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Sample records for probing intermolecular couplings

  1. Probing Intermolecular Coupled Vibrations between Two Molecules

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

  2. Tandem intermolecular Suzuki coupling/intramolecular vinyl triflate-arene coupling.

    PubMed

    Willis, Michael C; Claverie, Christelle K; Mahon, Mary F

    2002-04-21

    Treatment of a benzyl substituted meso-ditriflate with boronic acids in the presence of palladium acetate, triphenylphosphine and caesium fluoride results in intermolecular Suzuki coupling followed by vinyl triflate-arene cyclisation to provide, in high yields, single regioisomers of tricyclic-carbocycles.

  3. Rh(I)-Catalyzed Intermolecular Hydroacylation: Enantioselective Cross-Coupling of Aldehydes and Ketoamides

    PubMed Central

    2015-01-01

    Under Rh(I) catalysis, α-ketoamides undergo intermolecular hydroacylation with aliphatic aldehydes. A newly designed Josiphos ligand enables access to α-acyloxyamides with high atom-economy and enantioselectivity. On the basis of mechanistic and kinetic studies, we propose a pathway in which rhodium plays a dual role in activating the aldehyde for cross-coupling. A stereochemical model is provided to rationalize the sense of enantioinduction observed. PMID:24937681

  4. Density Analysis of Intra- and Intermolecular Vibronic Couplings toward Bath Engineering for Singlet Fission.

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2015-12-17

    Vibronic coupling plays a crucial role in singlet fission whereby a singlet exciton splits into two triplet excitons. In order to reveal the physicochemical origin of the vibronic coupling associated with singlet fission as well as to clarify its relationship with chemical structure, we evaluate relevant vibronic couplings from the viewpoint of their spatial contributions described by vibronic coupling density. From the analysis using a model tetracene dimer, a typical singlet fission system, the frequency dependence of vibronic couplings in each electronic state is found to be significantly different from that of another depending on the nature of the electronic structure (intra/intermolecular excitation) and the related vibrational motion. These findings contribute not only to the fundamental understanding of the singlet fission mechanism from the viewpoint of vibronic couplings but also to opening a new path to designing highly efficient singlet fission materials through phonon-bath engineering.

  5. 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.

  6. 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)

  7. Detection of intermolecular homonuclear dipolar coupling in organic rich shale by transverse relaxation exchange.

    PubMed

    Washburn, Kathryn E; Cheng, Yuesheng

    2017-03-04

    The mechanism behind surface relaxivity within organic porosity in shales has been an unanswered question. Here, we present results that confirm the existence of intermolecular homonuclear dipolar coupling between solid and liquid phases in sedimentary organic matter. Transverse magnetization exchange measurements were performed on an organic-rich shale saturated with liquid hydrocarbon. Liquid and solid constituents were identified through both sample resaturation and through their T1/T2 ratios. Extensive cross peaks are observed in the T2-T2 exchange spectra between the solid and liquid constituents, indicating an exchange of magnetization between the two phases. This result cannot arise from physical molecular diffusion, and the dissolution energies are too high for chemical exchange, such that the magnetization exchange must arise from intermolecular homonuclear dipolar coupling. These results both confirm a possible source of surface relaxivity in organic matter and emphasize caution in the use of standard porous media interpretations of relaxation results in shales because of coupling between different magnetization environments.

  8. 15N- 15N spin-spin coupling constants through intermolecular hydrogen bonds in the solid state

    NASA Astrophysics Data System (ADS)

    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.

  9. 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

  10. X-filtering for a range of coupling constants: application to the detection of intermolecular NOEs

    NASA Astrophysics Data System (ADS)

    Zangger, Klaus; Oberer, Monika; Keller, Walter; Sterk, Heinz

    2003-02-01

    A new method for heteronuclear X-filtering is presented, which relies on repetitive applications of 90°( 1H)-τ(1/4 1J HC)-180°( 1H, 13C)-τ(1/4 1J HC)-90°( 1H, 13C)- PFG building blocks employing gradient-mediated suppression of magnetization built up for directly heteronuclear coupled protons. Thereby, a range of heteronuclear coupling constants can be suppressed by varying the delays of scalar coupling evolution both within and between individual transients. To achieve efficient destruction of 13C-coupled protons in macromolecular systems, the scalar coupling evolution delays were optimized using simulated annealing by including transverse relaxation effects. With a combination of regular hard pulses, delays and pulsed field gradients only, this method yields sufficient X-filtering to allow the observation of intermolecular nuclear overhauser effects in a molecular complex consisting of a 13C, 15N double-labeled, and an unlabeled protein. This is achieved by exciting magnetization of 12C- and 14N-bound protons and detecting 13C-bound 1H magnetization in a 3D 13C-filtered, 13C-edited NOESY-HSQC experiment. The method is tested on the 18 kDa homodimeric bacterial antidote ParD.

  11. Hypervalent Iodine(III)-Promoted Intermolecular C–C Coupling of Vindoline with β-Ketoesters and Related Substrates

    PubMed Central

    Turner, Travis C.; Shibayama, Kotaro

    2013-01-01

    The regioselective intermolecular coupling reaction of vindoline with a wide range of substrates including β-ketoesters, β-diketones, β-ketoaldehydes, β-ketonitriles, malononitriles, and β-cyanoesters provides an opportunity for the synthesis of vinblastine analogues containing deep-seated changes in the upper velbanamine subunit. The transition-metal free hypervalent iodine(III)-promoted intermolecular sp3/sp2 coupling, representing a special class of selective C–H activation with direct carbon–carbon bond formation, proceeds with generation of a quaternary center capable of incorporation of the vinblastine C16′ methyl ester and functionalized for subsequent divergent heterocycle introduction. PMID:23421318

  12. 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

  13. 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.

