenium surfaces or nanoparticles with solid-state NMR. PMID:19842483

  6. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, Brian D.; Fought, Eric R.

    1987-01-01

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

  7. Electrophoresis-mass spectrometry probe

    DOEpatents

    Andresen, B.D.; Fought, E.R.

    1987-11-10

    The invention involves a new technique for the separation of complex mixtures of chemicals, which utilizes a unique interface probe for conventional mass spectrometers which allows the electrophoretically separated compounds to be analyzed in real-time by a mass spectrometer. This new chemical analysis interface, which couples electrophoresis with mass spectrometry, allows complex mixtures to be analyzed very rapidly, with much greater specificity, and with greater sensitivity. The interface or probe provides a means whereby large and/or polar molecules in complex mixtures to be completely characterized. The preferred embodiment of the probe utilizes a double capillary tip which allows the probe tip to be continually wetted by the buffer, which provides for increased heat dissipation, and results in a continually operating interface which is more durable and electronically stable than the illustrated single capillary tip probe interface. 8 figs.

  8. The ``primitive'' wave function in the theory of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Kutzelnigg, Werner

    1980-07-01

    The concept of the primitive wave function for a supermolecule consisting of interacting subsystems is critically analyzed. The distinction between formal and genuine primitive functions is stressed. The concept of uniformly complete basis sets as contrasted to simply complete basis is introduced. Primitive basis sets are defined and shown not to be uniformly complete for the expansion of the supersystem wave function while 'full supersystem basis sets' are. The conditions are specified under which a supersystem wave function can be decomposed into its 'primitive components' corresponding to different partitions of the electrons among the subsystems. These primitive components satisfy the Schrödinger equation asymptotically. The matrix representation of the Hamiltonian (both the full supersystem Hamiltonian H and the zeroth order Hamiltonian Ho) in terms of these partitions is analyzed. It is shown that in the standard application of RS-perturbation theory to intermolecular forces (the polarization approximation) the limiting processes λ→1 and R→∞ do not commute, that the λ-series is not uniformly convergent with respect to R and that the wave function to any finite order in λ is genuinely primitive. The symmetrized polarization approximation is justified for the 'coasymptotic ground state' in certain cases and a 'symmetrized polarization approximation with shifted eigenvalues' is proposed that connects the lowest eigenvalue of Ho with the physical ground state. A justification of simplified schemes in the region of 'small exchange' is given and alternative perturbation schemes are discussed. Finally the use of the primitive function in variational treatments is outlined. One advantage is that a genuinely (not a formally) primitive function is uniformly expandable in a primitive basis set.

  9. Interpretation of intermolecular geometric isotope effect in hydrogen bonds: nuclear orbital plus molecular orbital study.

    PubMed

    Ikabata, Yasuhiro; Imamura, Yutaka; Nakai, Hiromi

    2011-03-01

    The intermolecular geometric isotope effect (GIE) in hydrogen bond A-X···B (X = H and D) is investigated theoretically using the nuclear orbital plus molecular orbital (NOMO) theory. To interpret the GIE in terms of physically meaningful energy components such as electrostatic and exchange-repulsion interactions, the reduced variational space self-consistent-field method is extended to the NOMO scheme. The intermolecular GIE is analyzed as a two-stage process: the intramolecular bond shrinkage and the intermolecular bond elongation. According to the isotopic shifts of energy components described by the NOMO/MP2 method, the intermolecular GIE is approximately interpreted as a process reducing the exchange-repulsion interaction after the decrease of electrostatic interaction. PMID:21306139

  10. The palladium-catalyzed intermolecular C-H chalcogenation of arenes.

    PubMed

    Qiu, Renhua; Reddy, Vutukuri Prakash; Iwasaki, Takanori; Kambe, Nobuaki

    2015-01-01

    Palladium catalyzes the intermolecular chalcogenation of carbazole, 2-phenylpyridine, benzo[h]quinolone, and indole derivatives with disulfides and diselenides via selective C-H bond cleavage, providing a convenient route to thio and selenoethers. PMID:25437148

  11. Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.

    PubMed

    Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

    2002-05-01

    The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density.

  12. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  13. Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.

    PubMed

    Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

    2002-05-01

    The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density. PMID:12059561

  14. Determining the Intermolecular Potential Energy in a Gas: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Olbregts, J.; Walgraeve, J. P.

    1976-01-01

    Describes an experiment in which gas viscosity coefficients over a large temperature range are used to determine the parameters of the intermolecular potential energy and other properties such as virial coefficients. (MLH)

  15. Homologous genes for mouse 4.5S hybRNA are found in all eukaryotes and their low molecular weight RNA transcripts intermolecularly hybridize with eukaryotic 18S ribosomal RNAs.

    PubMed

    Trinh-Rohlik, Q; Maxwell, E S

    1988-07-11

    Previous work has reported the isolation and sequencing of a mouse low molecular weight RNA species designated 4.5S hybridizing RNA or hybRNA because of its ability to intermolecularly hybridize with mouse mRNA and 18S rRNA sequences. Using synthetic DNA oligonucleotide probes we have examined the conservation of this gene sequence and its expression as a lmwRNA transcript across evolution. Southern blot analysis has shown that homologous genes of single or low copy number are found in all eukaryotes examined as well as in E. coli. Northern blot analysis has demonstrated 4.5S hybRNA transcription in all mouse tissues as well as expression in yeast and Xenopus laevis as lmwRNAs of approximately 130 and 100 nucleotides, respectively, as compared with mouse/rat/hamster species of approximately 87 nucleotides. Yeast and X. laevis 4.5S hybRNA homologs, isolated by hybrid-selection, were shown by Northern blot analysis to intermolecularly hybridize with homologous as well as heterologous 18S rRNA sequences. The conservation of 4.5S hybRNA homologous genes and their expression as lmwRNA transcripts with common intermolecular RNA:RNA hybridization capabilities in fungi, amphibians, and mammals argues for a common, conserved and required biological function for this lmwRNA in all eukaryotes and potential utilization of its intermolecular RNA:RNA hybridization capabilities to carry out this function.

  16. Ice-Borehole Probe

    NASA Technical Reports Server (NTRS)

    Behar, Alberto; Carsey, Frank; Lane, Arthur; Engelhardt, Herman

    2006-01-01

    An instrumentation system has been developed for studying interactions between a glacier or ice sheet and the underlying rock and/or soil. Prior borehole imaging systems have been used in well-drilling and mineral-exploration applications and for studying relatively thin valley glaciers, but have not been used for studying thick ice sheets like those of Antarctica. The system includes a cylindrical imaging probe that is lowered into a hole that has been bored through the ice to the ice/bedrock interface by use of an established hot-water-jet technique. The images acquired by the cameras yield information on the movement of the ice relative to the bedrock and on visible features of the lower structure of the ice sheet, including ice layers formed at different times, bubbles, and mineralogical inclusions. At the time of reporting the information for this article, the system was just deployed in two boreholes on the Amery ice shelf in East Antarctica and after successful 2000 2001 deployments in 4 boreholes at Ice Stream C, West Antarctica, and in 2002 at Black Rapids Glacier, Alaska. The probe is designed to operate at temperatures from 40 to +40 C and to withstand the cold, wet, high-pressure [130-atm (13.20-MPa)] environment at the bottom of a water-filled borehole in ice as deep as 1.6 km. A current version is being outfitted to service 2.4-km-deep boreholes at the Rutford Ice Stream in West Antarctica. The probe (see figure) contains a sidelooking charge-coupled-device (CCD) camera that generates both a real-time analog video signal and a sequence of still-image data, and contains a digital videotape recorder. The probe also contains a downward-looking CCD analog video camera, plus halogen lamps to illuminate the fields of view of both cameras. The analog video outputs of the cameras are converted to optical signals that are transmitted to a surface station via optical fibers in a cable. Electric power is supplied to the probe through wires in the cable at a

  17. Investigation on intermolecular interaction between two solutes where one solute occurs in two states

    NASA Astrophysics Data System (ADS)

    Kang, Xiaoyan; He, Anqi; Guo, Ran; Chen, Jing; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2016-11-01

    The spectral behavior of a pair of 2D asynchronous spectra generated by using the double asynchronous orthogonal sample design (DAOSD) approach on a chemical system is investigated. Two solutes (P and Q) are dissolved in the solution and intermolecular interaction between P and Q is characterized. In this particular system, P occurs in two exchangeable states when it is dissolved in the solutions. Results on mathematical analysis and computer simulation demonstrated that interference unrelated to the intermolecular interaction can be completely removed. Hence the resultant 2D asynchronous spectra generated by using the DAOSD approach can reflect intermolecular interaction reliably. Moreover, properties of cross peaks in different regions of the pair of asynchronous spectra are discussed. In our previous works, cross peaks generated by using the DAOSD and relevant techniques reflect variations on peak position, bandwidth or absorptivity of the characteristic peaks of solutes caused by intermolecular interaction. However, we find that cross peak can still be produced even if intermolecular interaction do not bring about any changes on the characteristic peaks of solutes. Mathematical analysis demonstrates that cross peaks are related to the variations of chemical systems caused by intermolecular interaction at a network level.

  18. Conductivity Probe

    NASA Technical Reports Server (NTRS)

    2008-01-01

    The Thermal and Electrical Conductivity Probe (TECP) for NASA's Phoenix Mars Lander took measurements in Martian soil and in the air.

    The needles on the end of the instrument were inserted into the Martian soil, allowing TECP to measure the propagation of both thermal and electrical energy. TECP also measured the humidity in the surrounding air.

    The needles on the probe are 15 millimeters (0.6 inch) long.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  19. Cantilevered probe detector with piezoelectric element

    SciTech Connect

    Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

    2014-04-29

    A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

  20. Cantilevered probe detector with piezoelectric element

    SciTech Connect

    Adams, Jesse D; Sulchek, Todd A; Feigin, Stuart C

    2013-04-30

    A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

  1. Cantilevered probe detector with piezoelectric element

    DOEpatents

    Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

    2010-04-06

    A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

  2. Cantilevered probe detector with piezoelectric element

    DOEpatents

    Adams, Jesse D.; Sulchek, Todd A.; Feigin, Stuart C.

    2012-07-10

    A disclosed chemical detection system for detecting a target material, such as an explosive material, can include a cantilevered probe, a probe heater coupled to the cantilevered probe, and a piezoelectric element disposed on the cantilevered probe. The piezoelectric element can be configured as a detector and/or an actuator. Detection can include, for example, detecting a movement of the cantilevered probe or a property of the cantilevered probe. The movement or a change in the property of the cantilevered probe can occur, for example, by adsorption of the target material, desorption of the target material, reaction of the target material and/or phase change of the target material. Examples of detectable movements and properties include temperature shifts, impedance shifts, and resonant frequency shifts of the cantilevered probe. The overall chemical detection system can be incorporated, for example, into a handheld explosive material detection system.

  3. Single-molecule studies of DNA dynamics and intermolecular forces

    NASA Astrophysics Data System (ADS)

    Robertson, Rae Marie

    DNA molecules were used as a model system to investigate fundamental problems in polymer physics; namely, how molecular length, topology and concentration influence the dynamical properties of polymers. A set of DNA molecules suitable for polymer studies was prepared using molecular biology techniques. Video fluorescence microscopy and single-molecule tracking were used to determine self-diffusion coefficients of DNA molecules. Optical tweezers were used to measure the intermolecular forces confining entangled DNA molecules. Scaling of diffusion with molecular length was in agreement with the Zimm model for dilute solutions of linear and circular DNA, indicating that excluded volume effects are appreciable for both topologies. Scaling of diffusion with concentration was also determined for the four possible topological combinations of linear and circular molecules: linear DNA diffusing in a solution of linear DNA, linear DNA in circular DNA, circular in circular, and circular in linear. For lower concentrations molecular topology had little effect and scaling was in agreement with that of the Rouse model. As concentration was increased topology played a much larger role and scaling crossed over to that of the reptation model, predicted to describe the dynamics of entangled polymers. The notable exception was the strongly hindered diffusion observed for a circular molecule diffusing in an entangled linear solution, suggesting the importance of constraint release. Using a new experimental approach with optical tweezers, a tube-like field confining a single entangled molecule was measured, in accord with the key assumption of the reptation model. A time-dependent harmonic potential opposed displacement transverse to the molecular contour, and the force relaxations following displacement were composed of three distinct modes. A characteristic tube radius of the entangled solution was also determined, close to the classically predicted value. The dependence of the above

  4. Pollution Probe.

    ERIC Educational Resources Information Center

    Chant, Donald A.

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

  5. Ferromagnetic intermolecular interactions in a series of organic mixed crystals of galvinoxyl radical and its precursory closed shell compound

    NASA Astrophysics Data System (ADS)

    Awaga, Kunio; Sugano, Tadashi; Kinoshita, Minoru

    1986-08-01

    The magnetic properties of the 4:1, 6:1, 9:1, and 19:1 mixed crystals of galvinoxyl (4-[[3,5-bis(1,1-dimethylethyl)-4-oxo-2,5-cyclohexadien-1-ylidene]methyl]-2,6 -bis(1,1-dimethylethyl) phenoxy) radical and its precursory closed shell compound, hydrogalvinoxyl, have been studied. From the measurements of the temperature dependence of the magnetic susceptibility, it is found that the ferromagnetic intermolecular interactions, which are lost below about 85 K in pure galvinoxyl because of the phase transition, are maintained down to 2 K in these mixed crystals, and that the number of galvinoxyl radicals keeping the ferromagnetically coupled structure at low temperature increases as the concentration of hydrogalvinoxyl increases. The magnetic behavior of the mixed crystals at low temperature depends on the thermal history of the sample and is well interpreted by assuming the presence of a glassy state into which the high-temperature, ferromagnetically coupled phase is quenched. The magnetization curves show the spin multiplicity to be almost in proportion to the radical concentration in the mixed crystal and may be qualitatively understood by assuming that the mixed crystal is an assembly of one-dimensional chain segments partitioned by hydrogalvinoxyl within which the galvinoxyl radicals are coupled ferromagnetically.

  6. Accurate intermolecular ground state potential of the Ne-N2 van der Waals complex.

    PubMed

    Munteanu, Cristian R; López Cacheiro, Javier; Fernández, Berta

    2004-05-15

    Ab initio ground state potential energy surfaces are obtained from interaction energies calculated with the coupled cluster singles and doubles model including connected triples corrections [CCSD(T)] and the aug-cc-pVXZ (X=5,Q,T,D) basis sets augmented with two different sets of midbond functions (denoted 33221 and 33211). The aug-cc-pV5Z-33221 surface is characterized by a T-shaped 49.5 cm(-1) minimum at Re=3.38 Angstroms and a linear saddle point at 3.95 Angstroms with De=36.6 cm(-1). These results agree well with the values provided by the accurate semiempirical potentials available. The rovibronic spectroscopic properties are determined and compared to the available experimental data and previous theoretical results. We study the basis set convergence of the intermolecular potentials and the rotational frequencies. The aug-cc-pVTZ basis sets provide reasonable binding parameters, but seem not to be converged enough for the evaluation of the microwave spectra. The aug-cc-pVQZ basis sets considerably improve the triple zeta results. The differences between the results obtained with the aug-cc-pVTZ-33221 basis set surface and those with the aug-cc-pVQZ-33221 are smaller than those of the corresponding bases with the set of 33211 midbond functions. The aug-cc-pVQZ surfaces are close to the aug-cc-pV5Z, that are expected to be close to convergence. With our best surfaces the errors in the frequencies with respect to the accurate experimental results go down to 0.6%.

  7. Intermolecular interactions in a radiation field via the method of induced moments

    SciTech Connect

    Salam, A.

    2006-01-15

    Molecular quantum electrodynamics is employed to calculate a generalized formula for the energy shift between a pair of molecules that have electric polarizability of arbitrary multipole order and are in the presence of an intense electromagnetic field. In contrast to a previous calculation of the dipole-dipole contribution, which required fourth-order time-dependent perturbation theory for its evaluation, the present approach involves calculating the interaction between the multipole moments induced at each center by the incident beam and the resonant multipole-multipole coupling tensor together with the average value of the spatial correlation function of the displacement field for an N-photon state. The theory developed applies to the situation where the molecular pair is held fixed relative to the direction of propagation of the radiation field or is allowed to be completely randomly oriented. Explicit results are obtained for dipole-quadrupole and quadrupole-quadrupole polarizable molecules. For oriented systems the energy shift for linear and circular polarizations is examined for incident radiation propagating in directions parallel and perpendicular to the intermolecular join, and the asymptotic behavior is obtained at the limits of short and large separation distance. After performing a pair orientation average, the energy shift in the near zone is found to exhibit an R{sup -1} power-law behavior with separation distance, while the far zone has a modulated R{sup -2} dependence in all of the cases considered. None of the energy shifts obtained display discriminatory characteristics, with respect to either the handedness of the incident beam or the individual species.

  8. Iron-Catalyzed Enantioselective Cross-Coupling Reactions of α-Chloroesters with Aryl Grignard Reagents.

    PubMed

    Jin, Masayoshi; Adak, Laksmikanta; Nakamura, Masaharu

    2015-06-10

    The first iron-catalyzed enantioselective cross-coupling reaction between an organometallic compound and an organic electrophile is reported. Synthetically versatile racemic α-chloro- and α-bromoalkanoates were coupled with aryl Grignard reagents in the presence of catalytic amounts of an iron salt and a chiral bisphosphine ligand, giving the products in high yields with acceptable and synthetically useful enantioselectivities (er up to 91:9). The produced α-arylalkanoates were readily converted to the corresponding α-arylalkanoic acids with high optical enrichment (er up to >99:1) via simple deprotections/recrystallizations. The results of radical probe experiments are consistent with a mechanism that involves the formation of an alkyl radical intermediate, which undergoes subsequent enantioconvergent arylation in an intermolecular manner. The developed asymmetric coupling offers not only facile and practical access to various chiral α-arylalkanoic acid derivatives, which are of significant pharmaceutical importance, but also a basis of controlling enantioselectivity in an iron-catalyzed organometallic transformation. PMID:25955413

  9. Palladium-catalyzed Heck-type cross-couplings of unactivated alkyl iodides.

    PubMed

    McMahon, Caitlin M; Alexanian, Erik J

    2014-06-01

    A palladium-catalyzed, intermolecular Heck-type coupling of alkyl iodides and alkenes is described. This process is successful with a variety of primary and secondary unactivated alkyl iodides as reaction partners, including those with hydrogen atoms in the β position. The mild catalytic conditions enable intermolecular C-C bond formations with a diverse set of alkyl iodides and alkenes, including substrates containing base- or nucleophile-sensitive functionality.