  14. 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.

  15. Detection of complex formation and determination of intermolecular geometry through electrical anharmonic coupling of molecular vibrations using electron-vibration-vibration two-dimensional infrared spectroscopy.

    PubMed

    Guo, Rui; Fournier, Frederic; Donaldson, Paul M; Gardner, Elizabeth M; Gould, Ian R; Klug, David R

    2009-10-14

    Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species.

  16. Probing the self-association, intermolecular contacts, and folding propensity of amelogenin

    PubMed Central

    Ndao, Moise; Dutta, Kaushik; Bromley, Keith M; Lakshminarayanan, Rajamani; Sun, Zhi; Rewari, Gita; Moradian-Oldak, Janet; Evans, John Spencer

    2011-01-01

    Amelogenins are an intrinsically disordered protein family that plays a major role in the development of tooth enamel, one of the most highly mineralized materials in nature. Monomeric porcine amelogenin possesses random coil and residual secondary structures, but it is not known which sequence regions would be conformationally attractive to potential enamel matrix targets such as other amelogenins (self-assembly), other matrix proteins, cell surfaces, or biominerals. To address this further, we investigated recombinant porcine amelogenin (rP172) using “solvent engineering” techniques to simultaneously promote native-like structure and induce amelogenin oligomerization in a manner that allows identification of intermolecular contacts between amelogenin molecules. We discovered that in the presence of 2,2,2-trifluoroethanol (TFE) significant folding transitions and stabilization occurred primarily within the N- and C-termini, while the polyproline Type II central domain was largely resistant to conformational transitions. Seven Pro residues (P2, P127, P130, P139, P154, P157, P162) exhibited conformational response to TFE, and this indicates these Pro residues act as folding enhancers in rP172. The remaining Pro residues resisted TFE perturbations and thus act as conformational stabilizers. We also noted that TFE induced rP172 self-association via the formation of intermolecular contacts involving P4–H6, V19–P33, and E40–T58 regions of the N-terminus. Collectively, these results confirm that the N- and C-termini of amelogenin are conformationally responsive and represent potential interactive sites for amelogenin–target interactions during enamel matrix mineralization. Conversely, the Pro, Gln central domain is resistant to folding and this may have important functional significance for amelogenin. PMID:21351181

  17. Residence Times of Molecular Complexes in Solution from NMR Data of Intermolecular Hydrogen-Bond Scalar Coupling.

    PubMed

    Zandarashvili, Levani; Esadze, Alexandre; Kemme, Catherine A; Chattopadhyay, Abhijnan; Nguyen, Dan; Iwahara, Junji

    2016-03-03

    The residence times of molecular complexes in solution are important for understanding biomolecular functions and drug actions. We show that NMR data of intermolecular hydrogen-bond scalar couplings can yield information on the residence times of molecular complexes in solution. The molecular exchange of binding partners via the breakage and reformation of a complex causes self-decoupling of intermolecular hydrogen-bond scalar couplings, and this self-decoupling effect depends on the residence time of the complex. For protein-DNA complexes, we investigated the salt concentration dependence of intermolecular hydrogen-bond scalar couplings between the protein side-chain (15)N and DNA phosphate (31)P nuclei, from which the residence times were analyzed. The results were consistent with those obtained by (15)Nz-exchange spectroscopy. This self-decoupling-based kinetic analysis is unique in that it does not require any different signatures for the states involved in the exchange, whereas such conditions are crucial for kinetic analyses by typical NMR and other methods.

  18. Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

    NASA Astrophysics Data System (ADS)

    Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

    2016-12-01

    In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

  19. 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

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

    PubMed

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

    2014-04-11

    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.

  1. 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

  2. NMR Scalar Couplings across Intermolecular Hydrogen Bonds between Zinc-Finger Histidine Side Chains and DNA Phosphate Groups.

    PubMed

    Chattopadhyay, Abhijnan; Esadze, Alexandre; Roy, Sourav; Iwahara, Junji

    2016-10-10

    NMR scalar couplings across hydrogen bonds represent direct evidence for the partial covalent nature of hydrogen bonds and provide structural and dynamic information on hydrogen bonding. In this article, we report heteronuclear (15)N-(31)P and (1)H-(31)P scalar couplings across the intermolecular hydrogen bonds between protein histidine (His) imidazole and DNA phosphate groups. These hydrogen-bond scalar couplings were observed for the Egr-1 zinc-finger-DNA complex. Although His side-chain NH protons are typically undetectable in heteronuclear (1)H-(15)N correlation spectra due to rapid hydrogen exchange, this complex exhibited two His side-chain NH signals around (1)H 14.3 ppm and (15)N 178 ppm at 35 °C. Through various heteronuclear multidimensional NMR experiments, these signals were assigned to two zinc-coordinating His side chains in contact with DNA phosphate groups. The data show that the Nδ1 atoms of these His side chains are protonated and exhibit the (1)H-(15)N cross-peaks. Using heteronuclear (1)H, (15)N, and (31)P NMR experiments, we observed the hydrogen-bond scalar couplings between the His (15)Nδ1/(1)Hδ1 and DNA phosphate (31)P nuclei. These results demonstrate the direct involvement of the zinc-coordinating His side chains in the recognition of DNA by the Cys2His2-class zinc fingers in solution.

  3. Unusual intermolecular "through-space" j couplings in p-se heterocycles.

    PubMed

    Sanz Camacho, Paula; Athukorala Arachchige, Kasun S; Slawin, Alexandra M Z; Green, Timothy F G; Yates, Jonathan R; Dawson, Daniel M; Woollins, J Derek; Ashbrook, Sharon E

    2015-05-20

    Solid-state NMR spectra of new P-Se heterocycles based on peri-substituted naphthalene motifs show the presence of unusual J couplings between Se and P. These couplings are between atoms in adjacent molecules and occur "through space", rather than through conventional covalent bonds. Experimental measurements are supported by relativistic DFT calculations, which confirm the presence of couplings between nonbonded atoms, and provide information on the pathway of the interaction. This observation improves the understanding of J couplings and offers insight into the factors that affect crystal packing in solids, for future synthetic exploitation.

  4. Probing intermolecular interactions in a diethylcarbamazine citrate salt by fast MAS (1)H solid-state NMR spectroscopy and GIPAW calculations.

    PubMed

    Venâncio, Tiago; Oliveira, Lyege Magalhaes; Ellena, Javier; Boechat, Nubia; Brown, Steven P

    2017-03-02

    Fast magic-angle spinning (MAS) NMR is used to probe intermolecular interactions in a diethylcarbamazine salt, that is widely used as a treatment against adult worms of Wuchereria bancrofti which cause a common disease in tropical countries named filariasis. Specifically, a dihydrogen citrate salt that has improved thermal stability and solubility as compared to the free form is studied. One-dimensional (1)H, (13)C and (15)N and two-dimensional (1)H-(13)C and (14)N-(1)H heteronuclear correlation NMR experiments under moderate and fast MAS together with GIPAW (CASTEP) calculations enable the assignment of the (1)H, (13)C and (14)N/(15)N resonances. A two-dimensional (1)H-(1)H double-quantum (DQ) -single-quantum (SQ) MAS spectrum recorded with BaBa recoupling at 60kHz MAS identifies specific proton-proton proximities associated with citrate-citrate and citrate-diethylcarbamazine intermolecular interactions.

  5. Investigating Unusual Homonuclear Intermolecular "Through-Space" J Couplings in Organochalcogen Systems.

    PubMed

    Sanz Camacho, Paula; McKay, David; Dawson, Daniel M; Kirst, Christin; Yates, Jonathan R; Green, Timothy F G; Cordes, David B; Slawin, Alexandra M Z; Woollins, J Derek; Ashbrook, Sharon E

    2016-11-07

    Although the electron-mediated spin-spin or J coupling is conventionally viewed as transmitted via covalent bonds, examples of J couplings between atoms that are not formally bonded but are in close proximity (termed "through-space" J couplings) have been reported. In this work, we investigate the observation of homonuclear (31)P J couplings in organochalcogen heterocycles, which occur between (31)P in two separate molecules, confirming without doubt their through-space nature. The presence of this interaction is even more surprising for one compound, where it occurs between crystallographically equivalent species. Although crystallographically equivalent species need not be magnetically equivalent in the solid state, owing to the presence of anisotropic interactions, we demonstrate that it is not the shielding anisotropy that lifts magnetic equivalence, in this case, but the presence of heteronuclear couplings to (77)Se. We support our experimental observations with periodic scalar-relativistic density functional theory calculations and coupling density deformation plots to visualize the mechanism of these interesting interactions.

  6. 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.

  7. The origins of intra- and inter-molecular vibrational couplings: A case study of H{sub 2}O-Ar on full and reduced-dimensional potential energy surface

    SciTech Connect

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

    2016-01-07

    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{sub 2}O–Ar, which explicitly incorporates interdependence on the intramolecular (Q{sub 1},  Q{sub 2},  Q{sub 3}) normal-mode coordinates of the H{sub 2}O 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 (v{sub 1},  v{sub 2},  v{sub 3}) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H{sub 2}O 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{sup −1}, and required only 58 parameters. With the 3D PESs of H{sub 2}O–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{sup −1} for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H{sub 2}O in H{sub 2}O–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

  8. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy.

    PubMed

    Semenov, M A; Blyzniuk, Iu N; Bolbukh, T V; Shestopalova, A V; Evstigneev, M P; Maleev, V Ya

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (CO and NH(2)) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  9. Intermolecular hydrogen bonds in hetero-complexes of biologically active aromatic molecules probed by the methods of vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Semenov, M. A.; Blyzniuk, Iu. N.; Bolbukh, T. V.; Shestopalova, A. V.; Evstigneev, M. P.; Maleev, V. Ya.

    2012-09-01

    By the methods of vibrational spectroscopy (Infrared and Raman) the investigation of the hetero-association of biologically active aromatic compounds: flavin-mononucleotide (FMN), ethidium bromide (EB) and proflavine (PRF) was performed in aqueous solutions. It was shown that between the functional groups (Cdbnd O and NH2) the intermolecular hydrogen bonds are formed in the hetero-complexes FMN-EB and FMN-PRF, additionally stabilizing these structures. An estimation of the enthalpy of Н-bonding obtained from experimental shifts of carbonyl vibrational frequencies has shown that the H-bonds do not dominate in the magnitude of experimentally measured total enthalpy of the hetero-association reactions. The main stabilization is likely due to intermolecular interactions of the molecules in these complexes and their interaction with water environment.

  10. 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.