  10. Rational targeting of subclasses of intermolecular interactions: elimination of nonspecific binding for analyte sensing.

    PubMed

    Lane, Jordan S; Richens, Joanna L; Vere, Kelly-Ann; O'Shea, Paul

    2014-08-12

    The ability to target and control intermolecular interactions is crucial in the development of several different technologies. Here we offer a tool to rationally design liquid media systems that can modulate specific intermolecular interactions. This has broad implications in deciphering the nature of intermolecular forces in complex solutions and offers insight into the forces that govern both specific and nonspecific binding in a given system. Nonspecific binding still continues to be a problem when dealing with analyte detection across a range of different detection technologies. Here, we exemplify the problem of nonspecific binding on model membrane systems and when dealing with low-abundance protein detection on commercially available SPR technology. A range of different soluble reagents that target specific subclasses of intermolecular interactions have been tested and optimized to virtually eliminate nonspecific binding while leaving specific interactions unperturbed. Thiocyanate ions are used to target nonpolar interactions, and small reagents such as glycylglycylglycine are used to modulate the dielectric constant, which targets charge-charge and dipole interactions. We show that with rational design and careful modulation these reagents offer a step forward in dissecting the intermolecular forces that govern binding, alongside offering nonspecific binding elimination in detection systems.

  11. Probes labelled with energy transfer coupled dyes

    DOEpatents

    Mathies, R.A.; Glazer, A.; Ju, J.

    1997-11-18

    Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids. 7 figs.

  12. Probes labelled with energy transfer coupled dyes

    DOEpatents

    Mathies, Richard A.; Glazer, Alexander; Ju, Jingyue

    1997-01-01

    Compositions are provided comprising sets of fluorescent labels carrying pairs of donor and acceptor dye molecules, designed for efficient excitation of the donors at a single wavelength and emission from the acceptor in each of the pairs at different wavelengths. The different molecules having different donor-acceptor pairs can be modified to have substantially the same mobility under separation conditions, by varying the distance between the donor and acceptor in a given pair. Particularly, the fluorescent compositions find use as labels in sequencing nucleic acids.

  13. Theoretical analysis of anharmonic coupling and cascading Raman signals observed with femtosecond stimulated Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Mehlenbacher, Randy D.; Lyons, Brendon; Wilson, Kristina C.; Du, Yong; McCamant, David W.

    2009-12-01

    We present a classical theoretical treatment of a two-dimensional Raman spectroscopy based on the initiation of vibrational coherence with an impulsive Raman pump and subsequent probing by two-pulse femtosecond stimulated Raman spectroscopy (FSRS). The classical model offers an intuitive picture of the molecular dynamics initiated by each laser pulse and the generation of the signal field traveling along the probe wave vector. Previous reports have assigned the observed FSRS signals to anharmonic coupling between the impulsively driven vibration and the higher-frequency vibration observed with FSRS. However, we show that the observed signals are not due to anharmonic coupling, which is shown to be a fifth-order coherent Raman process, but instead due to cascades of coherent Raman signals. Specifically, the observed vibrational sidebands are generated by parallel cascades in which a coherent anti-Stokes or Stokes Raman spectroscopy (i.e., CARS or CSRS) field generated by the coherent coupling of the impulsive pump and the Raman pump pulses participates in a third-order FSRS transition. Additional sequential cascades are discussed that will give rise to cascade artifacts at the fundamental FSRS frequencies. It is shown that the intended fifth-order FSRS signals, generated by an anharmonic coupling mechanism, will produce signals of ˜10-4 ΔOD (change in the optical density). The cascading signals, however, will produce stimulated Raman signal of ˜10-2 ΔOD, as has been observed experimentally. Experiments probing deuterochloroform find significant sidebands of the CCl3 bend, which has an E type symmetry, shifted from the A1 type C-D and C-Cl stretching modes, despite the fact that third-order anharmonic coupling between these modes is forbidden by symmetry. Experiments probing a 50:50 mixture of chloroform and d-chloroform find equivalent intensity signals of low-frequency CDCl3 modes as sidebands shifted from both the C-D stretch of CDCl3 and the C-H stretch of

  14. Comment on 'Intermolecular interaction potentials of the methane dimer from the local density approximation'

    SciTech Connect

    Li, Arvin H.-T.; Chao, S.D.

    2006-01-15

    To verify the recently calculated intermolecular interaction potentials of the methane dimer within the density functional theory using the (Perdew) local density approximation (LDA) [Chen et al., Phys. Rev. A 69, 034701 (2004)], we have performed a parallel series of calculations using the LDA/6-311++G (3df, 3pd) level of theory with selected exchange functionals (B, G96, MPW, O, PBE, PW91, S, and XA). None of the above calculated intermolecular interaction potentials from the local density approximation reproduce the results reported in the commented paper. In addition, we point out the inappropriateness of using the Lennard-Jones function to model the long-range parts of the calculated intermolecular interaction potentials, as suggested positively by Chen et al.

  15. Localization of the dominant non-enzymatic intermolecular cross-linking sites on fibrous collagen.

    PubMed

    Chiue, Hiroko; Yamazoye, Tsutako; Matsumura, Sueo

    2015-06-01

    Previous studies have shown that fibrous collagen undergoes intermolecular cross-linking at multiple sites of the elongated triple-helical regions among adjacent juxtaposed collagen molecules on incubation with a very high concentration of reducing sugar such as 200 mM ribose, and the similarity of the changes in its physicochemical properties to that of senescent collagen aged in vivo has been emphasized. In the present study, however, it was found that when incubated with less than 30 mM ribose, fibrous collagen underwent intermolecular cross-linking primarily between the telopeptide region of a collagen molecule and the triple-helical region of another adjacent collagen molecule, and intermolecular cross-linking between the triple-helical regions of adjacent collagen molecules was very small. Physiological significance of the previous studies thus needs to be reevaluated.

  16. Intermolecular and intramolecular contributions to the relaxation process in sorbitol and maltitol

    NASA Astrophysics Data System (ADS)

    Sixou, B.; Faivre, A.; David, L.; Vigier, G.

    Molecular mobility in sorbitol and maltitol is studied with spectroscopic techniques and molecular dynamics simulations in order to evaluate the relative contributions of the intermolecular and intramolecular interactions involved in the relaxation processes. The results of the molecular dynamics simulations performed on the polyols in the bulk or in vacuum compares well with the results of the analysis of the relaxation diagrams in the framework of the Perez et al . model. They both imply that the difference in the relative contributions of the intermolecular and intramolecular interactions associated with the different chemical architectures of the two polyols must be taken into account. The intermolecular interactions cannot be neglected and they are stronger in sorbitol than in maltitol in relation with the linear structure of this polyol. The intramolecular barrier, higher in the maltitol molecule with a more complex structure, could be at the origin of the higher junction temperature between the αand βrelaxation processes.

  17. Copper-catalyzed synthesis of substituted quinolines via C–N coupling/condensation from ortho-acylanilines and alkenyl iodides.

    PubMed

    Kong, Lingkai; Zhou, Yuanyuan; Huang, He; Yang, Yang; Liu, Yuanyuan; Li, Yanzhong

    2015-01-16

    An efficient cascade copper-catalyzed intermolecular Ullmann-type C–N coupling/enamine condensation reaction is described, in which ortho-acylanilines and alkenyl iodides converted to multisubstituted quinolines in good to excellent yields.

  18. Fixed-bias floating double-probe technique with simple Langmuir-probe characteristics.

    NASA Technical Reports Server (NTRS)

    Szuszczewicz, E. P.

    1972-01-01

    A new floating double-probe method is presented which has advantages over other floated-probe systems heretofore described in the literature. The method utilizes two electrodes, one of constant area and the other with a variable area, and the two-electrode configuration is separated by a fixed bias voltage. The current-voltage characteristics of the new technique, which are generated by varying the area of one electrode, are identical to those of a simple Langmuir probe, thus coupling all the advantages of a floated-probe system with the simple analysis scheme generally applied to the Langmuir probe for the determination of plasma density and temperature.

  19. A fixed bias, floating double probe technique with simple Langmuir probe characteristics

    NASA Technical Reports Server (NTRS)

    Szuszczewicz, E. P.

    1971-01-01

    A new floating double-probe method is presented which has advantages over other floated-probe systems previously described in literature. The method utilized two electrodes, one of constant area and the other with a variable area. The two-electrode configuration is separated by a fixed bias voltage. The current-voltage characteristics of the new technique, which are generated by varying the area of the one electrode, are identical to those of a simple Langmuir probe, thus coupling all the advantages of a floated-probe system with the simple analysis scheme generally applied to the Langmuir probe for the determination of plasma density and temperature.

  20. Computational Analysis of Intermolecular Coulombic Decay Effects in DNA nucleotide Photoionization

    NASA Astrophysics Data System (ADS)

    Vargas, E. L.; Robertson, J.; Andrianarijaona, V. M.

    2016-03-01

    Intermolecular Coulombic Decay (ICD) is the process of how electrons return to their original state after excitation and how this affects their immediate environment. In a previous research presentationwe had considered the hypothetical applications of Intermolecular Coulombic Decay on the adhesiveness of coding proteins within DNA molecules. This presentation is a continuation of the previous in that the results of our DFT-based computational calculations of the ionization potentials of nucleotides and their excitation energies will be presented, as well as how they influence their surroundings. Author would like to acknowledge the PUC Student Senate for financial assistance.

  1. Study of gelatin-agar intermolecular aggregates in the supernatant of its coacervate.

    PubMed

    Singh, S Santinath; Bohidar, H B; Bandyopadhyay, S

    2007-05-15

    Intermolecular interaction leading to formation of aggregates between gelatin, a polyampholyte, and agar, a polysaccharide was studied in the supernatant of the complex coacervate formed by these biopolymers. Electrophoresis, laser light scattering and viscometry data were used to determine the interaction and the physical structure of these intermolecular soluble complexes by modeling these to be prolate ellipsoids of revolution (rod-like structures with well defined axial ratio and Perrin's factor). Solution ionic strength was found to reduce the axial ratio of these complexes implying the presence of screened polarization-induced electrostatic interaction between the two biopolymers.

  2. Intermolecular potential functions and high resolution molecular spectroscopy of weakly bound complexes. Final progress report

    SciTech Connect

    Muenter, J.S.

    1997-04-01

    This report describes accomplishments over the past year in research supported by this grant. Two papers published in this period are briefly discussed. The general goal of the work is to consolidate the understanding of experimental results through a theoretical model of intermolecular potential energy surfaces. Progress in the experimental and theoretical phases of the program are presented and immediate goals outlined. The ability to construct analytic intermolecular potential functions that accurately predict the energy of interaction between small molecules will have great impact in many areas of chemistry, biochemistry, and biology.

  3. Effects of competition for charge capture from the matrix on intermolecular electron-tunneling reactions

    SciTech Connect

    Huddleston, R.K.; Miller, J.R.

    1982-04-15

    A general method is presented for correcting for the direct capture of matrix charges by the acceptor in an intermolecular electron-transfer reaction in a rigid medium. The method is based on a two-step electron-tunneling model that takes into account the correlation between matrix charge capture and intermolecular electron transfer. As an experimental test of the method, electron transfer from the anion of cinnamaldehyde to neutral pryomellitic dianhydride was studied in 2-methyltetrahydrofuran glass at 77/sup 0/K. Good agreement between the model and the experimental kinetic results was obtained.

  4. [Intermolecular Interactions between Cytisine and Bovine Serum Albumin A Synchronous Fluorescence Spectroscopic Analysis and Molecular Docking Research].

    PubMed

    Wu, Yu-hang; Han, Zhong-bao; Ma, Jia-ze; He, Yan; Liu, Li-yan; Xin, Shi-gang; Yu, Zhan

    2016-03-01

    Cytisine (Cy) is one of the alkaloids that exist naturally in the plant genera Laburnum of the family Fabaceae. With strong bioactivities, Cy is commercialized for smoking cessation for years. In this work, the study of intermolecular interactions between Cy and bovine serum albumin (BSA) was performed by applying fluorescence spectroscopic methods under simulated physiological conditions. The mechanism of fluorescence quenching of BSA by Cy was also studied. Parameters such as bathing temperature, time and solution pH were investigated to optimize the fluorescence quenching. The binding type, binding ratio and binding constant between BSA and Cy were calculated by using the Stem-Volmer equation. Experimental results indicated that Cy can quench the fluorescent emission of BSA statically by forming a 1 : 1 type non-covalent complex and the binding constant is 5.6 x 10(3) L x mol(-1). Synchronous fluorescence spectral research shows Cy may affect the fluorescence emission of Trp residues of BSA. Furthermore, molecular docking is utilized to model the complex and probe the plausible quenching mechanism. It can be noted that the hydrogen bindings and hydrophobic interactions between Cy and BSA change the micro-environment of Trp213, which leads to the fluorescence quenching of BSA. PMID:27400521

  5. Accurate first principles model potentials for intermolecular interactions.

    PubMed

    Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

    2013-01-01

    The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

  6. Intramolecular vibrational energy redistribution and intermolecular energy transfer of benzene in supercritical CO 2: measurements from the gas phase up to liquid densities

    NASA Astrophysics Data System (ADS)

    von Benten, R.; Charvat, A.; Link, O.; Abel, B.; Schwarzer, D.

    2004-03-01

    Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within τ IVR(1)<0.5 ps. The slower IVR component has a time constant of τ IVR(2)=(48±5) ps in the gas phase and in scCO 2 is accelerated by interactions with the solvent. At the highest CO 2 density it is reduced to τ IVR(2)=(6±1) ps. The corresponding IVR rate constants show a similar density dependence as the VET rate constants. Model calculations suggest that both quantities correlate with the local CO 2 density in the immediate surrounding of the benzene molecule.

  7. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

    SciTech Connect

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D.

    2014-10-07

    We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  8. Accurate intermolecular ground state potential of the Ar-N2 van der Waals complex.

    PubMed

    Munteanu, Cristian R; Cacheiro, Javier López; Fernández, Berta

    2004-12-01

    After carrying out a systematic basis set convergence study, we evaluate several ground state potential energy surfaces of the Ar-N(2) van der Waals complex at the coupled cluster singles and doubles model including connected triples corrections. We use the aug-cc-pVXZ (X=5,Q,D) and the daug-cc-pVQZ basis sets augmented with a set of 3s3p2d1f1g (denoted 33211) and 3s3p2d2f1g (denoted 33221) midbond functions, respectively. aug-cc-pVTZ-33211 results were available in the literature. The aug-cc-pV5Z-33211 (daug-cc-pVQZ-33221) surface is characterized by a T-shaped minimum at R(e)=3.709 (3.701) A and of 99.01 (102.50) cm(-1), and a linear saddle point at 4.260 (4.257) A and D(e)=75.28 (79.73) cm(-1). These results are compared with the values provided by the semiempirical potentials available, and those of previous theoretical studies. The basis set convergence of the intermolecular potentials is also analyzed. From the potentials the rovibronic spectroscopic properties are determined. We study the basis set convergence of the rotational frequencies. The binding parameters that characterized the aug-cc-pVTZ-33211 surface are reasonable, but the surface is not good enough to evaluate the microwave spectra. The aug-cc-pVQZ-33211 basis set results considerably improve the triple zeta and are close to the aug-cc-pV5Z-33211. Considering the small differences between the quadruple and the quintuple zeta surfaces, the latter results can be expected to be close to convergence. At this level the differences with respect to the accurate experimental frequencies are in the order of 0.7%. In the case of the daug-cc-pVXZ-33211,33221 (X=5,Q,T,D) series, the convergence of the interaction energies with respect to basis set improvement is not so smooth. The errors in the frequencies obtained with the daug-cc-pVQZ-33221 basis set with respect to experiment are in the order of 0.4%.

  9. Copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides.

    PubMed

    Chen, Long; Xing, Haotian; Zhang, Huaibin; Jiang, Zhong-Xing; Yang, Zhigang

    2016-08-21

    A highly practical copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides has been described, giving a series of azidochlorides in good-to-excellent yields. The stable azidoiodine(iii) reagent and SOCl2 were used as azide and chlorine sources, respectively. The synthetic applications of this protocol were also explored by a variety of synthetically useful transformations. PMID:27462802

  10. An Analysis of Two Textbooks on the Topic of Intermolecular Forces

    ERIC Educational Resources Information Center

    Tan, Daniel Kim Chwee; Seng, Chan Kim

    2004-01-01

    This paper describes the analysis of two commonly used high school (Grades 11 and 12) chemistry textbooks in Singapore to determine if the content presented in the topic of intermolecular forces is consistent with the concepts and propositional knowledge identified by the authors as essential for the learning and understanding of the topic…

  11. Orthogonal adsorption onto nano-graphene oxide using different intermolecular forces for multiplexed delivery.

    PubMed

    Wang, Feng; Liu, Biwu; Ip, Alexander C-F; Liu, Juewen

    2013-08-14

    Nano-graphene oxide can adsorb both doxorubicin and zwitterionic dioleoyl-sn-glycero-3-phosphocholine (DOPC) liposomes in an orthogonal and non-competing manner with high capacities based on different surface and intermolecular forces taking place on the heterogeneous surface of the graphene oxide. The system forms stable colloids, allowing co-delivery of both cargos to cancer cells.

  12. Intermolecular forces and nonbonded interactions: Superoperator nonlinear time-dependent density-functional-theory response approach

    SciTech Connect

    Harbola, Upendra; Mukamel, Shaul

    2004-11-01

    Electrostatic and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge-density response functions of the isolated molecules, which in turn are expanded using the collective electronic oscillator (CEO) eigenmodes of linearized time-dependent density-functional theory. Closed expressions for the intermolecular energy are derived to sixth order in charge fluctuation amplitudes.

  13. Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

    ERIC Educational Resources Information Center

    Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

    2010-01-01

    This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

  14. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-28

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  15. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view.

    PubMed

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-28

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  16. The acid free asymmetric intermolecular α-alkylation of aldehydes in fluorinated alcohols.

    PubMed

    Xiao, Jian; Zhao, Kai; Loh, Teck-Peng

    2012-04-11

    The acid free asymmetric intermolecular α-alkylation of aldehydes with alcohols has been discovered using trifluoroethanol as solvent. This unprecedented system affords the enantioenriched functionalized primary alcohols (after NaBH(4) reduction) in high yields and good to excellent enantioselectivities with wide substrate scope in the absence of any acid additive.

  17. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-01

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  18. Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces

    ERIC Educational Resources Information Center

    Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

    2008-01-01

    Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

  19. Frontier orbital symmetry control of intermolecular electron transfer. Final report, September 15, 1988--December 31, 1994

    SciTech Connect

    Stevens, B.

    1997-07-01

    This report discusses the following topics: the recovery of intermolecular transfer parameters from fluorescence quenching in liquids; photoinduced intramolecular electron transfer in flexible donor/space/acceptor systems containing an extended unsaturated spacer; electron transfer sensitized reaction; the recovery of solute and fractal dimensions from electron transfer quenching data; and frontier orbital symmetry control of back electron transfer.

  20. Intermolecular C-H Quaternary Alkylation of Aniline Derivatives Induced by Visible-Light Photoredox Catalysis.

    PubMed

    Cheng, Jie; Deng, Xia; Wang, Guoqiang; Li, Ying; Cheng, Xu; Li, Guigen

    2016-09-16

    The intermolecular direct C-H alkylation of aniline derivatives with α-bromo ketones to build a quaternary carbon center was reported with a visible-light catalysis procedure. The reaction covers a variety of functional groups with good to excellent yields. A regioselectivity favoring the ortho position for the amine group was observed and investigated with Fukui indices and spectral methods.

  1. Copper-Catalyzed Intermolecular Amidation and Imidation of Unactivated Alkanes

    PubMed Central

    2015-01-01

    We report a set of rare copper-catalyzed reactions of alkanes with simple amides, sulfonamides, and imides (i.e., benzamides, tosylamides, carbamates, and phthalimide) to form the corresponding N-alkyl products. The reactions lead to functionalization at secondary C–H bonds over tertiary C–H bonds and even occur at primary C–H bonds. [(phen)Cu(phth)] (1-phth) and [(phen)Cu(phth)2] (1-phth2), which are potential intermediates in the reaction, have been isolated and fully characterized. The stoichiometric reactions of 1-phth and 1-phth2 with alkanes, alkyl radicals, and radical probes were investigated to elucidate the mechanism of the amidation. The catalytic and stoichiometric reactions require both copper and tBuOOtBu for the generation of N-alkyl product. Neither 1-phth nor 1-phth2 reacted with excess cyclohexane at 100 °C without tBuOOtBu. However, the reactions of 1-phth and 1-phth2 with tBuOOtBu afforded N-cyclohexylphthalimide (Cy-phth), N-methylphthalimide, and tert-butoxycyclohexane (Cy-OtBu) in approximate ratios of 70:20:30, respectively. Reactions with radical traps support the intermediacy of a tert-butoxy radical, which forms an alkyl radical intermediate. The intermediacy of an alkyl radical was evidenced by the catalytic reaction of cyclohexane with benzamide in the presence of CBr4, which formed exclusively bromocyclohexane. Furthermore, stoichiometric reactions of [(phen)Cu(phth)2] with tBuOOtBu and (Ph(Me)2CO)2 at 100 °C without cyclohexane afforded N-methylphthalimide (Me-phth) from β-Me scission of the alkoxy radicals to form a methyl radical. Separate reactions of cyclohexane and d12-cyclohexane with benzamide showed that the turnover-limiting step in the catalytic reaction is the C–H cleavage of cyclohexane by a tert-butoxy radical. These mechanistic data imply that the tert-butoxy radical reacts with the C–H bonds of alkanes, and the subsequent alkyl radical combines with 1-phth2 to form the corresponding N-alkyl imide product

  2. (S)-Styryl-α-alanine used to probe the intermolecular mechanism of an intramolecular MIO-aminomutase.

    PubMed

    Wanninayake, Udayanga; Deporre, Yvonne; Ondari, Mark; Walker, Kevin D

    2011-11-22

    A Taxus canadensis phenylalanine aminomutase (TcPAM) catalyzes the isomerization of (S)-α- to (R)-β-phenylalanine, making (E)-cinnamate (~10%) as a byproduct at steady state. A currently accepted mechanism for TcPAM suggests that the amino group is transferred from the substrate to a prosthetic group comprised of an amino acid triad in the active site and then principally rebinds to the carbon skeleton of the cinnamate intermediate to complete the α-β isomerization. In contrast, when (S)-styryl-α-alanine is used as a substrate, TcPAM produces (2E,4E)-styrylacrylate as the major product (>99%) and (R)-styryl-β-alanine (<1%). Comparison of the rates of conversion of the natural substrate (S)-α-phenylalanine and (S)-styryl-α-alanine to their corresponding products (k(cat) values of 0.053 ± 0.001 and 0.082 ± 0.002 s(-1), respectively) catalyzed by TcPAM suggests that the amino group resides in the active site longer than styrylacrylate. To demonstrate this principle, inhibition constants (K(I)) for selected acrylates ranging from 0.6 to 106 μM were obtained, and each had a lower K(I) compared to that of (2E,4E)-styrylacrylate (337 ± 12 μM). Evaluation of the inhibition constants and the rates at which both the α/β-amino acids (between 7 and 80% yield) and styrylacrylate were made from a corresponding arylacrylate and styryl-α-alanine, respectively, by TcPAM catalysis revealed that the reaction progress was largely dependent on the K(I) of the acrylate. Bicyclic amino donor substrates also transferred their amino groups to an arylacrylate, demonstrating for the first time that ring-fused amino acids are productive substrates in the TcPAM-catalyzed reaction.

  3. Methyl group dynamics in paracetamol and acetanilide: probing the static properties of intermolecular hydrogen bonds formed by peptide groups

    NASA Astrophysics Data System (ADS)

    Johnson, M. R.; Prager, M.; Grimm, H.; Neumann, M. A.; Kearley, G. J.; Wilson, C. C.

    1999-06-01

    Measurements of tunnelling and librational excitations for the methyl group in paracetamol and tunnelling excitations for the methyl group in acetanilide are reported. In both cases, results are compared with molecular mechanics calculations, based on the measured low temperature crystal structures, which follow an established recipe. Agreement between calculated and measured methyl group observables is not as good as expected and this is attributed to the presence of comprehensive hydrogen bond networks formed by the peptide groups. Good agreement is obtained with a periodic quantum chemistry calculation which uses density functional methods, these calculations confirming the validity of the one-dimensional rotational model used and the crystal structures. A correction to the Coulomb contribution to the rotational potential in the established recipe using semi-emipircal quantum chemistry methods, which accommodates the modified charge distribution due to the hydrogen bonds, is investigated.

  4. Intermolecular potential parameters and combining rules determined from viscosity data

    SciTech Connect

    Bastien, Lucas A.J.; Price, Phillip N.; Brown, Nancy J.

    2010-05-07

    The Law of Corresponding States has been demonstrated for a number of pure substances and binary mixtures, and provides evidence that the transport properties viscosity and diffusion can be determined from a molecular shape function, often taken to be a Lennard-Jones 12-6 potential, that requires two scaling parameters: a well depth {var_epsilon}{sub ij} and a collision diameter {sigma}{sub ij}, both of which depend on the interacting species i and j. We obtain estimates for {var_epsilon}{sub ij} and {sigma}{sub ij} of interacting species by finding the values that provide the best fit to viscosity data for binary mixtures, and compare these to calculated parameters using several 'combining rules' that have been suggested for determining parameter values for binary collisions from parameter values that describe collisions of like molecules. Different combining rules give different values for {sigma}{sub ij} and {var_epsilon}{sub ij} and for some mixtures the differences between these values and the best-fit parameter values are rather large. There is a curve in ({var_epsilon}{sub ij}, {sigma}{sub ij}) space such that parameter values on the curve generate a calculated viscosity in good agreement with measurements for a pure gas or a binary mixture. The various combining rules produce couples of parameters {var_epsilon}{sub ij}, {sigma}{sub ij} that lie close to the curve and therefore generate predicted mixture viscosities in satisfactory agreement with experiment. Although the combining rules were found to underpredict the viscosity in most of the cases, Kong's rule was found to work better than the others, but none of the combining rules consistently yields parameter values near the best-fit values, suggesting that improved rules could be developed.

  5. Accurate intermolecular ground-state potential-energy surfaces of the HCCH-He, Ne, and Ar van der Waals complexes.

    PubMed

    Munteanu, Cristian Robert; Fernández, Berta

    2005-07-01

    Accurate ground-state intermolecular potential-energy surfaces are obtained for the HCCH-He, Ne, and Ar van der Waals complexes. The interaction energies are calculated at the coupled cluster singles and doubles including connected triple excitations level and fitted to analytic functions. For the three complexes we start with systematic basis set studies carried out at several intermolecular geometries, and using augmented correlation consistent polarized valence basis sets x-aug-cc-pVXZ (x=-,d; X=D,T,Q,5), also extended with a set of 3s3p2d1f1g midbond functions. The aug-cc-pVQZ-33211 surfaces of HCCH-He, Ne, and Ar complexes are characterized by absolute minima of -24.22, -50.20, and -122.17 cm(-1) at distances R between the rare-gas atom and the HCCH centers of mass of 4.35, 3.95, and 3.99 A, respectively; and at angles between the vector R and the HCCH main symmetry axis of 0 degrees , 43.3 degrees , and 60.6 degrees . The results are compared and considerably improve those previously available.

  6. Molecular and intermolecular effects in collagen fibril mechanics: a multiscale analytical model compared with atomistic and experimental studies.

    PubMed

    Marino, Michele

    2016-02-01

    Both atomistic and experimental studies reveal the dependence of collagen fibril mechanics on biochemical and biophysical features such as, for instance, cross-link density, water content and protein sequence. In order to move toward a multiscale structural description of biological tissues, a novel analytical model for collagen fibril mechanics is herein presented. The model is based on a multiscale approach that incorporates and couples: thermal fluctuations in collagen molecules; the uncoiling of collagen triple helix; the stretching of molecular backbone; the straightening of the telopeptide in which covalent cross-links form; slip-pulse mechanisms due to the rupture of intermolecular weak bonds; molecular interstrand delamination due to the rupture of intramolecular weak bonds; the rupture of covalent bonds within molecular strands. The effectiveness of the proposed approach is verified by comparison with available atomistic results and experimental data, highlighting the importance of cross-link density in tuning collagen fibril mechanics. The typical three-region shape and hysteresis behavior of fibril constitutive response, as well as the transition from a yielding-like to a brittle-like behavior, are recovered with a special insight on the underlying nanoscale mechanisms. The model is based on parameters with a clear biophysical and biochemical meaning, resulting in a promising tool for analyzing the effect of pathological or pharmacological-induced histochemical alterations on the functional mechanical response of collagenous tissues.

  7. The weakly bound He-HCCCN complex: High-resolution microwave spectra and intermolecular potential-energy surface

    NASA Astrophysics Data System (ADS)

    Topic, Wendy C.; Jäger, Wolfgang

    2005-08-01

    Rotational spectra of the weakly bound He-HCCCN and He-DCCCN van der Waals complexes were observed using a pulsed-nozzle Fourier-transform microwave spectrometer in the 7-26-GHz frequency region. Nuclear quadrupole hyperfine structures due to the N14 and D nuclei (both with nuclear-spin quantum number I =1) were resolved and assigned. Both strong a and weaker b-type transitions were observed and the assigned transitions were used to fit the parameters of a distortable asymmetric rotor model. The dimers are floppy, near T-shaped complexes. Three intermolecular potential-energy surfaces were calculated using the coupled-cluster method with single and double excitations and noniterative inclusion of triple excitations. Bound-state rotational energy levels supported by these surfaces were determined. The quality of the potential-energy surfaces was assessed by comparing the experimental and calculated transition frequencies and also the corresponding spectroscopic parameters. Simple scaling of the surfaces improved both the transition frequencies and spectroscopic constants. Five other recently reported surfaces [O. Akin-Ojo, R. Bukowski, and K. Szalewicz, J. Chem. Phys. 119, 8379 (2003)], calculated using a variety of methods, and their agreement with spectroscopic properties of He-HCCCN are discussed.

  8. Gas Phase Hydration of Model Peptide Chains: Far/mid Infrared Signature of Water Intermolecular Motions in the Monohydrate

    NASA Astrophysics Data System (ADS)

    Cirtog, M.; Loquais, Y.; Brenner, V.; Tardivel, B.; Mons, M.; Gloaguen, E.; Rijs, A. M.

    2012-06-01

    The far/mid infrared region (100 - 800 cm-1) of two hydrated conformations of the model peptide chain N-acetyl-phenylalanine-amide (Ac-Phe-NH_2) have been investigated in a supersonic jet expansion by conformational selective double-resonance IR/UV spectroscopy, using the free electron laser FELIX for the far IR tunability. The two folded conformations (identified in a previous work share the same H-bonding network, with the water molecule bridging the peptide ends as a donor and acceptor but differ by the orientation of the free hydrogen. By comparison with the isolated peptide, hydration gives rise to new spectroscopic features locate in three different spectral regions namely around 160, 400 and 600 cm-1. The analysis of a series of quantum chemical harmonic frequency calculations using various approaches (DFT and DFT-D) suggests that this spectral region constitutes a real challenge to the theory. As expected, the low frequency modes present a strong anharmonicity and sensitivity to the position of the water molecule. It has nevertheless allowed us to assign the new experimental signatures to a direct excitation of normal modes widely involving intermolecular libration and wagging motions of the water molecule in the complex, and revealed an extended coupling with the peptide backbone deformation motions. H.S. Biswal, Y. Loquais, B. Tardivel, E. Gloaguen and M. Mons, J. Am. Chem. Soc. 133, 3931 (2011). S. Jaeqx, M. Schmit, W.J. van der Zande, and A.M. Rijs, manuscript in preparation

  9. New probe of naturalness.

    PubMed

    Craig, Nathaniel; Englert, Christoph; McCullough, Matthew

    2013-09-20

    Any new scalar fields that perturbatively solve the hierarchy problem by stabilizing the Higgs boson mass also generate new contributions to the Higgs boson field-strength renormalization, irrespective of their gauge representation. These new contributions are physical, and in explicit models their magnitude can be inferred from the requirement of quadratic divergence cancellation; hence, they are directly related to the resolution of the hierarchy problem. Upon canonically normalizing the Higgs field, these new contributions lead to modifications of Higgs couplings that are typically great enough that the hierarchy problem and the concept of electroweak naturalness can be probed thoroughly within a precision Higgs boson program. Specifically, at a lepton collider this can be achieved through precision measurements of the Higgs boson associated production cross section. This would lead to indirect constraints on perturbative solutions to the hierarchy problem in the broadest sense, even if the relevant new fields are gauge singlets.

  10. Heat transfer probe

    DOEpatents

    Frank, Jeffrey I.; Rosengart, Axel J.; Kasza, Ken; Yu, Wenhua; Chien, Tai-Hsin; Franklin, Jeff

    2006-10-10

    Apparatuses, systems, methods, and computer code for, among other things, monitoring the health of samples such as the brain while providing local cooling or heating. A representative device is a heat transfer probe, which includes an inner channel, a tip, a concentric outer channel, a first temperature sensor, and a second temperature sensor. The inner channel is configured to transport working fluid from an inner inlet to an inner outlet. The tip is configured to receive at least a portion of the working fluid from the inner outlet. The concentric outer channel is configured to transport the working fluid from the inner outlet to an outer outlet. The first temperature sensor is coupled to the tip, and the second temperature sensor spaced apart from the first temperature sensor.

  11. Intramolecular and intermolecular hydrogen-bonding effects on photophysical properties of 2'-aminoacetophenone and its derivatives in solution.

    PubMed

    Shimada, Hirofumi; Nakamura, Akihito; Yoshihara, Toshitada; Tobita, Seiji

    2005-04-01

    Effects of intra- and intermolecular hydrogen-bonds on the photophysical properties of 2'-aminoacetophenone derivatives (X-C6H4-COCH3) having a substituted amino group (X) with different hydrogen-bonding ability to the carbonyl oxygen (X: NH2(AAP), NHCH3(MAAP), N(CH3)2(DMAAP), NHCOCH3(AAAP), NHCOCF3(TFAAP)) are investigated by means of steady-state and time-resolved fluorescence spectroscopy and time-resolved thermal lensing. Based on the photophysical parameters obtained in aprotic solvents with different polarity and protic solvents with different hydrogen-bonding ability, the characteristic photophysical behavior of the 2'-aminoacetophenone derivatives is discussed in terms of hydrogen-bonding and n,pi*-pi,pi* vibronic coupling. The dominant deactivation process of AAP and MAAP in nonpolar aprotic solvents is the extremely fast internal conversion (k(ic)= 1.0 x 10(11) s(-1) for AAP and 3.9 x 10(10) s(-1) for MAAP in n-hexane). The internal conversion rates of both compounds decrease markedly with increasing solvent polarity, suggesting that vibronic interactions between close-lying S1(pi,pi*) and S2(n,pi*) states lead to the large increase in the non-radiative decay rate of the lowest excited singlet state. It is also suggested that for MAAP, which has a stronger hydrogen-bond as compared to AAP, an intramolecular hydrogen-bonding induced deactivation is involved in the dissipation of the S1 state. For DMAAP, which cannot possess an intramolecular hydrogen-bond, the primary relaxation mechanism of the S1 state in nonpolar aprotic solvents is the intersystem crossing to the triplet state, whereas in protic solvents very efficient internal conversion due to intermolecular hydrogen-bonding is induced. In contrast, the fluorescence spectra of AAAP and TFAAP, which have an amino group with a much stronger hydrogen-bonding ability, give strongly Stokes-shifted fluorescence, indicating that these compounds undergo excited-state intramolecular proton transfer reaction

  12. Chemical Force Microscopy: Probing Chemical Origin of Interfacial Forces and Adhesion

    SciTech Connect

    Vezenov, D V; Noy, A; Ashby, P

    2005-03-21

    Experimental methods of measuring intermolecular interactions have had several recent developments which have improved our understanding of chemical forces. First, they allowed direct exploration of the role that different functionalities, solvents and environmental variables play in shaping the strength of intermolecular interactions. Chemical force microscopy approach, in particular, became an extremely effective tool for exploring the contributions of each of these factors. Second, CFM studies clearly debunked the naive notion that intermolecular interaction strength is determined only by the nature of the interacting groups. These studies showed that the interaction strength between two chemical species must always considered in context of the environment surrounding these species. Third, CFM studies highlighted the critical role solvent plays in shaping intermolecular interactions in condensed phases. Emerging kinetic view of the intermolecular interactions introduced a completely new paradigm for understanding these interactions. Kinetic modeling showed that the measured interactions strength depends not only on the energy landscape of the system, but also on the loading history prior to the bond break-up. This new paradigm refocused our attention to the energy landscape as a fundamental characteristic of the interaction. Moreover, dynamic force spectroscopy, derived from kinetic models, allowed direct characterization of the geometry of the potential energy barrier, while some other methods attempt to probe the equilibrium energy landscape directly. Further investigations of the interactions in different systems, especially interactions between biomolecules, will uncover many interesting characteristics of intermolecular potentials. These studies have the potential to reveal, for the first time, a true picture of the energy landscapes of adhesion processes in complex chemical and biological systems.