  11. Closed-shell ring coupled cluster doubles theory with range separation applied on weak intermolecular interactions.

    PubMed

    Toulouse, Julien; Zhu, Wuming; Savin, Andreas; Jansen, Georg; Ángyán, János G

    2011-08-28

    We explore different variants of the random phase approximation to the correlation energy derived from closed-shell ring-diagram approximations to coupled cluster doubles theory. We implement these variants in range-separated density-functional theory, i.e., by combining the long-range random phase approximations with short-range density-functional approximations. We perform tests on the rare-gas dimers He(2), Ne(2), and Ar(2), and on the weakly interacting molecular complexes of the S22 set of Jurečka et al. [P. Jurečka, J. Šponer, J. Černý, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The two best variants correspond to the ones originally proposed by Szabo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977)]. With range separation, they reach mean absolute errors on the equilibrium interaction energies of the S22 set of about 0.4 kcal/mol, corresponding to mean absolute percentage errors of about 4%, with the aug-cc-pVDZ basis set.

  12. Probing anomalous Higgs couplings in H → ZV decays

    NASA Astrophysics Data System (ADS)

    Modak, Tanmoy; Srivastava, Rahul

    2017-01-01

    We analyze the possibility of probing anomalous Higgs couplings in the rare decays H → ZV, V being a vector quarkonium state. These rare decays involve both gauge as well as the Yukawa sectors and either of them can potentially be anomalous. We show that the branching fractions for H → ZV decays in Standard Model (SM) are small, making it a sensitive probe for anomalous Higgs couplings originating from physics beyond SM. Moreover, as both V and Z can decay into pair of charged leptons, they provide experimentally clean channels and future LHC runs should observe such decays. We perform a model independent analysis and show how angular asymmetries can be used to probe these anomalous Higgs couplings, taking further decays of V and Z to pair of charged leptons into account. The angular asymmetries can provide significant information about anomalous Higgs couplings in both gauge and Yukawa sectors.

  13. Intermolecular forces.

    PubMed

    Buckingham, A D

    1975-11-06

    The nature of molecular interactions is examined. Intermolecular forces are divided into long-range and short-range components; the former operate at distances where the effects of electron exchange are negligible and decrease as an inverse power of the separation. The long-range interactions may be subdividied into electrostatic, induction and dispersion contributions, where the electrostatic component is the interaction of the permanent charge distributions and the others originate in the fluctuations in the distributions. Typical magnitudes of the various contributions are given. The forces between macroscopic bodies are briefly considered, as are the effects of a medium. Some of the manifestations of molecular interactions are discussed.

  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. 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.

  16. Probing electroweak top quark couplings at hadron colliders

    SciTech Connect

    Baur, U.; Juste, A.; Orr, L.H.; Rainwater, D.

    2005-03-01

    We consider QCD tt{gamma} and ttZ production at hadron colliders as a tool to measure the tt{gamma} and ttZ couplings. At the Tevatron it may be possible to perform a first, albeit not very precise, test of the tt{gamma} vector and axial vector couplings in tt{gamma} production, provided that more than 5 fb{sup -1} of integrated luminosity are accumulated. The ttZ cross section at the Tevatron is too small to be observable. At the CERN Large Hadron Collider (LHC) it will be possible to probe the tt{gamma} couplings at the few-percent level, which approaches the precision which one hopes to achieve with a next-generation e{sup +}e{sup -} linear collider. The LHC's capability of associated QCD ttV (V={gamma},Z) production has the added advantage that the tt{gamma} and ttZ couplings are not entangled. For an integrated luminosity of 300 fb{sup -1}, the ttZ vector (axial vector) coupling can be determined with an uncertainty of 45-85% (15-20%), whereas the dimension-five dipole form factors can be measured with a precision of 50-55%. The achievable limits improve typically by a factor of 2-3 for the luminosity-upgraded (3 ab{sup -1}) LHC.

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-01

    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 Cs-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.

  20. 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.

  1. Solute-solvent intermolecular vibronic coupling as manifested by the molecular near-field effect in resonance hyper-Raman scattering.

    PubMed

    Shimada, Rintaro; Hamaguchi, Hiro-o

    2011-01-21

    Vibronic coupling within the excited electronic manifold of the solute all-trans-β-carotene through the vibrational motions of the solvent cyclohexane is shown to manifest as the "molecular near-field effect," in which the solvent hyper-Raman bands are subject to marked intensity enhancements under the presence of all-trans-β-carotene. The resonance hyper-Raman excitation profiles of the enhanced solvent bands exhibit similar peaks to those of the solute bands in the wavenumber region of 21,700-25,000 cm(-1) (10,850-12,500 cm(-1) in the hyper-Raman exciting wavenumber), where the solute all-trans-β-carotene shows a strong absorption assigned to the 1A(g) → 1B(u) transition. This fact indicates that the solvent hyper-Raman bands gain their intensities through resonances with the electronic states of the solute. The observed excitation profiles are quantitatively analyzed and are successfully accounted for by an extended vibronic theory of resonance hyper-Raman scattering that incorporates the vibronic coupling within the excited electronic manifold of all-trans-β-carotene through the vibrational motions of cyclohexane. It is shown that the major resonance arises from the B-term (vibronic) coupling between the first excited vibrational level (v = 1) of the 1B(u) state and the ground vibrational level (v = 0) of a nearby A(g) state through ungerade vibrational modes of both the solute and the solvent molecules. The inversion symmetry of the solute all-trans-β-carotene is preserved, suggesting the weak perturbative nature of the solute-solvent interaction in the molecular near-field effect. The present study introduces a new concept, "intermolecular vibronic coupling," which may provide an experimentally accessible∕theoretically tractable model for understanding weak solute-solvent interactions in liquid.