  13. Changes of microstructure characteristics and intermolecular interactions of preserved egg white gel during pickling.

    PubMed

    Zhao, Yan; Chen, Zhangyi; Li, Jianke; Xu, Mingsheng; Shao, Yaoyao; Tu, Yonggang

    2016-07-15

    Changes in gel microstructure characteristics and in intermolecular interactions of preserved egg whites during pickling were investigated. Spin-spin relaxation times of preserved egg whites significantly decreased in the first 8 days and remained unchanged after the 16th day. SEM images revealed a three-dimensional gel network, interwoven with a loose linear fibrous mesh structure. The protein gel mesh structure became more regular, smaller, and compacted with pickling time. Free sulfhydryl contents in the egg whites increased significantly, while total sulfhydryl contents dramatically decreased during pickling. The primary intermolecular forces in the preserved egg white gels were ionic and disulfide bonds. Secondary forces included hydrophobic interaction and relatively few hydrogen bonds. During the first 8 days, the proportion of ionic bonds sharply decreased, and that of disulfide bonds increased over the first 24 days.

  14. Cation-π interactions: accurate intermolecular potential from symmetry-adapted perturbation theory.

    PubMed

    Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd

    2013-09-01

    Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent.

  15. Distinguishability and chiral stability in solution: Effects of decoherence and intermolecular interactions

    SciTech Connect

    Han, Heekyung; Wardlaw, David M.; Frolov, Alexei M.

    2014-05-28

    We examine the effect of decoherence and intermolecular interactions (chiral discrimination energies) on the chiral stability and the distinguishability of initially pure versus mixed states in an open chiral system. Under a two-level approximation for a system, intermolecular interactions are introduced by a mean-field theory, and interaction between a system and an environment is modeled by a continuous measurement of a population difference between the two chiral states. The resultant equations are explored for various parameters, with emphasis on the combined effects of the initial condition of the system, the chiral discrimination energies, and the decoherence in determining: the distinguishability as measured by a population difference between the initially pure and mixed states, and the decoherence process; the chiral stability as measured by the purity decay; and the stationary state of the system at times long relative to the time scales of the system dynamics and of the environmental effects.

  16. Charge dependence of solvent-mediated intermolecular Coster-Kronig decay dynamics of aqueous ions.

    PubMed

    Ohrwall, G; Ottosson, N; Pokapanich, W; Legendre, S; Svensson, S; Björneholm, O

    2010-12-30

    The 2s and 2p photoelectron spectra have been measured for Na(+), Mg(2+), and Al(3+) ions in aqueous solution. In all cases, the 2s lines are significantly broader than the 2p features, which is attributed to a shorter lifetime of the respective 2s hole. Since intraionic Coster-Kronig decay channels from the (2s)(-1) state are closed for free Na(+), Mg(2+), and Al(3+) ions, this is evidence for an intermolecular Coster-Kronig-like process, reminiscent of intermolecular Coulombic decay (ICD), involving neighboring water solvent molecules. The observed 2s Lorentzian line widths correspond to lifetimes of the (2s)(-1) state of 3.1, 1.5, and 0.98 fs for the solvated Na, Mg, and Al ions, respectively.

  17. Theoretical study on intermolecular interactions in BrF/H nX adducts

    NASA Astrophysics Data System (ADS)

    Wu, Junyong; Zhang, Jingchang; Wang, Zhaoxu; Cao, Weiliang

    2007-09-01

    Equilibrium geometries, interaction energies, and charge transfer for the intermolecular interactions between BrF and H nX (HF, H 2O, and NH 3) were studied at the MP2/6-311++G(3d,3p) level. The halogen-bonded geometry and hydrogen-bonded geometry are observed in these interactions. The calculated interaction energies show that the halogen-bonded structures are more stable than the corresponding hydrogen-bonded structures. To study the nature of the intermolecular interactions, symmetry-adapted perturbation theory (SAPT) calculations were carried out and the results indicate that the halogen bonding interactions are dominantly inductive energy in nature, while electrostatic energy governs the hydrogen bonding interactions.

  18. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    NASA Astrophysics Data System (ADS)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  19. Changes of microstructure characteristics and intermolecular interactions of preserved egg white gel during pickling.

    PubMed

    Zhao, Yan; Chen, Zhangyi; Li, Jianke; Xu, Mingsheng; Shao, Yaoyao; Tu, Yonggang

    2016-07-15

    Changes in gel microstructure characteristics and in intermolecular interactions of preserved egg whites during pickling were investigated. Spin-spin relaxation times of preserved egg whites significantly decreased in the first 8 days and remained unchanged after the 16th day. SEM images revealed a three-dimensional gel network, interwoven with a loose linear fibrous mesh structure. The protein gel mesh structure became more regular, smaller, and compacted with pickling time. Free sulfhydryl contents in the egg whites increased significantly, while total sulfhydryl contents dramatically decreased during pickling. The primary intermolecular forces in the preserved egg white gels were ionic and disulfide bonds. Secondary forces included hydrophobic interaction and relatively few hydrogen bonds. During the first 8 days, the proportion of ionic bonds sharply decreased, and that of disulfide bonds increased over the first 24 days. PMID:26948621

  20. Intermolecular C-H Quaternary Alkylation of Aniline Derivatives Induced by Visible-Light Photoredox Catalysis.

    PubMed

    Cheng, Jie; Deng, Xia; Wang, Guoqiang; Li, Ying; Cheng, Xu; Li, Guigen

    2016-09-16

    The intermolecular direct C-H alkylation of aniline derivatives with α-bromo ketones to build a quaternary carbon center was reported with a visible-light catalysis procedure. The reaction covers a variety of functional groups with good to excellent yields. A regioselectivity favoring the ortho position for the amine group was observed and investigated with Fukui indices and spectral methods. PMID:27571116

  1. Intermolecular interactions in rifabutin-2-hydroxypropyl-β-cyclodextrin-water solutions, according to solubility data

    NASA Astrophysics Data System (ADS)

    Anshakova, A. V.; Vinogradov, E. V.; Sedush, N. G.; Kurtikyan, T. S.; Zhokhov, S. S.; Polshakov, V. I.; Ermolenko, Yu. V.; Konyukhov, V. Yu.; Maksimenko, O. O.; Gelperin, S. E.

    2016-05-01

    The formulations of rifabutin (RB) and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), obtained using different preparation techniques, are studied by means of differential scanning calorimetry and molecular spectroscopy (FTIR, NMR, Raman scattering, and photon correlation light scattering). It is established that molecules of RB do not form inclusion complexes with the molecules of HP-β-CD, and an increase in the solubility of RB determined earlier is caused by the formation of weak intermolecular associates.

  2. Estimation of Some Parameters from Morse-Morse-Spline-Van Der Waals Intermolecular Potential

    SciTech Connect

    Coroiu, I.

    2007-04-23

    Some parameters such as transport cross-sections and isotopic thermal diffusion factor have been calculated from an improved intermolecular potential, Morse-Morse-Spline-van der Waals (MMSV) potential proposed by R.A. Aziz et al. The treatment was completely classical and no corrections for quantum effects were made. The results would be employed for isotope separations of different spherical and quasi-spherical molecules.

  3. Long range intermolecular forces in change-of-phase heat transfer

    SciTech Connect

    Wayner, P.C. Jr.

    1999-07-01

    The variation of long range intermolecular forces near interfaces profoundly affects the performance of change-of-phase heat exchangers. Starting with the fundamental electromagnetic force between molecules (dielectric properties), the effects of shape, temperature and concentration on the heat transfer characteristics and stability of thin films and larger systems are reviewed. A judicious selection of literature gives a consistent set of models of particular use in heat transfer. Examples of experimental verification in this rapidly developing field are also presented.

  4. Enantioselective Intermolecular Cyclopropanations for the Synthesis of Chiral Pyrimidine Carbocyclic Nucleosides.

    PubMed

    Xie, Ming-Sheng; Zhou, Peng; Niu, Hong-Ying; Qu, Gui-Rong; Guo, Hai-Ming

    2016-09-01

    A direct route to chiral cyclopropylpyrimidine carbocyclic nucleoside analogues has been reported via highly enantioselective intermolecular cyclopropanation reactions of N1-vinylpyrimidines with α-diazoesters. With chiral ruthenium(II)-phenyloxazoline complex (2 mol %) as the catalyst, cyclopropyl pyrimidine nucleoside analogues could be obtained in good yields (71-96% yields) with high levels of diastereo- and enantioselectivities (10:1 to >20:1 dr and 96-99% ee) in 1 min. PMID:27526779

  5. Total Synthesis and Structural Reassignment of Lyngbyaloside C Highlighted by Intermolecular Ketene Esterification.

    PubMed

    Chang, Chia-Fu; Stefan, Eric; Taylor, Richard E

    2015-07-20

    Lyngbyaloside C, a classic macrolide, isolated from Lyngbya bouilloni, has shown moderate anticancer activity against several cancer cell lines. Here, we report the first total synthesis and stereochemical configuration reassignment of lyngbyaloside C. The synthesis highlights a one-pot intermolecular ketene esterification reaction to form the crucial tertiary ester and tetrahydropyran. In addition, a novel and concise synthetic pathway towards the 1,3-syn secondary, tertiary diol fragment is described using a regio- and stereospecific electrophilic ether transfer reaction.

  6. Cupric-Superoxo Mediated Inter-Molecular C-H Activation Chemistry

    PubMed Central

    Peterson, Ryan L.; Himes, Richard A.; Kotani, Hiroaki; Suenobu, Tomoyoshi; Tian, Li; Siegler, Maxime A.; Solomon, Edward I.; Fukuzumi, Shunichi; Karlin, Kenneth D.

    2011-01-01

    A new cupric-superoxo complex [LCuII(O2•−)]+, which possesses particularly strong O–O and Cu–O bonding, is capable of intermolecular C-H activation of the NADH analogue 1-benzyl-1,4-dihydronicotinamide (BNAH). Kinetic studies indicate a first-order dependence on both the Cu-complex and BNAH with a deuterium kinetic isotope effect (KIE) of 12.1, similar to that observed for certain copper monooxygenases. PMID:21265534

  7. Copper-catalyzed regio- and stereoselective intermolecular three-component oxyarylation of allenes.

    PubMed

    Itoh, Taisuke; Shimizu, Yohei; Kanai, Motomu

    2014-05-16

    A copper(II)-catalyzed intermolecular three-component oxyarylation of allenes using arylboronic acids as a carbon source and TEMPO as an oxygen source is described. The reaction proceeded under mild conditions with high regio- and stereoselectivity and functional group tolerance. A plausible reaction mechanism is proposed, involving carbocupration of allenes, homolysis of the intervening allylcopper(II), and a radical TEMPO trap. PMID:24766635

  8. Metal-free intermolecular formal cycloadditions enable an orthogonal access to nitrogen heterocycles

    PubMed Central

    Xie, Lan-Gui; Niyomchon, Supaporn; Mota, Antonio J.; González, Leticia; Maulide, Nuno

    2016-01-01

    Nitrogen-containing heteroaromatic cores are ubiquitous building blocks in organic chemistry. Herein, we present a family of metal-free intermolecular formal cycloaddition reactions that enable highly selective and orthogonal access to isoquinolines and pyrimidines at will. Applications of the products are complemented by a density functional theory mechanistic analysis that pinpoints the crucial factors responsible for the selectivity observed, including stoichiometry and the nature of the heteroalkyne. PMID:26975182

  9. Blind test of density-functional-based methods on intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Taylor, DeCarlos E.; Ángyán, János G.; Galli, Giulia; Zhang, Cui; Gygi, Francois; Hirao, Kimihiko; Song, Jong Won; Rahul, Kar; Anatole von Lilienfeld, O.; Podeszwa, Rafał; Bulik, Ireneusz W.; Henderson, Thomas M.; Scuseria, Gustavo E.; Toulouse, Julien; Peverati, Roberto; Truhlar, Donald G.; Szalewicz, Krzysztof

    2016-09-01

    In the past decade, a number of approaches have been developed to fix the failure of (semi)local density-functional theory (DFT) in describing intermolecular interactions. The performance of several such approaches with respect to highly accurate benchmarks is compared here on a set of separation-dependent interaction energies for ten dimers. Since the benchmarks were unknown before the DFT-based results were collected, this comparison constitutes a blind test of these methods.

  10. Optical probing of cold trapped atoms

    NASA Technical Reports Server (NTRS)

    Fox, R. W.; Gilbert, S. L.; Hollberg, L.; Marquardt, J. H.; Robinson, H. G.

    1993-01-01

    Transitions between excited states of laser-cooled and laser-trapped rubidium and cesium atoms are probed by use of fiber and diode lasers. High-resolution Doppler-free spectra are detected by observation of the absorption and fluorescence of light from the intermediate level of two-step cascade systems. The optical double-resonance spectra show Autler-Townes splitting in the weak probe limit and more complicated spectra for a strongly coupled three-level system.

  11. Broad-band magnetic induction probe calibration using a frequency-corrected reference probe.

    PubMed

    Hill, Carrie

    2013-10-01

    Finite impedances of magnetic induction probes attenuate and shift the field fluctuations measured by the probe so that they differ from the measured signal at the digitizer. These effects vary with frequency. Traditionally, impedance effects have been accounted for in the calibration process by sweeping the frequency of the magnetic field source through a range of frequencies. Situations arise where the conventional calibration method is not feasible due to probe geometry or hardware constraints. A new calibration technique is presented in this paper which calibrates the probe in situ at a single frequency and uses impedance measurements of the probe assembly across the desired frequency range to account for broad-band effects. The in situ calibration technique requires a reference probe with a known proportionality constant NA and known impedances. Impedance effects are corrected in the probe signal using broad-band impedance measurements included in a transfer function in frequency space. The in situ calibration technique is shown to be complicated by capacitive coupling between the probes and the high voltage source coil. Circuit modeling demonstrates that this coupling introduces negligible attenuation and a small phase-delay so that the relative phase-delay between the reference and target probe signals can be corrected by shifting the signals in time. In summary, this calibration method extends traditional single-frequency calibration techniques to broad-band applications, accounting for important non-ideal effects to improve the accuracy of the magnetic field measurement.

  12. Inelastic x-ray scattering of dense solid oxygen: Evidence for intermolecular bonding

    SciTech Connect

    Meng, Yue; Eng, Peter J.; Tse, John S.; Shaw, Dawn M.; Hu, Michael Y.; Shu, Jinfu; Gramsch, Stephen A.; Kao, Chichang; Hemley, Russell J.; Mao, Ho-kwang

    2008-08-14

    The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O{sub 2} molecules interact predominantly through the half-filled 1{pi}{sub g}* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1{pi}{sub g}* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O{sub 2} molecules at the transition to the {epsilon}-phase. The {epsilon}-phase, which consists of (O{sub 2}){sub 4} clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O{sub 2}){sub 4} clusters develop upon compression of the {epsilon}-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.

  13. Intermolecular interactions in multi-component crystals of acridinone/thioacridinone derivatives: Structural and energetics investigations

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Trzybiński, Damian; Zadykowicz, Beata

    2016-12-01

    A single crystal X-ray analysis of two multi-component crystals consisting of an acridinone/thioacridinone moiety and a solvent moiety - water and ammonia (1 and 2), respectively, was carried out to determine the crystal structures of obtained crystals. A theoretical approach was undertaken - using the DFT method, lattice energies calculations and Hirshfeld surfaces (HS) - to qualitatively and quantitatively assess the intermolecular interactions within the crystal. HS analysis was showed that the H⋯H, C⋯H/H⋯C and C⋯C contacts for both structures (altogether 81.6% of total Hirshfeld surface area for 1 and 79.3% for 2) and the O⋯H/H⋯O (14.3%) for 1 and the S⋯H/H⋯S (15.2%) contacts for 2 were the characteristic intermolecular contacts in the related crystal structures. Using a computational methods were confirmed that the main contribution to the stabilization of the crystal lattice of compound 1 comes from the Coulombic interactions, whereas in compound 2 electrostatic and van der Waals appear to have similar contribution to the crystal lattice energy. Theoretical calculations of the investigated compounds have also allowed to determine the energy of a single specific intermolecular interaction.

  14. Boiling points of halogenated ethanes: an explanatory model implicating weak intermolecular hydrogen-halogen bonding.

    PubMed

    Beauchamp, Guy

    2008-10-23

    This study explores via structural clues the influence of weak intermolecular hydrogen-halogen bonds on the boiling point of halogenated ethanes. The plot of boiling points of 86 halogenated ethanes versus the molar refraction (linked to polarizability) reveals a series of straight lines, each corresponding to one of nine possible arrangements of hydrogen and halogen atoms on the two-carbon skeleton. A multiple linear regression model of the boiling points could be designed based on molar refraction and subgroup structure as independent variables (R(2) = 0.995, standard error of boiling point 4.2 degrees C). The model is discussed in view of the fact that molar refraction can account for approximately 83.0% of the observed variation in boiling point, while 16.5% could be ascribed to weak C-X...H-C intermolecular interactions. The difference in the observed boiling point of molecules having similar molar refraction values but differing in hydrogen-halogen intermolecular bonds can reach as much as 90 degrees C.

  15. The intermolecular hydrogen-hydrogen structure of chain-molecule liquids from neutron diffraction

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Turner, J. Z.; Soper, A. K.

    1994-11-01

    Neutron diffraction isotopic substitution experiments on liquid n-decane (C10H22) and n-eicosane (C20H42) are described. The intermolecular H-H structure function hHH(Q) and the intermolecular H-H correlation function ginterHH(r) are obtained without recourse to models of the intramolecular structure. The structure of the ginterHH(r) found at 2.5, 5.0, and 7.0 Å corresponds to different shells in the H-H pair correlation function. In addition, ginterHH(r)<1 for a considerable range, due to the screening of intermolecular correlations by intramolecular correlations. This ``correlation hole'' effect is accentuated by extrapolation of the structure functions to the expected infinite wavelength limit, and shows good agreement with values determined from small-angle neutron scattering (SANS) data. All of these features are in good agreement with the results of molecular dynamics simulations for the closely related system C13H28.