  2. Coupling efficiency of ultra-small gradient-index fiber probe

    NASA Astrophysics Data System (ADS)

    Wang, Chi; Sun, Jianmei; Sun, Fan; Zhu, Jun; Yuan, Zhiwen; Asundi, Anand

    2017-04-01

    In this paper, the coupling efficiency of ultra-small GRIN fiber probe is studied for its focusing performance. Based on the light transmission characteristics of a Gaussian beam and the principle of optical imaging, with the analytical methods, the theoretical formula is deduced for the coupling efficiency of ultra-small GRIN fiber probe. Experiments were set-up and conducted for verification. Per the experimental results, for an ultra-small GRIN fiber probe with the focal length of 0.4 mm, the coupling efficiency measured at the focusing position was 57%, and above 44% within the 0-0.6 mm range. However, for a single-mode fiber, the coupling efficiency dropped to 17% when the distance increased to 0.2 mm. Thus, the ultra-small GRIN fiber probe boasts a superior focusing performance and coupling efficiency. This paper provides a theoretical basis for the application and research on ultra-small GRIN fiber probe.

  3. Coupled Cluster and Møller-Plesset Perturbation Theory Calculations of Noncovalent Intermolecular Interactions using Density Fitting with Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Pitoňák, Michal; Aquilante, Francesco; Neogrády, Pavel; Pedersen, Thomas Bondo; Lindh, Roland

    2012-06-12

    We compute noncovalent intermolecular interaction energies for the S22 test set [Phys. Chem. Chem. Phys.2006, 8, 1985-1993] of molecules at the Møller-Plesset and coupled cluster levels of supermolecular theory using density fitting (DF) to approximate all two-electron integrals. The error due to the DF approximation is analyzed for a range of auxiliary basis sets derived from Cholesky decomposition (CD) in conjunction with correlation consistent and atomic natural orbital valence basis sets. A Cholesky decomposition threshold of 10(-4)Eh for full molecular CD and its one-center approximation (1C-CD) generally yields errors below 0.03 kcal/mol, whereas 10(-3)Eh is sufficient to obtain the same level of accuracy or better with the atomic CD (aCD) and atomic compact CD (acCD) auxiliary basis sets. Comparing to commonly used predefined auxiliary basis sets, we find that while the aCD and acCD sets are larger by a factor of 2-4 with triple-ζ AO basis sets, they provide results 1-2 orders of magnitude more accurate.

  4. 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.

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

    PubMed

    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.

  6. 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.

  7. Higgs coupling constants as a probe of new physics

    SciTech Connect

    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.

  8. 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.

  9. 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.

  10. 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.

  11. NDE of a 3-D surface crack using closely coupled probes for DCPD technique

    SciTech Connect

    Saka, M.; Abe, H.; Hirota, D.; Komura, I.

    1998-11-01

    A procedure of applying the d-c potential drop technique using the closely coupled probes to NDE of a 3-D surface crack is newly developed. The calibration equation for three sensors which differ in the distance between the probes is derived. Experiments validated the use of the calibration equation for the NDE of cracks. The method to use the three sensors properly based on the measuring sensitivity is shown.

  12. Probing gravitational non-minimal coupling with dark energy surveys

    NASA Astrophysics Data System (ADS)

    Geng, Chao-Qiang; Lee, Chung-Chi; Wu, Yi-Peng

    2017-03-01

    We investigate observational constraints on a specific one-parameter extension to the minimal quintessence model, where the quintessence field acquires a quadratic coupling to the scalar curvature through a coupling constant ξ . The value of ξ is highly suppressed in typical tracker models if the late-time cosmic acceleration is driven at some field values near the Planck scale. We test ξ in a second class of models in which the field value today becomes a free model parameter. We use the combined data from type-Ia supernovae, cosmic microwave background, baryon acoustic oscillations and matter power spectrum, to weak lensing measurements and find a best-fit value ξ {>}0.289 where ξ = 0 is excluded outside the 95% confidence region. The effective gravitational constant G_eff subject to the hint of a non-zero ξ is constrained to -0.003< 1- G_eff/G < 0.033 at the same confidence level on cosmological scales, and it can be narrowed down to 1- G_eff/G < 2.2 × 10^{-5} when combining with Solar System tests.

  13. 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.

  14. 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.

  15. 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.

  16. Probing anomalous couplings using di-Higgs production in electron-proton collisions

    NASA Astrophysics Data System (ADS)

    Kumar, Mukesh; Ruan, Xifeng; Islam, Rashidul; Cornell, Alan S.; Klein, Max; Klein, Uta; Mellado, Bruce

    2017-01-01

    A proposed high energy Future Circular Hadron-Electron Collider would provide sufficient energy in a clean environment to probe di-Higgs production. Using this channel we show that the azimuthal angle correlation between the missing transverse energy and the forward jet is a very good probe for the non-standard hhh and hhWW couplings. We give the exclusion limits on these couplings as a function of integrated luminosity at a 95% C.L. using the fiducial cross sections. With appropriate error fitting methodology we find that the Higgs boson self coupling could be measured to be ghhh(1) = 1.00-0.17(0.12)+0.24(0.14) of its expected Standard Model value at √{ s} = 3.5 (5.0) TeV for an ultimate 10 ab-1 of integrated luminosity.