  16. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    PubMed Central

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  17. Engine spectrometer probe and method of use

    NASA Technical Reports Server (NTRS)

    Barkhoudarian, Sarkis (Inventor); Kittinger, Scott A. (Inventor)

    2006-01-01

    The engine spectrometer probe and method of using the same of the present invention provides a simple engine spectrometer probe which is both lightweight and rugged, allowing an exhaust plume monitoring system to be attached to a vehicle, such as the space shuttle. The engine spectrometer probe can be mounted to limit exposure to the heat and debris of the exhaust plume. The spectrometer probe 50 comprises a housing 52 having an aperture 55 and a fiber optic cable 60 having a fiber optic tip 65. The fiber optic tip 65 has an acceptance angle 87 and is coupled to the aperture 55 so that the acceptance angle 87 intersects the exhaust plume 30. The spectrometer probe can generate a spectrum signal from light in the acceptance angle 506 and the spectrum signal can be provided to a spectrometer 508.

  18. Hydrodynamic ultrasonic probe

    DOEpatents

    Day, Robert A.; Conti, Armond E.

    1980-01-01

    An improved probe for in-service ultrasonic inspection of long lengths of a workpiece, such as small diameter tubing from the interior. The improved probe utilizes a conventional transducer or transducers configured to inspect the tubing for flaws and/or wall thickness variations. The probe utilizes a hydraulic technique, in place of the conventional mechanical guides or bushings, which allows the probe to move rectilinearly or rotationally while preventing cocking thereof in the tube and provides damping vibration of the probe. The probe thus has lower friction and higher inspection speed than presently known probes.

  19. Molecular orientation transition of organic thin films on graphite: the effect of intermolecular electrostatic and interfacial dispersion forces.

    PubMed

    Chen, Wei; Huang, Han; Thye, Andrew; Wee, Shen

    2008-09-28

    In situ low-temperature scanning tunnelling microscopy investigation reveals a molecular orientation transition of organic thin films of pentacene and p-sexiphenyl on graphite, arising from the delicate balance between the intermolecular electrostatic and interfacial dispersion forces.

  20. Interplay between molecular conformation and intermolecular interactions in conformational polymorphism: a molecular perspective from electronic calculations of tolfenamic acid.

    PubMed

    Mattei, Alessandra; Li, Tonglei

    2011-10-14

    Tolfenamic acid exhibits conformational polymorphism. The molecules in its two commonly occurred crystal structures form similar hydrogen-bonded dimers but differ in conformation. The conformational variance was analyzed by electronic calculation methods with the aim to unravel intrinsic connection between the conformational flexibility and intermolecular interactions in the polymorphs. The study was conducted mainly by conceptual density functional theory (DFT) and natural bond orbital (NBO) analysis. It is found that the conformational polymorphism is resulted from the energy competition between intramolecular π-conjugation and intermolecular hydrogen bonding. By adapting conformation that departs from being the most energetically stable, tolfenamic acid molecules can strengthen the intermolecular hydrogen-bonding interactions in the crystals. The study illustrates how the molecule's electronic properties are influenced by conformational variation and, inherently, how the intermolecular interactions become regulated. Moreover, understanding molecular interaction and crystal packing necessitates electronic structure calculation and analysis, which can be further facilitated by utilizing DFT and NBO concepts.

  1. Simulations of the THz spectrum of liquid water incorporating the effects of intermolecular charge fluxes through hydrogen bonds

    SciTech Connect

    Torii, Hajime

    2015-12-31

    The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper shows how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.

  2. Millimeter-wave active probe

    DOEpatents

    Majidi-Ahy, Gholamreza; Bloom, David M.

    1991-01-01

    A millimeter-wave active probe for use in injecting signals with frequencies above 50GHz to millimeter-wave and ultrafast devices and integrated circuits including a substrate upon which a frequency multiplier consisting of filter sections and impedance matching sections are fabricated in uniplanar transmission line format. A coaxial input and uniplanar 50 ohm transmission line couple an approximately 20 GHz input signal to a low pass filter which rolls off at approximately 25 GHz. An input impedance matching section couples the energy from the low pass filter to a pair of matched, antiparallel beam lead diodes. These diodes generate odd-numberd harmonics which are coupled out of the diodes by an output impedance matching network and bandpass filter which suppresses the fundamental and third harmonics and selects the fifth harmonic for presentation at an output.

  3. Vibrational dynamics of hydrogen-bonded complexes in solutions studied with ultrafast infrared pump-probe spectroscopy.

    PubMed

    Banno, Motohiro; Ohta, Kaoru; Yamaguchi, Sayuri; Hirai, Satori; Tominaga, Keisuke

    2009-09-15

    acceleration may be due to increased coupling between the OH stretching mode and the accepting mode of the VER, because the low-frequency shift caused by hydrogen bond formation is very large. Unlike phenol oligomers, however, the pump-probe signals of phenol-base complexes did not exhibit probe frequency dependence. For these complexes, rapid interconversion between different conformations causes rapid fluctuations in the vibrational frequency of the OH stretching modes, and these fluctuations level the VER times of different conformations. For the benzoic acid dimer, a quantum beat at a frequency of around 100 cm(-1) is superimposed on the pump-probe signal. This result indicates the presence of strong anharmonic coupling between the intramolecular OH stretching and the intermolecular stretching modes. From a two-dimensional plot of the OH stretching wavenumber and the low-frequency wavenumber, the wavenumber of the low-frequency mode is found to increase monotonically as the probe wavenumber is shifted toward lower wavenumbers. Our results represent a quantitative determination of the acceleration of VER by the formation of hydrogen bonds. Our studies merit further evaluation and raise fundamental questions about the current theory of vibrational dynamics in the condensed phase.

  4. Bioconjugation Methods for Coupling Targeting Ligands with Fluorescent Dyes.

    PubMed

    Ling, Xiaoxi

    2016-01-01

    Targeted molecular imaging probes are essential tools for visualization of specific molecular processes in cells and living systems. Among these, targeted fluorescent probes are widely used due to the high sensitivity and resolution of fluorescence imaging. The conventional strategy for developing targeted fluorescent probes is to couple targeting ligands with fluorescent dyes by covalent bond via bioconjugation. Here, we describe several commonly used bioconjugation methods, from traditional amide and thiol coupling, to metal-catalyzed coupling reaction and catalyst free cycloaddition. PMID:27283413

  5. Surface enhanced Raman gene probe and methods thereof

    DOEpatents

    Vo-Dinh, T.

    1998-02-24

    The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  6. Surface enhanced Raman gene probe and methods thereof

    DOEpatents

    Vo-Dinh, Tuan

    1998-01-01

    The subject invention disclosed herein is a new gene probe biosensor and methods thereof based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays.

  7. Surface enhanced Raman gene probe and methods thereof

    DOEpatents

    Vo-Dinh, T.

    1998-09-29

    The subject invention disclosed herein is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed thereon. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  8. Surface enhanced Raman gene probe and methods thereof

    DOEpatents

    Vo-Dinh, T.

    1998-07-21

    The subject invention disclosed is a new gene probe biosensor and methods based on surface enhanced Raman scattering (SERS) label detection. The SER gene probe biosensor comprises a support means, a SER gene probe having at least one oligonucleotide strand labeled with at least one SERS label, and a SERS active substrate disposed on the support means and having at least one of the SER gene probes adsorbed. Biotargets such as bacterial and viral DNA, RNA and PNA are detected using a SER gene probe via hybridization to oligonucleotide strands complementary to the SER gene probe. The support means supporting the SERS active substrate includes a fiberoptic probe, an array of fiberoptic probes for performance of multiple assays and a waveguide microsensor array with charge-coupled devices or photodiode arrays. 18 figs.

  9. Controlling electronic effects and intermolecular packing in contorted polyaromatic hydrocarbons (c-PAHs): towards high mobility field effect transistors.

    PubMed

    Bhattacharyya, Kalishankar; Mukhopadhyay, Titas Kumar; Datta, Ayan

    2016-06-01

    We have investigated the electronic and charge transport properties of two regioisomeric contorted polyaromatic hydrocarbons at the molecular level as well as in the crystalline state. Electron and hole transport is studied on the basis of an incoherent charge hopping model through DFT calculations. For trifluro-dibenzoperylene (CF3-DBP, ), which crystallizes as a herringbone network, the computed drift hole and electron mobilities are 0.234 and 0.008 cm(2) V(-1) S(-1), respectively. The greater hole mobility in the DBP crystal (μh/μe = 29) can be rationalized by its lower hole reorganization energy and higher hole transfer integral simultaneously. These calculations for the pristine DBP crystal differ from recent experiments indicating its preferential electron conductivity. This might be attributed to the interaction of the molecules with the gold source/drain electrodes. Its second regioisomer, , having a HOMO-LUMO gap of 3.2 eV and thus expectedly inefficient, can be converted into an effective OFET material by replacing the Ph-CF3 groups by oxo groups (>C[double bond, length as m-dash]O) in the 9 and 10 positions (9,10-dioxotribenzopyrene, ). has a suitable HOMO-LUMO gap of 2.18 eV. This bowl-shaped molecule is predicted to pack in a stacked orientation with preferential concaveconcave pairs having a short intermolecular distance of 4.15 Å and identical inter-chromophoric electron/hole coupling (th ∼ te). This creates an ambipolar charge transport behavior in . Clearly, fine tuning the structure-property relationship opens up the possibility of implanting tailored OFET properties in the existing library of molecules. PMID:27189183

  10. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    PubMed

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  11. Using corresponding state theory to obtain intermolecular potentials to calculate pure liquid shock Hugoniots

    SciTech Connect

    Hobbs, M.L.

    1997-12-01

    Determination of product species, equations-of-state (EOS) and thermochemical properties of high explosives and pyrotechnics remains a major unsolved problem. Although, empirical EOS models may be calibrated to replicate detonation conditions within experimental variability (5--10%), different states, e.g. expansion, may produce significant discrepancy with data if the basic form of the EOS model is incorrect. A more physically realistic EOS model based on intermolecular potentials, such as the Jacobs Cowperthwaite Zwisler (JCZ3) EOS, is needed to predict detonation states as well as expanded states. Predictive capability for any EOS requires a large species data base composed of a wide variety of elements. Unfortunately, only 20 species have known JCZ3 molecular force constants. Of these 20 species, only 10 have been adequately compared to experimental data such as molecular scattering or shock Hugoniot data. Since data in the strongly repulsive region of the molecular potential is limited, alternative methods must be found to deduce force constants for a larger number of species. The objective of the present study is to determine JCZ3 product species force constants by using a corresponding states theory. Intermolecular potential parameters were obtained for a variety of gas species using a simple corresponding states technique with critical volume and critical temperature. A more complex, four parameter corresponding state method with shape and polarity corrections was also used to obtain intermolecular potential parameters. Both corresponding state methods were used to predict shock Hugoniot data obtained from pure liquids. The simple corresponding state method is shown to give adequate agreement with shock Hugoniot data.

  12. Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

    SciTech Connect

    Bai, Yang; He, Hui-Min; Li, Ying; Zhou, Zhong-Jun; Wang, Jia-Jun; Wu, Di; Chen, Wei; Gu, Feng-Long; Sumpter, Bobby G.; Huang, Jingsong

    2015-02-19

    Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field, the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H2O)2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.

  13. Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

    DOE PAGES

    Bai, Yang; He, Hui-Min; Li, Ying; Zhou, Zhong-Jun; Wang, Jia-Jun; Wu, Di; Chen, Wei; Gu, Feng-Long; Sumpter, Bobby G.; Huang, Jingsong

    2015-02-19

    Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H2O)2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

  14. Intermolecular disulfide bond formation promotes immunoglobulin aggregation: investigation by fluorescence correlation spectroscopy.

    PubMed

    Nag, Moupriya; Bera, Kallol; Basak, Soumen

    2015-01-01

    Protein aggregation generally results from association between hydrophobic regions of individual monomers. However, additional mechanisms arising from specific interactions, such as intermolecular disulfide bond formation, may also contribute to the process. The latter is proposed to be the initiating pathway for aggregation of immunoglobulin (IgG), which is essential for triggering its immune response. To test the veracity of this hypothesis, we have employed fluorescence correlation spectroscopy to measure the kinetics of aggregation of IgG in separate experiments either allowing or inhibiting disulfide formation. Fluorescence correlation spectroscopy measurements yielded a diffusion time (τ(D)) of ∼200 µsec for Rhodamine-labeled IgG, corresponding to a hydrodynamic radius (R(H)) of 56 Å for the IgG monomer. The aggregation kinetics of the protein was followed by monitoring the time evolution of τ(D) under conditions in which its cysteine residues were either free or blocked. In both cases, the progress curves confirmed that aggregation proceeded via the nucleation-dependent polymerization pathway. However, for aggregation in the presence of free cysteines, the lag times were shorter, and the aggregate sizes bigger, than their respective counterparts for aggregation in the presence of blocked cysteines. This result clearly demonstrates that formation of intermolecular disulfide bonds represents a preferred pathway in the aggregation process of IgG. Fluorescence spectroscopy showed that aggregates formed in experiments where disulfide formation was prevented denatured at lower concentration of guanidine hydrochloride than those obtained in experiments where the disulfides were free to form, indicating that intermolecular disulfide bridging is a valid pathway for IgG aggregation. PMID:25371040

  15. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  16. Protein Mediated Magnetic Coupling between Lactate and Water Protons

    NASA Astrophysics Data System (ADS)

    Swanson, Scott D.

    1998-11-01

    The magnetic coupling between methyl lactate protons and water protons in samples of cross-linked bovine serum albumin (BSA) is studied. Cross-relaxation spectroscopy shows efficient magnetization transfer from immobilized BSA to both water and methyl lactate protons. Transient and steady-state NOE experiments reveal a negative intermolecular NOE between methyl lactate and water protons. Lactate is indirectly detected by selectively saturating the methyl lactate protons and measuring the decrease in water proton magnetization. Indirect detection of methyl lactate protons is an order of magnitude more sensitive than direct detection in these model systems. Lactate was indirectly imaged, via the water proton resonance, with 1.1-μl voxels in 2 min. Immobilized BSA reduces the intermolecular correlation time between water and lactate protons into the spin-diffusion limit where the NOE is negative. Possible molecular mechanisms for this coupling and applications toin vivospectroscopy are discussed.

  17. New openings for porous systems research from intermolecular double-quantum NMR.

    PubMed

    Capuani, S; Alesiani, M; Branca, R T; Maraviglia, B

    2004-01-01

    It has been recently recognized that residual intermolecular double-quantum coherences (iDQcs) provide a novel contrast mechanism to study heterogeneity in liquid systems. This is of much interest in the field of the physics of matter and biomedicine. Nowadays, literature concerning the behaviour of the iDQc signal originated by highly heterogeneous systems such as fluids in porous media is scarce. In this paper, we report and discuss our principal results about iDQc signal behaviour in confined liquid systems (trabecular bone, travertine, porous standard systems) and also some new results obtained on doped water in glass capillary pipes. PMID:14698403

  18. Intermolecular forces in phase-change heat transfer: 1998 Kern award review

    SciTech Connect

    Wayner, P.C. Jr.

    1999-10-01

    The variation of long-range intermolecular forces near interfaces profoundly affects the performance of change-of-phase heat exchangers. Starting with the fundamental electromagnetic force between molecules (dielectric properties), the effects of shape (Kelvin effect), temperature (Clapeyron effect) and concentration on the heat-transfer characteristics of thin films and larger systems are reviewed and connected. A judicious selection of literature gives a consistent set of models of particular use in heat transfer. Examples of experimental verification of these interfacial models in this rapidly developing field are also presented.

  19. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution.

    PubMed

    Robertson, Rae M; Smith, Douglas E

    2007-09-21

    We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tubelike confining field was measured in accord with the key assumption of reptation models. A time-dependent harmonic potential opposed transverse displacement, in accord with recent simulation findings. A tube radius of 0.8 microm was determined, close to the predicted value (0.5 microm). Three relaxation modes (approximately 0.4, 5, and 34 s) were measured following transverse displacement, consistent with predicted relaxation mechanisms.

  20. Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.

    2006-09-20

    Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

  1. Profile of the intermolecular forces governing the interaction of drugs with mucin.

    PubMed

    Caron, Giulia; Visentin, Sonja; Pontremoli, Carlotta; Ermondi, Giuseppe

    2015-07-01

    The study highlights the balance of the intermolecular forces governing the interaction between drugs and mucin. The interaction strength is expressed as a retention factor k (data retrieved from the literature (Gargano et al., 2014)) obtained by a new bio-affinity chromatographic method in which the stationary phase is based on covalently immobilized mucin (porcine gastric mucin, PGM). A quantitative structure-property relationship (QSPR) between logk and 82 VolSurf+ descriptors was established and mechanistically interpreted. Results evidence that all blocks contribute similarly to the model; moreover, hydrogen bonding donor (HBD) properties of solutes favor the interaction with mucin; and thus, support their detrimental role on drug permeability.

  2. Iron(II)-Catalyzed Intermolecular Aminofluorination of Unfunctionalized Olefins Using Fluoride Ion.

    PubMed

    Lu, Deng-Fu; Zhu, Cheng-Liang; Sears, Jeffrey D; Xu, Hao

    2016-09-01

    We herein report a new catalytic method for intermolecular olefin aminofluorination using earth-abundant iron catalysts and nucleophilic fluoride ion. This method tolerates a broad range of unfunctionalized olefins, especially nonstyrenyl olefins that are incompatible with existing olefin aminofluorination methods. This new iron-catalyzed process directly converts readily available olefins to internal vicinal fluoro carbamates with high regioselectivity (N vs F), many of which are difficult to prepare using known methods. Preliminary mechanistic studies demonstrate that it is possible to exert asymmetric induction using chiral iron catalysts and that both an iron-nitrenoid and carbocation species may be reactive intermediates. PMID:27529196

  3. Copper-catalyzed intermolecular trifluoromethylarylation of alkenes: mutual activation of arylboronic acid and CF3+ reagent.

    PubMed

    Wang, Fei; Wang, Dinghai; Mu, Xin; Chen, Pinhong; Liu, Guosheng

    2014-07-23

    A novel copper-catalyzed intermolecular trifluoromethylarylation of alkenes is developed using less active ether-type Togni's reagent under mild reaction conditions. Various alkenes and diverse arylboronic acids are compatible with these conditions. Preliminary mechanistic studies reveal that a mutual activation process between arylboronic acid and CF3(+) reagent is essential. In addition, the reaction might involve a rate-determining transmetalation, and the final aryl C-C bond is derived from reductive elimination of the aryl(alkyl)Cu(III) intermediate. PMID:24983408

  4. Flat versus twisted rotamers of 2,4-disubstituted thiazoles: the effect of intermolecular hydrogen bonds.

    PubMed

    Bernès, Sylvain; Berros, Martha I; Rodríguez de Barbarín, Cecilia; Sánchez-Viesca, Francisco

    2002-03-01

    In the title compounds, 2-amino-4-(2-chloro-4,5-dimethoxyphenyl)-1,3-thiazole, C(11)H(11)ClN(2)O(2)S, (I), and 4-(2-chloro-4,5-dimethoxyphenyl)-2-methyl-1,3-thiazole, C(12)H(12)ClNO(2)S, (II), the dihedral angles between the thiazole moiety and the chloroaryl group are 51.61 (10) and 8.44 (14), respectively. This difference is a consequence of intermolecular hydrogen bonds forcing the stabilization of a twisted rotamer in (I). Substitution of the amino function by a methyl group precludes these contacts, giving a flat rotamer in (II).