  17. Influence of intermolecular interactions on magnetic observables

    NASA Astrophysics Data System (ADS)

    Schnack, Jürgen

    2016-02-01

    Very often it is an implied paradigm of molecular magnetism that magnetic molecules in a crystal interact so weakly that measurements of dc magnetic observables reflect ensemble properties of single molecules. But the number of cases where the assumption of virtually noninteracting molecules does not hold grows steadily. A deviation from the noninteracting case can especially clearly be seen in clusters with antiferromagnetic couplings, where steps of the low-temperature magnetization curve are smeared out with increasing intermolecular interaction. In this investigation we demonstrate with examples in one, two, and three space dimensions how intermolecular interactions influence typical magnetic observables such as magnetization, susceptibility, and specific heat.

  18. Probing electromechanical coupling in collagen at the nanoscale via scanning probe microscopy

    NASA Astrophysics Data System (ADS)

    Denning, Denise

    Electromechanical coupling is ubiquitous in nature and is a functional characteristic in a large range of inorganic and organic materials, including collagen type I -- a fibrous protein abundant in mammals. Understanding the biofunctionality of electromechanical coupling in its linear form -- piezoelectricity, has been a topic of research spanning over seven decades and yet many questions still remain unanswered. Piezoelectricity in bone and connective tissues such as tendon has been investigated at the macroscopic scale since the discovery of piezoelectricity in bone in 1957 and induced currents via the piezoelectric effect have been shown to activate the healing process in tissues under tension. Biological systems consist of complex hierarchical structures which results from a high degree of organization from the macroscale down to the nanoscale. These complex structures, however, make quantitative piezoelectric measurements difficult. Therefore, there exists a need to understand these processes at the individual protein level -- i.e. at the nanoscale. In this thesis, a voltage-modulated form of atomic force microscopy called piezoresponse force microscopy is utilized to investigate the counterpart which is responsible for piezoelectricity in bone and connective tissues -- collagen. The polar properties of collagen were revealed at the nanoscale and were shown to result in a highly complex polar architecture in natural tissue, which is important for understanding tissue development. Shear piezoelectricity was discovered to persist in engineered collagen hydrogels, a study intended to highlight the importance of replicating both structural and functional properties in replacement tissues. The electromechanical properties of collagen type II were investigated which were previously unknown. Collagen type II was shown to be a shear piezoelectric, exhibiting an angle dependence of the piezoelectric signal with cantilever-fibril angle. In addition, the piezoelectric

  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. Near-Field Infrared Pump-Probe Imaging of Surface Phonon Coupling in Boron Nitride Nanotubes.

    PubMed

    Gilburd, Leonid; Xu, Xiaoji G; Bando, Yoshio; Golberg, Dmitri; Walker, Gilbert C

    2016-01-21

    Surface phonon modes are lattice vibrational modes of a solid surface. Two common surface modes, called longitudinal and transverse optical modes, exhibit lattice vibration along or perpendicular to the direction of the wave. We report a two-color, infrared pump-infrared probe technique based on scattering type near-field optical microscopy (s-SNOM) to spatially resolve coupling between surface phonon modes. Spatially varying couplings between the longitudinal optical and surface phonon polariton modes of boron nitride nanotubes are observed, and a simple model is proposed.

  1. Fluorescent probe environment and the structural and charge changes in energy coupling of mitochondrial membranes.

    PubMed

    Chance, B

    1970-10-01

    The use of fluorescent probes to give continuous readouts of the structural states of mitochondrial membranes during energy coupling seems a logical extension of their use in the study of protein structural changes. A clear correlation of the probes' fluorescence characteristics with the acquisition of energy coupling can be demonstrated in fragmented and natural membrane using 1-anilinonaphthalene-8-sulfonate (ANS) and ethidium bromide respectively. The present contribution attempts to bring together contemporary viewpoints of this and other laboratories and the recent experimental data and give some detailed information on probe environment and on the structural or charge changes occurring upon energization. The energy-dependent region of the membrane is located at an aqueous interface between an outer layer of proteins (presumably cytochromes) and the membrane permeability barrier; the aromatic portion of ANS appears to be located in the lipid phase and the sulfonic acid group in the aqueous phase. The aqueous phase is probably a structured water region near paramagnetic membrane components such as cytochrome. Membrane energization arising from altered redox potential changes of cytochromes (b(T)) is communicated to the water structure through altered structural states of the hemoproteins, causing a decreased volume of the structured water region and increased interaction with the paramagnetic components in the energized state. Attendant alterations of protonic equilibria of membrane components induce both local and transmembrane changes in charge distribution, with consequent movements of ions, including the probe molecules themselves.

  2. Development of (trimethylsilyl)ethyl ester protected enolates and applications in palladium-catalyzed enantioselective allylic alkylation: intermolecular cross-coupling of functionalized electrophiles.

    PubMed

    Reeves, Corey M; Behenna, Douglas C; Stoltz, Brian M

    2014-05-02

    The development of (trimethylsilyl)ethyl ester protected enolates is reported. The application of this class of compounds in palladium-catalyzed asymmetric allylic alkylation is explored, yielding a variety of α-quaternary six- and seven-membered ketones and lactams. Independent coupling partner synthesis engenders enhanced allyl substrate scope relative to traditional β-ketoester substrates; highly functionalized α-quaternary ketones generated by the union of (trimethylsilyl)ethyl β-ketoesters and sensitive allylic alkylation coupling partners serve to demonstrate the utility of this method for complex fragment coupling.

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

    PubMed

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

    2014-11-07

    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.