  5. Regiodivergent Intermolecular [3+2] Cycloadditions of Vinyl Aziridines and Allenes: Stereospecific Synthesis of Chiral Pyrrolidines.

    PubMed

    Lin, Tao-Yan; Zhu, Chao-Ze; Zhang, Peichao; Wang, Yidong; Wu, Hai-Hong; Feng, Jian-Jun; Zhang, Junliang

    2016-08-26

    The first rhodium-catalyzed intermolecular [3+2] cycloaddition reaction of vinyl aziridines and allenes for the synthesis of enantioenriched functionalized pyrrolidines was realized. [3+2] cycloaddition with the proximal C=C bond of N-allenamides gave 3-methylene-pyrrolidines in high regio- and diastereoselectivity, whereas, 2-methylene-pyrrolidines were obtained as the major products by the cycloadditions of vinyl aziridines with the distal C=C bond of allenes. Use of readily available starting materials, a broad substrate scope, high selectivity, mild reaction conditions, as well as versatile functionalization of the cycloadducts make this approach very practical and attractive. PMID:27485044

  6. Intermolecular Interactions between Eosin Y and Caffeine Using 1H-NMR Spectroscopy

    PubMed Central

    Okuom, Macduff O.; Wilson, Mark V.; Jackson, Abby; Holmes, Andrea E.

    2014-01-01

    DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using 1H-NMR, 1H-COSY, and 1H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed. PMID:25018772

  7. Intermolecular Interactions between Eosin Y and Caffeine Using (1)H-NMR Spectroscopy.

    PubMed

    Okuom, Macduff O; Wilson, Mark V; Jackson, Abby; Holmes, Andrea E

    2013-12-31

    DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using (1)H-NMR, (1)H-COSY, and (1)H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed. PMID:25018772

  8. Catalytic Selenium-Promoted Intermolecular Friedel-Crafts Alkylation with Simple Alkenes.

    PubMed

    Tang, E; Zhao, Yinjiao; Li, Wen; Wang, Weilin; Zhang, Meng; Dai, Xin

    2016-03-01

    A method for conducting selenium-promoted intermolecular Friedel-Crafts (F-C) alkylation reactions has been developed with simple alkenes using trimethylsilyl trifluoromethanesulfonate as a catalyst and N-phenylselenophthalimide as an efficient selenium source. Electron-rich arenes smoothly underwent F-C alkylation with a variety of alkenes to afford alkylated products in good yield and with high regioselectivity and diastereoselectivity. The regioselectivity and stereoselectivity of arenes and alkenes as well as a preliminary mechanism of the F-C alkylation reaction are discussed. PMID:26882088

  9. ORGANIC CHEMISTRY. Iron-catalyzed intermolecular [2+2] cycloadditions of unactivated alkenes.

    PubMed

    Hoyt, Jordan M; Schmidt, Valerie A; Tondreau, Aaron M; Chirik, Paul J

    2015-08-28

    Cycloadditions, such as the [4+2] Diels-Alder reaction to form six-membered rings, are among the most powerful and widely used methods in synthetic chemistry. The analogous [2+2] alkene cycloaddition to synthesize cyclobutanes is kinetically accessible by photochemical methods, but the substrate scope and functional group tolerance are limited. Here, we report iron-catalyzed intermolecular [2+2] cycloaddition of unactivated alkenes and cross cycloaddition of alkenes and dienes as regio- and stereoselective routes to cyclobutanes. Through rational ligand design, development of this base metal-catalyzed method expands the chemical space accessible from abundant hydrocarbon feedstocks.

  10. Iridium-catalyzed intermolecular dehydrogenative silylation of polycyclic aromatic compounds without directing groups.

    PubMed

    Murai, Masahito; Takami, Keishi; Takai, Kazuhiko

    2015-03-16

    This study describes the iridium-catalyzed intermolecular dehydrogenative silylation of C(sp(2))-H bonds of polycyclic aromatic compounds without directing groups. The reaction produced various arylsilanes through both Si-H and C-H bond activation, with hydrogen as the sole byproduct. Reactivity was affected by the electronic nature of the aromatic compounds, and silylation of electron-deficient and polycyclic aromatic compounds proceeded efficiently. Site-selectivity was controlled predominantly by steric factors. Therefore, the current functionalization proceeded with opposite chemo- and site-selectivity compared to that observed for general electrophilic functionalization of aromatic compounds.

  11. DFT Study of Pd(0)-Promoted Intermolecular C-H Amination with O-Benzoyl Hydroxylamines.

    PubMed

    Zhou, Yunfei; Bao, Xiaoguang

    2016-09-16

    Computational studies were carried out to explore the mechanism of Pd-catalyzed intermolecular C-H amination with O-benzoyl hydroxylamines in which both Pd(0) and Pd(II) catalysts are effective. For the Pd(0)-catalyzed reaction, the generally assumed Pd(0)/Pd(II) catalytic cycle might not be feasible. Instead, Pd(0), being essentially a catalyst precursor, could be oxidized to Pd(II), and the C-H amination proceeds through the Pd(II)/Pd(IV) catalytic cycle. PMID:27573977

  12. Iridium(III)-Catalyzed Regioselective Intermolecular Unactivated Secondary Csp(3) -H Bond Amidation.

    PubMed

    Xiao, Xinsheng; Hou, Cheng; Zhang, Zhenhui; Ke, Zhuofeng; Lan, Jianyong; Jiang, Huanfeng; Zeng, Wei

    2016-09-19

    For the first time, a highly regioselective intermolecular sulfonylamidation unactivated secondary Csp(3) -H bond has been achieved using Ir(III) catalysts. The introduced N,N'-bichelating ligand plays a crucial role in enabling iridium-nitrene insertion into a secondary Csp(3) -H bond via an outer-sphere pathway. Mechanistic studies and density functional theory (DFT) calculations demonstrated that a two-electron concerted nitrene insertion was involved in this Csp(3) -H amidation process. This method tolerates a broad range of linear and branched-chain N-alkylamides, and provides efficient access to diverse γ-sulfonamido-substituted aliphatic amines. PMID:27561950

  13. Modification of PEGylated enzyme with glutaraldehyde can enhance stability while avoiding intermolecular crosslinking†

    PubMed Central

    McShane, M. J.

    2015-01-01

    We demonstrate an enzyme stabilization approach whereby a model enzyme is PEGylated, followed by controlled chemical modification with glutaraldehyde. Using this stabilization strategy, size increases and aggregation due to intermolecular crosslinking are avoided. Immediately following synthesis, the PEGylated enzyme with and without glutaraldehyde modification possessed specific activities of 372.9 ± 20.68 U/mg and 373.9 ± 15.14 U/mg, respectively (vs. 317.7 ± 19.31 U/mg for the native enzyme). The glutaraldehyde-modified PEGylated enzyme retains 73% original activity after 4 weeks at 37 °C (vs. 2% retention for control). PMID:26052433

  14. Intermolecular hydroaminoalkylation of alkenes and dienes using a titanium mono(formamidinate) catalyst.

    PubMed

    Dörfler, Jaika; Preuss, Till; Brahms, Christian; Scheuer, Dennis; Doye, Sven

    2015-07-21

    An easily accessible formamidinate ligand-bearing titanium complex initially synthesized by Eisen et al. is used as catalyst for intermolecular hydroaminoalkylation reactions of unactivated, sterically demanding 1,1- and 1,2-disubstituted alkenes and styrenes with secondary amines. The corresponding reactions, which have never been achieved with titanium catalysts before, take place with excellent regioselectivity (up to 99 : 1) and in addition, corresponding reactions of 1,3-butadienes with N-methylbenzylamine are also described for the first time.

  15. Predicting and managing heat dissipation from a neural probe.

    PubMed

    Smith, Andrew N; Christian, Matthew P; Firebaugh, Samara L; Cooper, Garret W; Jamieson, Brian G

    2015-08-01

    Light stimulating neural probes are rapidly increasing our understanding of neural pathways. Relocating the externally coupled light source to the probe tip has the potential to dramatically improve the flexibility of the technique. However, this approach would generate heat within the embedded probe where even minor temperature excursions could easily damage tissues under study. A COMSOL model was used to study the thermal effects of these heated probes in the brain including blood perfusion and metabolic heating, and to investigate the effect of passive methods for improving heat dissipation. The probe temperature initially decreases with insertion depth, and then becomes steady. Extending the probe beyond the heated region has a similar effect, while increasing the size of the heated region steadily decreases the probe temperature. Increasing the thermal conductivity of the probe promotes spreading, decreasing the probe temperature. The effects of insertion depth and probe power dissipation were experimentally tested with a microfabricated, heated mock neural probe. The heated probe was tested in 0.65 % agarose gel at room temperature and in ex vivo cow brain at body temperature. The thermal resistance between the probe and the neural tissue or agarose gel was determined at a range of insertion depths and compared to the COMSOL model.

  16. Predicting and managing heat dissipation from a neural probe.

    PubMed

    Smith, Andrew N; Christian, Matthew P; Firebaugh, Samara L; Cooper, Garret W; Jamieson, Brian G

    2015-08-01

    Light stimulating neural probes are rapidly increasing our understanding of neural pathways. Relocating the externally coupled light source to the probe tip has the potential to dramatically improve the flexibility of the technique. However, this approach would generate heat within the embedded probe where even minor temperature excursions could easily damage tissues under study. A COMSOL model was used to study the thermal effects of these heated probes in the brain including blood perfusion and metabolic heating, and to investigate the effect of passive methods for improving heat dissipation. The probe temperature initially decreases with insertion depth, and then becomes steady. Extending the probe beyond the heated region has a similar effect, while increasing the size of the heated region steadily decreases the probe temperature. Increasing the thermal conductivity of the probe promotes spreading, decreasing the probe temperature. The effects of insertion depth and probe power dissipation were experimentally tested with a microfabricated, heated mock neural probe. The heated probe was tested in 0.65 % agarose gel at room temperature and in ex vivo cow brain at body temperature. The thermal resistance between the probe and the neural tissue or agarose gel was determined at a range of insertion depths and compared to the COMSOL model. PMID:26223563

  17. Eddy-Current Probes For Inspecting Graphite-Fiber Composites

    NASA Technical Reports Server (NTRS)

    Workman, Gary L.; Wang, Morgan

    1992-01-01

    Eddy-current probes with E-shaped and U-shaped magnetic cores developed to detect flaws in graphite-fiber/epoxy and other composites. Magnetic fields more concentrated, yielding better coupling with specimens.

  18. Vertically aligned nanostructure scanning probe microscope tips

    DOEpatents

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.

    2006-12-19

    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  19. Galileo Probe Battery System

    NASA Technical Reports Server (NTRS)

    Dagarin, B. P.; Taenaka, R. K.; Stofel, E. J.

    1997-01-01

    The conclusions of the Galileo probe battery system are: the battery performance met mission requirements with margin; extensive ground-based and flight tests of batteries prior to probe separation from orbiter provided good prediction of actual entry performance at Jupiter; and the Li-SO2 battery was an important choice for the probe's main power.

  20. A Practical and Catalytic Reductive Olefin Coupling

    PubMed Central

    2015-01-01

    A redox-economic method for the direct coupling of olefins that uses an inexpensive iron catalyst and a silane reducing agent is reported. Thus, unactivated olefins can be joined directly to electron-deficient olefins in both intra- and intermolecular settings to generate hindered bicyclic systems, vicinal quaternary centers, and even cyclopropanes in good yield. The reaction is not sensitive to oxygen or moisture and has been performed on gram-scale. Most importantly, it allows access to many compounds that would be difficult or perhaps impossible to access using other methods. PMID:24428607

  1. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components.

    PubMed

    Makarewicz, Jan; Shirkov, Leonid

    2016-05-28

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm(-1) is close to that of 387 cm(-1) calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  2. Character of intermolecular interaction in pyridine-argon complex: Ab initio potential energy surface, internal dynamics, and interrelations between SAPT energy components

    NASA Astrophysics Data System (ADS)

    Makarewicz, Jan; Shirkov, Leonid

    2016-05-01

    The pyridine-Ar (PAr) van der Waals (vdW) complex is studied using a high level ab initio method. Its structure, binding energy, and intermolecular vibrational states are determined from the analytical potential energy surface constructed from interaction energy (IE) values computed at the coupled cluster level of theory with single, double, and perturbatively included triple excitations with the augmented correlation consistent polarized valence double-ζ (aug-cc-pVDZ) basis set complemented by midbond functions. The structure of the complex at its global minimum with Ar at a distance of 3.509 Å from the pyridine plane and shifted by 0.218 Å from the center of mass towards nitrogen agrees well with the corresponding equilibrium structure derived previously from the rotational spectrum of PAr. The PAr binding energy De of 392 cm-1 is close to that of 387 cm-1 calculated earlier at the same ab initio level for the prototypical benzene-Ar (BAr) complex. However, under an extension of the basis set, De for PAr becomes slightly lower than De for BAr. The ab initio vdW vibrational energy levels allow us to estimate the reliability of the methods for the determination of the vdW fundamentals from the rotational spectra. To disclose the character of the intermolecular interaction in PAr, the symmetry-adapted perturbation theory (SAPT) is employed for the analysis of different physical contributions to IE. It is found that SAPT components of IE can be approximately expressed in the binding region by only two of them: the exchange repulsion and dispersion energy. The total induction effect is negligible. The interrelations between various SAPT components found for PAr are fulfilled for a few other complexes involving aromatic molecules and Ar or Ne, which indicates that they are valid for all rare gas (Rg) atoms and aromatics.

  3. Remote Adjustable focus Raman Spectroscopy Probe

    SciTech Connect

    Schmucker, John E.; Blasi, Raymond J.; Archer, William B.

    1998-07-28

    A remote adjustable focus Raman spectroscopy probe allows for analyzing Raman scattered light from a point of interest external to the probe. An environmental barrier including at least one window separates the probe from the point of interest. An optical tube is disposed adjacent to the environmental barrier and includes along working length compound lens objective next to the window. A beam splitter and a mirror are at the other end. A mechanical means is used to translate the probe body in the X, Y, and Z directions resulting in a variable focus optical apparatus. Laser light is reflected by the beam splitter and directed toward the compound lens objective, then through the window and focused on the point of interest. Raman scattered light is then collected by the compound lens objective and directed through the beam splitter to a mirror. A device for analyzing the light, such as a monochrometer, is coupled to the mirror.

  4. Fine positioning of a poloidal probe array

    SciTech Connect

    Yamada, T.; Nagashima, Y.; Inagaki, S.; Kawai, Y.; Yagi, M.; Itoh, S.-I.; Maruta, T.; Shinohara, S.; Terasaka, K.; Kawaguchi, M.; Fukao, M.; Fujisawa, A.; Itoh, K.

    2007-12-15

    Multipoint detection is an essential requirement for investigating plasma turbulence which is a highly nonlinear phenomenon in space and time. We have fabricated an array of 64-channel poloidal probes surrounding the linear cylindrical plasma named LMD-U in order to study turbulence properties, particularly the nonlinear mode couplings, in the domain of poloidal wave number and frequency. However, misalignments of probe tips produce spurious modes, which do not exist in the real plasma, to distort the precise wave number measurements. The paper presents the description of the 64-channel poloidal probe array with means to adjust the probe positions, with discussion on the effects of the misalignments on the wave number measurements.

  5. Intra- and intermolecular hydrogen bonding in acetylacetone and benzoylacetone derived enaminone derivatives

    NASA Astrophysics Data System (ADS)

    Lazić, Vedrana; Jurković, Mihaela; Jednačak, Tomislav; Hrenar, Tomica; Vuković, Jelena Parlov; Novak, Predrag

    2015-01-01

    The structure and hydrogen bonding in solution of acetylacetone and benzoylacetone derived enaminone derivatives, 1a-1d and 2a-2d, have been studied by a combination of experimental (NMR and UV spectroscopies) and theoretical (PM6 and DFT) methods. It has been shown that all studied compounds predominantly existed in the localised keto-amine tautomeric form in solution as found also in the solid state. Significant line-broadening and down-field chemical shifts of NH and OH protons have strongly indicated that both groups formed hydrogen bonds, which has further been supported by quantum chemical calculations. Temperature and concentration dependent NMR measurements have pointed towards the fact that NH protons are engaged in strong intramolecular hydrogen bonds of the NH⋯Odbnd C type in both solvents. On the other hand, OH protons are involved in weaker intermolecular hydrogen bonding with solvent molecules in DMSO, while in chloroform intermolecular interactions between two molecules dominate. The results presented in this paper can be used for better understanding and further exploiting properties these ligands possess, especially their bioactivity.

  6. Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics

    NASA Astrophysics Data System (ADS)

    Casey, Ryan E.; Pittman, Faith A.

    2005-02-01

    Environmental education for undergraduate nonscience majors and high school students is key in fostering an increased understanding of environmental issues among the general public. We have developed an environmental chemistry module that can be used in high schools or undergraduate nonscience courses to relate chemical structures and properties to the macroscopic behavior of environmentally relevant organic chemicals like pesticides, PCBs, and solvents. The module introduces the concepts of intermolecular forces, polarity, and partitioning to explain complex phenomena such as environmental transport and biomagnification of xenobiotics (human-made chemicals). The level 1 version 2.11 model, developed by Trent University, is used in a laboratory segment that allows students to explore the relationship between chemical properties and environmental distribution. The initial material on polarity and intermolecular forces can lead to additional applications, including: bioaccumulation and biomagnification of organic chemicals; toxicology or pharmacology (ability of molecules to cross membranes); and groundwater contamination. This module can enhance chemistry courses by presenting detailed applications and allowing students to make powerful, verifiable predictions. See Featured Molecules .