  5. Exclusive radiative Higgs decays as probes of light-quark Yukawa couplings

    NASA Astrophysics Data System (ADS)

    König, Matthias; Neubert, Matthias

    2015-08-01

    We present a detailed analysis of the rare exclusive Higgs boson decays into a single vector meson and a photon and investigate the possibility of using these processes to probe the light-quark Yukawa couplings. We work with an effective Lagrangian with modified Higgs couplings to account for possible new-physics effects in a model-independent way. The h → Vγ decay rate is governed by the destructive interference of two amplitudes, one of which involves the Higgs coupling to the quark anti-quark pair inside the vector meson. We derive this amplitude at next-to-leading order in α s using QCD factorization, including the resummation of large logarithmic corrections and accounting for the effects of flavor mixing. The high factorization scale μ ˜ m h ensures that our results are rather insensitive to the hadronic parameters characterizing the light-cone distribution amplitude of the vector meson. The second amplitude arises from the loop-induced effective hγγ * and hγZ * couplings, where the off-shell gauge boson converts into the vector meson. We devise a strategy to eliminate theoretical uncertainties related to this amplitude to almost arbitrary precision. This opens up the possibility to probe for modifications of the c- and b-quark Yukawa couplings and modifications of the s-quark Yukawa coupling in the high-luminosity LHC run. In particular, we show that measurements of the ratios Br( h → Υ( nS) γ)/Br( h → γγ) and can provide complementary information on the real and imaginary parts of the b-quark Yukawa coupling. More accurate measurements would be possible at a future 100 TeV proton-proton collider.

  6. Probe And Enhancement Of SBS Based Phonons In Infrared Fibers Using Waveguide Coupled External Radiation

    NASA Astrophysics Data System (ADS)

    Yu, Chung; Chong, Yat C.; Fong, Chee K.

    1989-06-01

    Interaction of GHz and MHz radiation with CO2 laser propagation in a silver halide fiber using sBs based phonon coupling is furthet investigated. The external signal serves to both probe and enhance laser generated sBs phonons in the fiber. Efficient coupling of microwave radiation into the fiber is accomplished by placing the fiber in a hollow metallic waveguide, designed and constructed to transmit the dominant mode in the 0.9-2.0 GHz band. MHz radiation is conveniently coupled into the fiber using the guided microwave radiation as carrier. Phonon emissions from the fiber under CO2 laser pumping are first established on a spectrum analyzer; low frequency generators ale then tuned to match these frequencies and their maximum interaction recorded. Such interactions are systematically studied by monitoring the amplitude and waveform of the reflected and transmitted laser pulse at various power levels and frequencies of the externally coupled radiation. A plot of reflected laser power versus incident laser power reveals a distinct sBs generated phonon threshold. Variouslaunch directions of the GHz and MHz radiation with respect to the direction of laser propagation are realized to verify theory governing sBs interactions. The MHz radiation and its associated phonons in the fiber are convenient tools for probing sBs related phenomenon in infrared fibers.

  7. Prospective Real Time Head Motion Correction Using Inductively Coupled Wireless NMR Probes

    PubMed Central

    Sengupta, Saikat; Tadanki, Sasidhar; Gore, John C.; Welch, E. Brian

    2014-01-01

    Purpose Head motion continues to be a major source of artifacts and data quality degradation in MRI. The goal of this work was to develop and demonstrate a novel technique for prospective, 6 degrees of freedom (6DOF) rigid body motion estimation and real time motion correction using inductively coupled wireless nuclear magnetic resonance (NMR) probe markers. Methods Three wireless probes that are inductively coupled with the scanner’s RF setup serve as fiducials on the subject’s head. A 12 ms linear navigator module is interleaved with the imaging sequence for head position estimation, and scan geometry is updated in real time for motion compensation. Flip angle amplification in the markers allows the use of extremely small navigator flip angles (~1°). A novel algorithm is presented to identify marker positions in the absence of marker specific receive channels. The method is demonstrated for motion correction in 1 mm3 gradient recalled echo experiments in phantoms and humans. Results Significant improvement of image quality is demonstrated in phantoms and human volunteers under different motion conditions. Conclusion A novel real time 6 DOF head motion correction technique based on wireless NMR probes is demonstrated in high resolution imaging at 7 Tesla. PMID:24243810

  8. 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.

  9. 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.

  10. 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.

  11. Probing the flat band of optically trapped spin-orbital-coupled Bose gases using Bragg spectroscopy

    NASA Astrophysics Data System (ADS)

    Li, Wu; Chen, Lei; Chen, Zhu; Hu, Ying; Zhang, Zhidong; Liang, Zhaoxin

    2015-02-01

    Motivated by recent efforts in creating flat bands in ultracold atomic systems, we investigate how to probe a flat band in an optically trapped spin-orbital-coupled Bose-Einstein condensate using Bragg spectroscopy. We find that the excitation spectrum and the dynamic structure factor of the condensate are dramatically altered when the band structure exhibits various levels of flatness. In particular, when the band exhibits perfect flatness around the band minima corresponding to a near-infinite effective mass, a quadratic dispersion emerges in the low-energy excitation spectrum; in sharp contrast, for the opposite case when an ordinary band is present, the familiar linear dispersion arises. Such linear-to-quadratic crossover in the low-energy spectrum presents a striking manifestation of the transition of an ordinary band into a flat band, thereby allowing a direct probe of the flat band by using Bragg spectroscopy.