  7. Relating organic fouling of reverse osmosis membranes to intermolecular adhesion forces.

    PubMed

    Lee, Sangyoup; Elimelech, Menachem

    2006-02-01

    Organic fouling of reverse osmosis (RO) membranes and its relation to foulant--foulant intermolecular adhesion forces has been investigated. Alginate and Suwannee River natural organic matter were used as model organic foulants. Atomic force microscopy was utilized to determine the adhesion force between bulk organic foulants and foulants deposited on the membrane surface under various solution chemistries. The measured adhesion force was related to the RO fouling rate determined from fouling experiments under solution chemistries similar to those used in the AFM measurements. A remarkable correlation was obtained between the measured adhesion force and the fouling rate under the solution chemistries investigated. Fouling was more severe at solution chemistries that resulted in larger adhesion forces, namely, lower pH, higher ionic strength, presence of calcium ions (but not magnesium ions), and higher mass ratio of alginate to Suwannee River natural organic matter. The significant adhesion force measured with alginate in the presence of calcium ions indicated the formation of a crossed-linked alginate gel layer during fouling through intermolecular bridging among alginate molecules.

  8. Pressure Effects on the Intermolecular Interaction Potential of Condensed Protein Solutions.

    PubMed

    Winter, Roland

    2015-01-01

    Knowledge of the intermolecular interaction potential of proteins as a function of their solution conditions is essential for understanding protein aggregation, crystallization, and the phase behavior of proteins in general. Here, we report on a combined small-angle X-ray scattering and liquid-state theoretical approach to study dense lysozyme solutions as a function of temperature and pressure, but also in the presence of salts and osmolytes of different nature. We show that the pressure-dependent interaction potential of lysozyme changes in a nonlinear fashion over a wide range of temperatures, salt and protein concentrations, indicating that changes of the bulk water structure mediate the pressure dependence of the intermolecular forces. We present also results on the effect of high hydrostatic pressure on the phase behavior of dense lysozyme solutions in the liquid-liquid phase-coexistence region. As also shown in this study, the application of pressure can be used to fine-tune the second virial coefficient of protein solutions, which can be used to control nucleation rates and hence protein crystallization, or to prevent protein aggregation. Moreover, these results are also important for understanding the hydration behavior of biological matter under extreme environmental conditions, and the high stability of dense protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the 100 MPa-level are reached.

  9. Terahertz notch filter using intermolecular hydrogen bonds in a sucrose crystal

    NASA Astrophysics Data System (ADS)

    Rungsawang, Rakchanok; Ueno, Yuko; Tomita, Isao; Ajito, Katsuhiro

    2006-06-01

    We propose a THz notch filter that uses the absorption of the intermolecular hydrogen bonds in a molecular crystal such as sucrose. Terahertz (THz) time-domain spectroscopy was used to investigate the absorption characteristics of a rotationally oriented sucrose single crystal in the 0.3 - 3.0 THz frequency range. The crystal was set so that the (100) face (cleavage) was normal to the THz propagation direction. The two lowest frequency intermolecular hydrogen bonding bands clearly exist at room temperature and at 1.45 and 1.64 THz when the b-axis of the crystal is parallel and perpendicular to the THz polarization, respectively. In contrast, they disappear when the b-axis is reversed. This absorption feature means that it would be possible to utilize a sucrose crystal as a notch filter with a 1.45-THz band center for the 0.1-1.7 THz range and with a 1.64-THz band center for the 0.1-1.9 THz range. When the crystal is rotated, the transmitted intensities of the frequency components near the absorption bands alternate as a sine function against angle. The spectroscopic properties of the sucrose filter were confirmed by continuous THz wave imaging.

  10. The Effect of Intermolecular Modes on the Xh-Stretching Vibrations in Hydrogen Bonded Complexes

    NASA Astrophysics Data System (ADS)

    Mackeprang, Kasper; Kjaergaard, Henrik G.

    2016-06-01

    Vibrational spectra of hydrogen bonded bimolecular complexes (XH\\cdotsY, where X is the hydrogen bond donor atom, and Y is the acceptor atom) have long been a theoretical challenge. Specifically, the XH-stretching motion is difficult to describe due to the effect of the large amplitude intermolecular modes inherent to complexes. We have developed a vibrational model, the Local Mode Perturbation Theory (LMPT) model, to accurately determine the transition wavenumber and oscillator strength of the XH-stretching transition in hydrogen bonded bimolecular complexes. The model is based on a local mode (LM) model of the XH-stretching transition and the effect of the intermolecular modes is included via Rayleigh-Schrödinger perturbation theory. Our model has significantly improved results obtained using the LM model (see Figure). Additionally, our LMPT model does not require a full-dimensional anharmonic calculation, which enables application to large systems and the usage of higher level ab initio theory for the required potential energy surfaces. This work was inspired by our recent efforts to accurately determine equilibrium constants of complex formation, which rely on an accurate determination of the oscillator strength of the XH-stretching transition.

  11. Intermolecular cope-type hydroamination of alkenes and alkynes using hydroxylamines.

    PubMed

    Moran, Joseph; Gorelsky, Serge I; Dimitrijevic, Elena; Lebrun, Marie-Eve; Bédard, Anne-Catherine; Séguin, Catherine; Beauchemin, André M

    2008-12-31

    The development of the Cope-type hydroamination as a method for the metal- and acid-free intermolecular hydroamination of hydroxylamines with alkenes and alkynes is described. Aqueous hydroxylamine reacts efficiently with alkynes in a Markovnikov fashion to give oximes and with strained alkenes to give N-alkylhydroxylamines, while unstrained alkenes are more challenging. N-Alkylhydroxylamines also display similar reactivity with strained alkenes and give modest to good yields with vinylarenes. Electron-rich vinylarenes lead to branched products while electron-deficient vinylarenes give linear products. A beneficial additive effect is observed with sodium cyanoborohydride, the extent of which is dependent on the structure of the hydroxylamine. The reaction conditions are found to be compatible with common protecting groups, free OH and NH bonds, as well as bromoarenes. Both experimental and theoretical results suggest the proton transfer step of the N-oxide intermediate is of vital importance in the intermolecular reactions of alkenes. Details are disclosed concerning optimization, reaction scope, limitations, and theoretical analysis by DFT, which includes a detailed molecular orbital description for the concerted hydroamination process and an exhaustive set of calculated potential energy surfaces for the reactions of various alkenes, alkynes, and hydroxylamines.

  12. Exploring the extent of magnetic field effect on intermolecular photoinduced electron transfer in different organized assemblies.

    PubMed

    Choudhury, Sharmistha Dutta; Basu, Samita

    2005-09-15

    Magnetic field effect (MFE) on the photoinduced electron transfer (PET) between phenazine (PZ) and the amines, N,N-dimethylaniline , N,N-diethylaniline, 4,4'-bis(dimethylamino)diphenylmethane (DMDPM), and triethylamine, has been studied in micelles, reverse micelles, and small unilamellar vesicles (SUVs) with a view to understand the effect of spatial location of the donor and acceptor moieties on the magnetic field behavior. The structure of the assembly is found to influence greatly the PET dynamics and hence the MFE of all the systems studied. The magnetic field behavior in micelles is consistent with the hyperfine mechanism, but high B(1/2) values have been obtained which have been ascribed to hopping and lifetime broadening. The variation of MFE with W(0), in reverse micelles, proves yet again that the MFE maximizes at an optimum separation distance between the acceptor and donor. This is the first example of such behavior for intermolecular PET in heterogeneous medium. We have also reported for the first time MFE on intermolecular PET in SUVs. In this case, the PZ-DMDPM system responds most appreciably to an external field compared to the other acceptor-donor systems because it is appropriately positioned in the bilayer. The differential behavior of the amines has been discussed in terms of their confinement in different zones of the organized assemblies depending on their bulk, hydrophobic, and electrostatic effects.

  13. Intermolecular stabilization of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) compressed to 20 GPa.

    PubMed

    Chellappa, Raja S; Dattelbaum, Dana M; Coe, Joshua D; Velisavljevic, Nenad; Stevens, Lewis L; Liu, Zhenxian

    2014-08-01

    The room temperature stability of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) has been investigated using synchrotron far-infrared, mid-infrared, Raman spectroscopy, and synchrotron X-ray diffraction (XRD) up to 20 GPa. The as-loaded DAAF samples exhibited subtle pressure-induced ordering phenomena (associated with positional disorder of the azoxy "O" atom) resulting in doubling of the a-axis, to form a superlattice similar to the low-temperature polymorph. Neither high pressure synchrotron XRD, nor high pressure infrared or Raman spectroscopies indicated the presence of structural phase transitions up to 20 GPa. Compression was accommodated in the unit cell by a reduction of the c-axis between the planar DAAF layers, distortion of the β-angle of the monoclinic lattice, and an increase in intermolecular hydrogen bonding. Changes in the ring and -NH2 deformation modes and increased intermolecular hydrogen bonding interactions with compression suggest molecular reorganizations and electronic transitions at ∼ 5 GPa and ∼ 10 GPa that are accompanied by a shifting of the absorption band edge into the visible. A fourth-order Birch-Murnaghan fit to the room temperature isotherm afforded an estimate of the zero-pressure isothermal bulk modulus, K0 = 12.4 ± 0.6 GPa and its pressure derivative K0' = 7.7 ± 0.3. PMID:25011055

  14. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

    PubMed Central

    Pyzer-Knapp, Edward O.; Thompson, Hugh P. G.; Day, Graeme M.

    2016-01-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  15. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

    NASA Astrophysics Data System (ADS)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  16. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

    NASA Astrophysics Data System (ADS)

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-01

    In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  17. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  18. Optimization of intermolecular potential parameters for the CO2/H2O mixture.

    PubMed

    Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2014-10-01

    Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures. PMID:25198539

  19. Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids

    NASA Astrophysics Data System (ADS)

    Siodłak, Dawid; Bujak, Maciej; Staś, Monika

    2013-09-01

    Esters of dehydroamino acids occur in nature. To investigate their conformational properties, the low-temperature structures of Ac-ΔAla-OMe, Ac-ΔVal-OMe, Z-(Z)-ΔAbu-OMe, and Z-(Z)-ΔAbu-NHMe were studied by single-crystal X-ray diffraction. The ΔAla ester prefers the fully extended conformation C5. Both the ΔVal and (Z)-ΔAbu esters assume the conformation β, whereas the amide analogue of the latter prefers the conformation α. For the conformations found, DFT calculations using B3LYP/6-311++G(d,p) with the SCRF-PCM and M062X/6-311++G(d,p) with the SCRF-SMD method were applied to mimicking chloroform and water environment. The tendency of the ΔVal and (Z)-ΔAbu esters towards the conformation β, and their amide analogues towards the conformation α, with increase of the polarity of environment was found. The analysis of both intra- and intermolecular interactions including hydrogen bonds, carbonyl dipole attraction, and π-electron conjugation, enabled to understand and elucidate the conformational preferences of studied compounds. The studies show how the molecular structure, and in consequence, the conformation adopted by molecules is influenced by the different intra- and intermolecular forces.

  20. Problem-Based Learning in 9th Grade Chemistry Class: `Intermolecular Forces'

    NASA Astrophysics Data System (ADS)

    Tarhan, Leman; Ayar-Kayali, Hulya; Urek, Raziye Ozturk; Acar, Burcin

    2008-05-01

    This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students’ understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student’s alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified by cognitive levels and then randomly assigned to experimental (PBL, 40 students) and control (lecture-style teaching, 38 students) groups. Following a preparatory lesson where activation and remediation of existing knowledge occur, a pre-test was given, and no significant difference was found between the two groups of students ( p > .05). After the instruction was completed, a post-test and also a questionnaire related to the quality of the problem, the teacher’s role and group functioning were administered. Results from the post-test of both groups ( p < .05) and questionnaire showed that PBL is affective on students’ achievement, remedying formation of alternate conceptions and also social skills.

  1. Conformational diversity in prion protein variants influences intermolecular [beta]-sheet formation

    SciTech Connect

    Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J.; Surewicz, Krystyna; Surewicz, Witold K.; Yee, Vivien C.

    2010-04-19

    A conformational transition of normal cellular prion protein (PrP{sup C}) to its pathogenic form (PrP{sup Sc}) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular {beta}-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular {beta}-sheets involving the M/V129 polymorphic residue.

  2. Intermolecular stabilization of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) compressed to 20 GPa.

    PubMed

    Chellappa, Raja S; Dattelbaum, Dana M; Coe, Joshua D; Velisavljevic, Nenad; Stevens, Lewis L; Liu, Zhenxian

    2014-08-01

    The room temperature stability of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) has been investigated using synchrotron far-infrared, mid-infrared, Raman spectroscopy, and synchrotron X-ray diffraction (XRD) up to 20 GPa. The as-loaded DAAF samples exhibited subtle pressure-induced ordering phenomena (associated with positional disorder of the azoxy "O" atom) resulting in doubling of the a-axis, to form a superlattice similar to the low-temperature polymorph. Neither high pressure synchrotron XRD, nor high pressure infrared or Raman spectroscopies indicated the presence of structural phase transitions up to 20 GPa. Compression was accommodated in the unit cell by a reduction of the c-axis between the planar DAAF layers, distortion of the β-angle of the monoclinic lattice, and an increase in intermolecular hydrogen bonding. Changes in the ring and -NH2 deformation modes and increased intermolecular hydrogen bonding interactions with compression suggest molecular reorganizations and electronic transitions at ∼ 5 GPa and ∼ 10 GPa that are accompanied by a shifting of the absorption band edge into the visible. A fourth-order Birch-Murnaghan fit to the room temperature isotherm afforded an estimate of the zero-pressure isothermal bulk modulus, K0 = 12.4 ± 0.6 GPa and its pressure derivative K0' = 7.7 ± 0.3.

  3. Effect of the electronic structure of quinoline and its derivatives on the capacity for intermolecular interactions

    SciTech Connect

    Privalova, N.Yu.; Sokolova, I.V.

    1985-05-01

    Calculations of the ground and excited states of quinoline and its 20H-, 70H-, 7NH2-, 7N(CH3)2-, and 7N(C2H5)2- substituted derivatives were undertaken by the INDO method, and the effect of intramolecular proton transfer (IPT) on their electronic structure was studied. The proton-accepting capacity of the compounds for intermolecular interactions was estimated by the molecular electrostatic potential method. It was shown that the proton-accepting capacity with respect to intermolecular interactions increases during the tautomeric transformation of the enolic form of 2-OH-quinoline to its keto form. The change in the basicity of the two forms of the molecules is affected by the orbital nature, and the multiplicity of the state is also important for the keto form. Substitution by electron-donating groups leads to increase in the proton-accepting capacity of both forms of the compounds in the S0, S/sub */, and T/sub */ states.

  4. REDOR solid-state NMR as a probe of the membrane locations of membrane-associated peptides and proteins

    NASA Astrophysics Data System (ADS)

    Jia, Lihui; Liang, Shuang; Sackett, Kelly; Xie, Li; Ghosh, Ujjayini; Weliky, David P.

    2015-04-01

    Rotational-echo double-resonance (REDOR) solid-state NMR is applied to probe the membrane locations of specific residues of membrane proteins. Couplings are measured between protein 13CO nuclei and membrane lipid or cholesterol 2H and 31P nuclei. Specific 13CO labeling is used to enable unambiguous assignment and 2H labeling covers a small region of the lipid or cholesterol molecule. The 13CO-31P and 13CO-2H REDOR respectively probe proximity to the membrane headgroup region and proximity to specific insertion depths within the membrane hydrocarbon core. One strength of the REDOR approach is use of chemically-native proteins and membrane components. The conventional REDOR pulse sequence with 100 kHz 2H π pulses is robust with respect to the 2H quadrupolar anisotropy. The 2H T1's are comparable to the longer dephasing times (τ's) and this leads to exponential rather than sigmoidal REDOR buildups. The 13CO-2H buildups are well-fitted to A × (1 - e-γτ) where A and γ are fitting parameters that are correlated as the fraction of molecules (A) with effective 13CO-2H coupling d = 3γ/2. The REDOR approach is applied to probe the membrane locations of the "fusion peptide" regions of the HIV gp41 and influenza virus hemagglutinin proteins which both catalyze joining of the viral and host cell membranes during initial infection of the cell. The HIV fusion peptide forms an intermolecular antiparallel β sheet and the REDOR data support major deeply-inserted and minor shallowly-inserted molecular populations. A significant fraction of the influenza fusion peptide molecules form a tight hairpin with antiparallel N- and C-α helices and the REDOR data support a single peptide population with a deeply-inserted N-helix. The shared feature of deep insertion of the β and α fusion peptide structures may be relevant for fusion catalysis via the resultant local perturbation of the membrane bilayer. Future applications of the REDOR approach may include samples that contain cell

  5. Observation of Combination Bands Involving Intermolecular Vibrations of N_2O-N_2, N_2O-OCS and N_2O-CO_2 Complexes Using AN External Cavity Quantum Cascade Laser

    NASA Astrophysics Data System (ADS)

    Rezaei, M.; Sheybani-Deloui, S.; Moazzen-Ahmadi, N.; McKellar, A. R. W.

    2013-06-01

    Spectra of the weakly-bound N_2O-CO_2, N_2O-OCS, and N_2O-N_2 complexes in the region of the N_2O ν_1 fundamental band (˜2224 cm^{-1}) are observed in a pulsed supersonic slit jet expansion probed with a quantum cascade laser. One new band is observed for each complex: two combination bands involving the intermolecular in-plane bending for N_2O-CO_2 and N_2O-N_2 complexes, and the out-of-plane torsional vibration for N_2O-OCS. The resulting intermolecular frequencies are 34.17, 17.11 and 22.33 cm^{-1} for N_2O-CO_2, N_2O-OCS, and N_2O-N_2 complexes, respectively. The intermolecular vibrations provide clear spectroscopic data against which theory can be benchmarked. These results will be discussed, along with a brief introduction to our pulsed-jet supersonic apparatus which has been retrofitted by an infrared cw external-cavity quantum cascade laser (QCL) manufactured by Daylight Solutions. The QCL is used in the rapid-scan signal averaging mode. Although the repetition rate of the QCL is limited by its PZT scan rate, which is 100 Hz, we describe a simple technique to increase the effective repetition rate to 625 Hz. In addition, we have significantly reduced the long term frequency drift of the QCL by locking the laser frequency to the sides of a reference line. Limin Zheng, Soo-Ying Lee, Yunpeng Lu, and Minghui Yang, J. Chem. Phys. 138, 044302 (2013).

  6. Double Electron-Electron Resonance Probes Ca2+-induced Conformational Changes and Dimerization of Recoverin†

    PubMed Central

    Myers, William K.; Xu, Xianzhong; Li, Congmin; Lagerstedt, Jens O.; Budamagunta, Madhu S.; Voss, John C.; Britt, R. David; Ames, James B.

    2013-01-01

    Recoverin, a member of the neuronal calcium sensor (NCS) branch of the calmodulin superfamily, is expressed in retinal photoreceptor cells and serves as a calcium sensor in vision. Ca2+-induced conformational changes in recoverin cause extrusion of its covalently attached myristate (termed Ca2+-myristoyl switch) that promote translocation of recoverin to disk membranes during phototransduction in retinal rod cells. Here we report double electron-electron resonance (DEER) experiments on recoverin that probe Ca2+-induced changes in distance as measured by the dipolar coupling between spin labels strategically positioned at engineered cysteine residues on the protein surface. The DEER distance between nitroxide spin-labels attached at C39 and N120C is 2.5 ±0.1 nm for Ca2+-free recoverin and 3.7 ±0.1 nm for Ca2+-bound recoverin. An additional DEER distance (5 - 6 nm) observed for Ca2+-bound recoverin may represent an intermolecular distance between C39 and N120. 15N NMR relaxation analysis and CW-EPR experiments both confirm that Ca2+-bound recoverin forms a dimer at protein concentrations above 100 μM, whereas Ca2+-free recoverin is monomeric. We propose that Ca2+-induced dimerization of recoverin at the disk membrane surface may play a role in regulating Ca2+-dependent phosphorylation of dimeric rhodopsin. The DEER approach will be useful for elucidating dimeric structures of NCS proteins in general for which Ca2+-induced dimerization is functionally important but not well understood. PMID:23906368

  7. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, Shimon; Chemla, Daniel S.; Ogletree, D. Frank; Botkin, David

    1995-01-01

    An ultrafast scanning probe microscopy method for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample.

  8. Ultrafast scanning probe microscopy

    DOEpatents

    Weiss, S.; Chemla, D.S.; Ogletree, D.F.; Botkin, D.

    1995-05-16

    An ultrafast scanning probe microscopy method is described for achieving subpicosecond-temporal resolution and submicron-spatial resolution of an observation sample. In one embodiment of the present claimed invention, a single short optical pulse is generated and is split into first and second pulses. One of the pulses is delayed using variable time delay means. The first pulse is then directed at an observation sample located proximate to the probe of a scanning probe microscope. The scanning probe microscope produces probe-sample signals indicative of the response of the probe to characteristics of the sample. The second pulse is used to modulate the probe of the scanning probe microscope. The time delay between the first and second pulses is then varied. The probe-sample response signal is recorded at each of the various time delays created between the first and second pulses. The probe-sample response signal is then plotted as a function of time delay to produce a cross-correlation of the probe sample response. In so doing, the present invention provides simultaneous subpicosecond-temporal resolution and submicron-spatial resolution of the sample. 6 Figs.

  9. Traversing probe system

    DOEpatents

    Mashburn, Douglas N.; Stevens, Richard H.; Woodall, Harold C.

    1977-01-01

    This invention comprises a rotatable annular probe-positioner which carries at least one radially disposed sensing probe, such as a Pitot tube having a right-angled tip. The positioner can be coaxially and rotatably mounted within a compressor casing or the like and then actuated to orient the sensing probe as required to make measurements at selected stations in the annulus between the positioner and compressor casing. The positioner can be actuated to (a) selectively move the probe along its own axis, (b) adjust the yaw angle of the right-angled probe tip, and (c) revolve the probe about the axis common to the positioner and casing. A cam plate engages a cam-follower portion of the probe and normally rotates with the positioner. The positioner includes a first-motor-driven ring gear which effects slidable movement of the probe by rotating the positioner at a time when an external pneumatic cylinder is actuated to engage the cam plate and hold it stationary. When the pneumatic cylinder is not actuated, this ring gear can be driven to revolve the positioner and thus the probe to a desired circumferential location about the above-mentioned common axis. A second motor-driven ring gear included in the positioner can be driven to rotate the probe about its axis, thus adjusting the yaw angle of the probe tip. The positioner can be used in highly corrosive atmosphere, such as gaseous uranium hexafluoride.

  10. Electrical resistivity probes

    DOEpatents

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

    2003-10-21

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

  11. Probing the nano-bio interface with nanoplasmonic optical probes

    NASA Astrophysics Data System (ADS)

    Yu, X.; Wu, Linxi; Khanehzar, Ali; Feizpour, Amin; Xu, Fangda; Reinhard, Björn M.

    2014-08-01

    Noble metal nanoparticles have large cross-sections in both optical and electron microscopy and plasmon coupling between noble metal nanoparticles facilitate the characterization of subdiffraction limit separations through spectral analysis of the scattered light in Plasmon Coupling Microscopy (PCM). The size compatibility of noble metal nanoparticles together with the ability to encode specific functionality in a rational fashion by control of the nanoparticle surface makes noble metal nanoparticles unique probes for a broad range of biological processes. Recent applications of the technology include i.) characterization of cellular heterogeneity in nanomaterial uptake and processing through macrophages, ii.) testing the role of viral membrane lipids in mediating viral binding and trafficking, and iii.) characterizing the spatial organization of cancer biomarkers in plasma membranes. This paper reviews some of these applications and introduces the physical and material science principles underlying them. We will also introduce the use of membrane wrapped noble metal nanoparticles, which combine the superb photophysical properties of a nanoparticle core with the biological functionality of a membrane, as probes in PCM.

  12. Role of silver ions in destabilization of intermolecular adhesion forces measured by atomic force microscopy in Staphylococcus epidermidis biofilms.

    PubMed

    Chaw, K C; Manimaran, M; Tay, Francis E H

    2005-12-01

    In this paper, we report on the potential use of atomic force microscopy (AFM) as a tool to measure the intermolecular forces in biofilm structures and to study the effect of silver ions on sessile Staphylococcus epidermidis cell viability and stability. We propose a strategy of destabilizing the biofilm matrix by reducing the intermolecular forces within the extracellular polymeric substances (EPSs) using a low concentration (50 ppb) of silver ions. Our AFM studies on the intermolecular forces within the EPSs of S. epidermidis RP62A and S.epidermidis 1457 biofilms suggest that the silver ions can destabilize the biofilm matrix by binding to electron donor groups of the biological molecules. This leads to reductions in the number of binding sites for hydrogen bonds and electrostatic and hydrophobic interactions and, hence, the destabilization of the biofilm structure.

  13. Spin excitations used to probe the nature of exchange coupling in the magnetically ordered ground state of Pr0.5Ca0.5MnO3

    NASA Astrophysics Data System (ADS)

    Ewings, R. A.; Perring, T. G.; Sikora, O.; Abernathy, D. L.; Tomioka, Y.; Tokura, Y.

    2016-07-01

    We have used time-of-flight inelastic neutron scattering to measure the spin wave spectrum of the canonical half-doped manganite Pr0.5Ca0.5MnO3 in its magnetic and orbitally ordered phase. The data, which cover multiple Brillouin zones and the entire energy range of the excitations, are compared with several different models that are all consistent with CE-type magnetic order, but arise through different exchange coupling schemes. The Goodenough model, i.e., an ordered state comprising strong nearest-neighbor ferromagnetic interactions along zigzag chains with antiferromagnetic interchain coupling, provides the best description of the data, provided that further neighbor interactions along the chains are included. We are able to rule out a coupling scheme involving formation of strongly bound ferromagnetic dimers, i.e., Zener polarons, on the basis of gross features of the observed spin wave spectrum. A model with weaker dimerization reproduces the observed dispersion but can be ruled out on the basis of discrepancies between the calculated and observed structure factors at certain positions in reciprocal space. Adding further neighbor interactions results in almost no dimerization, i.e., recovery of the Goodenough model. These results are consistent with theoretical analysis of the degenerate double exchange model for half-doping, and provide a recipe for how to interpret future measurements away from half-doping, where degenerate double exchange models predict more complex ground states.

  14. Ultrasensitive quantification of the CYP2E1 probe chlorzoxazone and its main metabolite 6-hydroxychlorzoxazone in human plasma using ultra performance liquid chromatography coupled to tandem mass spectrometry after chlorzoxazone microdosing.

    PubMed

    Witt, Lukas; Suzuki, Yosuke; Hohmann, Nicolas; Mikus, Gerd; Haefeli, Walter E; Burhenne, Jürgen

    2016-08-01

    Chlorzoxazone is a probe drug to assess cytochrome P450 (CYP) 2E1 activity (phenotyping). If the pharmacokinetics of the probe drug is linear, pharmacologically ineffective doses are sufficient for the purpose of phenotyping and adverse effects can thus be avoided. For this reason, we developed and validated an assay for the ultrasensitive quantification of chlorzoxazone and 6-hydroxychlorzoxazone in human plasma. Plasma (0.5mL) and liquid/liquid partitioning were used for sample preparation. Extraction recoveries ranged between 76 and 93% for both analytes. Extracts were separated within 3min on a Waters BEH C18 Shield 1.7μm UPLC column with a fast gradient consisting of aqueous formic acid and acetonitrile. Quantification was achieved using internal standards labeled with deuterium or (13)C and tandem mass spectrometry in the multiple reaction monitoring mode using negative electrospray ionization, which yielded lower limits of quantification of 2.5pgmL(-1), while maintaining a precision always below 15%. The calibrated concentration ranges were linear for both analytes (2.5-1000pgmL(-1)) with correlation coefficients of >0.99. Within-batch and batch-to-batch precision in the calibrated ranges for both analytes were <15% and <11% and plasma matrix effects always were below 50%. The assay was successfully applied to assess the pharmacokinetics of chlorzoxazone in two human volunteers after administration of single oral doses (2.5-5000μg). This ultrasensitive assay allowed the determination of chlorzoxazone pharmacokinetics for 8h after microdosing of 25μg chlorzoxazone.

  15. Strong anisotropy of momentum-relaxation time induced by intermolecular vibrations of single-crystal organic semiconductors

    NASA Astrophysics Data System (ADS)

    Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

    2013-11-01

    We present a theoretical study of the relationships between intermolecular vibrations and anisotropic transport properties of pentacene and rubrene single-crystal organic semiconductors. Using our wave-packet approach based on the Kubo formula beyond the effective-mass approximation with the assumption of an isotropic momentum-relaxation time, we find that the intermolecular vibrations induce a strong anisotropic momentum-relaxation time but moderate the anisotropy of carrier mobility much more than that of the effective mass. This clarifies the mechanism behind the deviation of the anisotropic ratio of mobility from that of effective mass observed in angle-resolved photoelectron spectroscopy experiments.

  16. Squeezing water clusters between graphene sheets: energetics, structure, and intermolecular interactions.

    PubMed

    McKenzie, S; Kang, H C

    2014-12-21

    The behavior of water confined at the nanoscale between graphene sheets has attracted much theoretical and experimental attention recently. However, the interactions, structure, and energy of water at the molecular scale underpinning the behavior of confined water have not been characterized by first-principles calculations. In this work we consider small water clusters up to the hexamer adsorbed between graphene sheets using density functional theory calculations with van der Waals corrections. We investigate the effects on structure, energy, and intermolecular interactions due to confinement between graphene sheets. For interlayer distances of about one nanometer or more, the cluster adsorption energy increases approximately linearly with the cluster size by 0.1 eV per molecule in the cluster. As the interlayer distance decreases, the cluster adsorption energy reaches a maximum at 6 to 7 Å with approximately 0.16 eV stabilization energy relative to large interlayer distances. This suggests the possibility of controlling the amount of adsorption in graphene nanomaterials by varying the interlayer distance. We also quantify the intermolecular hydrogen bonding in the clusters by calculating the dissociation energy required to remove one molecule from each cluster. For each cluster size, this is constant for interlayer distances larger than approximately 6 to 8 Å. For smaller distances the intermolecular interaction decreases rapidly thus leading to weaker cohesion between molecules in a squeezed cluster. We expect a mechanism of concerted motion for hydrogen-bonded water molecules confined between graphene sheets, as has been observed for water confined within the carbon nanotubes. Thus, the decrease in the dissociation energy we observed here is consistent with experimental results for water transport through graphene and related membranes that are of interest in nanofiltration. We also calculate the corrugation in the interaction potential between graphene

  17. CO2 Dimer: Four Intermolecular Modes Observed via Infrared Combination Bands

    NASA Astrophysics Data System (ADS)

    Norooz Oliaee, Jalal; Dehghany, Mehdi; Rezaei, Mojtaba; McKellar, Bob; Moazzen-Ahmadi, Nasser

    2016-06-01

    Study of the carbon dioxide dimer has a long history, but there is only one previous observation of an intermolecular vibration [1]. Here we analyze four new combination bands of (CO2)2 in the CO2 νb{3} region (˜2350 wn), observed using tunable infrared lasers and a pulsed slit-jet supersonic expansion. The previous combination band at 2382.2 wn was simple to assign [1]. A much more complicated band (˜2370 wn) turns out to involve two upper states, one at 2369.0 wn (Bu symmetry), and the other at 2370.0 wn (Au). The spectrum can be nicely fit by including the Coriolis interactions between these states. Another complicated band around 2443 wn also involves two nearby upper states which are highly perturbed in so-far unexplained ways (possibly related to tunneling shifts). With the help of new ab initio calculations [2], we assign the results as follows. The 2369.0 wn band is the combination of the forbidden Ag intramolecular fundamental (probably [1] at about 2346.76 wn) and the intermolecular geared bend (Bu). The 2370.0 wn band is the combination of the same Ag fundamental and the intermolecular torsion (Au). This gives about 22.3 and 23.2 wn for the geared bend and torsion. The previous 2382.2 wn band [1] is the allowed Bu fundamental (2350.771 wn) plus two quanta of the geared bend (Bu), giving 31.509 wn for this overtone. The highly perturbed 2442.7 wn band is the Bu fundamental plus the antigeared bend (Ag), giving about 91.9 wn for the antigeared bend. Finally, the perturbed 2442.1 wn band is due to an unknown combination of modes which gains intensity from the antigeared bend by a Fermi-type interaction. Calculated values [2] are: 20.64 (geared bend), 24.44 (torsion), 32.34 (geared bend overtone), and 92.30 wn (antigeared bend), in good agreement with experiment. \\vskip 0.2 truecm [1] M. Dehghany, A.R.W. McKellar, Mahin Afshari, and N. Moazzen-Ahmadi, Mol. Phys. 108, 2195 (2010). [2] X.-G. Wang, T. Carrington, Jr., and R. Dawes, private communication.

  18. Photoinduced intermolecular cross-linking of gas phase triacylglycerol lipid ions.

    PubMed

    Nie, Shuai; Pham, Huong T; Blanksby, Stephen J; Reid, Gavin E

    2015-01-01

    Complex mixtures of plant derived triglycerol (TG) lipids are commonly used as feedstock components for the production of industrial polymers. However, there remains a need for the development of analytical strategies to investigate the intrinsic intermolecular cross-linking reactivity of individual TG molecules within these mixtures as a function of their structures and physicochemical properties, and for the characterization of the resultant products. Here, to address this need, we describe a novel multistage tandem mass spectrometry based method for intermolecular cross-linking and subsequent structural characterization of TG lipid ions in the gas phase. Cross-linking reactions were initiated using 266 nm ultraviolet photodissociation tandem mass spectrometry (UVPD-MS/MS) of saturated or unsaturated TG dimers introduced via electrospray ionization into a linear ion trap mass spectrometer as noncovalent complexes with protonated 3,4-, 2,4- or 3,5- diiodoaniline (diIA). UVPD resulted in the initial formation of an anilinyl biradical via the sequential loss of two iodine radicals, which underwent further reaction to yield multiple cross-linked TG products along with competing noncross-linking processes. These chemistries are proposed to occur via sequential combinations of hydrogen abstraction (H-abstraction), radical addition and radical recombination. Multistage collision induced dissociation tandem mass spectrometry (CID-MS(n)) was used to obtain evidence for the structures and mechanisms of formation for these products, as a function of both the TG lipid and diIA ion structures. The efficiency of the UVPD reaction was shown to be dependent on the number of unsaturation sites present within the TG lipids. However, when unsaturation sites were present, formation of the cross-linked and noncross-linked product ions via H-abstraction and radical addition mechanisms was found to be competitive. Finally, the identity of the anilinyl biradical (e.g., 3,4- versus 2

  19. High temperature probe

    DOEpatents

    Swan, Raymond A.

    1994-01-01

    A high temperature probe for sampling, for example, smokestack fumes, and is able to withstand temperatures of 3000.degree. F. The probe is constructed so as to prevent leakage via the seal by placing the seal inside the water jacket whereby the seal is not exposed to high temperature, which destroys the seal. The sample inlet of the probe is also provided with cooling fins about the area of the seal to provide additional cooling to prevent the seal from being destroyed. Also, a heated jacket is provided for maintaining the temperature of the gas being tested as it passes through the probe. The probe includes pressure sensing means for determining the flow velocity of an efficient being sampled. In addition, thermocouples are located in various places on the probe to monitor the temperature of the gas passing there through.

  20. Integrated microfluidic probe station

    NASA Astrophysics Data System (ADS)

    Perrault, C. M.; Qasaimeh, M. A.; Brastaviceanu, T.; Anderson, K.; Kabakibo, Y.; Juncker, D.

    2010-11-01

    The microfluidic probe (MFP) consists of a flat, blunt tip with two apertures for the injection and reaspiration of a microjet into a solution—thus hydrodynamically confining the microjet—and is operated atop an inverted microscope that enables live imaging. By scanning across a surface, the microjet can be used for surface processing with the capability of both depositing and removing material; as it operates under immersed conditions, sensitive biological materials and living cells can be processed. During scanning, the MFP is kept immobile and centered over the objective of the inverted microscope, a few micrometers above a substrate that is displaced by moving the microscope stage and that is flushed continuously with the microjet. For consistent and reproducible surface processing, the gap between the MFP and the substrate, the MFP's alignment, the scanning speed, the injection and aspiration flow rates, and the image capture need all to be controlled and synchronized. Here, we present an automated MFP station that integrates all of these functionalities and automates the key operational parameters. A custom software program is used to control an independent motorized Z stage for adjusting the gap, a motorized microscope stage for scanning the substrate, up to 16 syringe pumps for injecting and aspirating fluids, and an inverted fluorescence microscope equipped with a charge-coupled device camera. The parallelism between the MFP and the substrate is adjusted using manual goniometer at the beginning of the experiment. The alignment of the injection and aspiration apertures along the scanning axis is performed using a newly designed MFP screw holder. We illustrate the integrated MFP station by the programmed, automated patterning of fluorescently labeled biotin on a streptavidin-coated surface.