  12. Remote estimation of phycocyanin (PC) for inland waters coupled with YSI PC fluorescence probe.

    PubMed

    Song, Kaishan; Li, Lin; Tedesco, Lenore; Clercin, Nicole; Hall, Bob; Li, Shuai; Shi, Kun; Liu, Dawei; Sun, Ying

    2013-08-01

    Nuisance cyanobacterial blooms degrade water resources through accelerated eutrophication, odor generation, and production of toxins that cause adverse effects on human health. Quick and effective methods for detecting cyanobacterial abundance in drinking water supplies are urgently needed to compliment conventional laboratory methods, which are costly and time consuming. Hyperspectral remote sensing can be an effective approach for rapid assessment of cyanobacterial blooms. Samples (n=250) were collected from five drinking water sources in central Indiana (CIN), USA, and South Australia (SA), which experience nuisance cyanobacterial blooms. In situ hyperspectral data were used to develop models by relating spectral signal with handheld fluorescence probe (YSI 6600 XLM-SV) measured phycocyanin (PC in cell/ml), a proxy pigment unique for indicating the presence of cyanobacteria. Three-band model (TBM), which is effective for chlorophyll-a estimates, was tuned to quantify cyanobacteria coupled with the PC probe measured cyanobacteria. As a comparison, two band model proposed by Simis et al. (Limnol Oceanogr, 50(11): 237-245, 2005; denoted as SM05) was paralleled to evaluate TBM model performance. Our observation revealed a high correlation between measured and estimated PC for SA dataset (R (2) =0.96; range: 534-20,200 cell/ml) and CIN dataset (R (2) =0.88; range: 1,300-44,500 cell/ml). The potential of this modeling approach for imagery data were assessed by simulated ESA/Centinel3/OLCI spectra, which also resulted in satisfactory performance with the TBM for both SA dataset (RMSE % =26.12) and CIN dataset (RMSE % =34.49). Close relationship between probe-measured PC and laboratory measured cyanobacteria biovolume was observed (R (2) =0.93, p<0.0001) for the CIN dataset, indicating a stable performance for PC probe. Based on our observation, field spectroscopic measurement coupled with PC probe measurements can provide quantitative cyanobacterial bloom

  13. Intermolecular interactions in solid benzene.

    PubMed

    Kearley, G J; Johnson, M R; Tomkinson, J

    2006-01-28

    The lattice dynamics and molecular vibrations of benzene and deuterated benzene crystals are calculated from force constants derived from density-functional theory (DFT) calculations and compared with measured inelastic neutron-scattering spectra. A very small change (0.5%) in lattice parameter is required to obtain real lattice-mode frequencies across the Brillouin zone. There is a strong coupling between wagging and breathing modes away from the zone center. This coupling and sensitivity to cell size arises from two basic interactions. Firstly, comparatively strong interactions that hold the benzene molecules together in layers. These include an intermolecular interaction in which H atoms of one molecule link to the center of the aromatic ring of a neighboring molecule. The layers are held to each other by weaker interactions, which also have components that hold molecules together within a layer. Small changes in the lattice parameters change this second type of interaction and account for the changes to the lattice dynamics. The calculations also reveal a small auxetic effect in that elongation of the crystal along the b axis leads to an increase in internal pressure in the ac plane, that is, elongation in the b direction induces expansion in the a and c directions.

  14. Probing ultrafast energy transfer between excitons and plasmons in the ultrastrong coupling regime

    NASA Astrophysics Data System (ADS)

    Balci, Sinan; Kocabas, Coskun; Küçüköz, Betül; Karatay, Ahmet; Akhüseyin, Elif; Gul Yaglioglu, H.; Elmali, Ayhan

    2014-08-01

    We investigate ultrafast energy transfer between excitons and plasmons in ensembles of core-shell type nanoparticles consisting of metal core covered with a concentric thin J-aggregate (JA) shell. The high electric field localization by the Ag nanoprisms and the high oscillator strength of the JAs allow us to probe this interaction in the ultrastrong plasmon-exciton coupling regime. Linear and nonlinear optical properties of the coupled system have been measured using transient absorption spectroscopy revealing that the hybrid system shows half-plasmonic and half-excitonic properties. The tunability of the nanoprism plasmon resonance provides a flexible platform to study the dynamics of the hybrid state in a broad range of wavelengths.

  15. Using magnetic coupling to implement 1H, 19F, 13C experiments in routine high resolution NMR probes

    NASA Astrophysics Data System (ADS)

    Bowyer, Paul; Finnigan, Jim; Marsden, Brian; Taber, Bob; Zens, Albert

    2015-12-01

    We report in this paper the design of 1H, 19F, 13C circuitry using magnetic coupling which can do on demand experiments where one of the three nuclei is observed and the other two are decoupled. The implementation of this circuitry in routine NMR probes is compared with capacitive coupling methods where it was found that by using magnetic coupling the performance of the routine NMR probe was not impacted by the addition of this circuitry. It is surmised that using this type of circuitry would be highly desirable for those chemists doing routine 19F NMR.

  16. Desensitization of metastable intermolecular composites

    SciTech Connect

    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.

  17. Alignment, vibronic level splitting, and coherent coupling effects on the pump-probe polarization anisotropy.

    PubMed

    Smith, Eric R; Jonas, David M

    2011-04-28

    The pump-probe polarization anisotropy is computed for molecules with a nondegenerate ground state, two degenerate or nearly degenerate excited states with perpendicular transition dipoles, and no resonant excited-state absorption. Including finite pulse effects, the initial polarization anisotropy at zero pump-probe delay is predicted to be r(0) = 3/10 with coherent excitation. During pulse overlap, it is shown that the four-wave mixing classification of signal pathways as ground or excited state is not useful for pump-probe signals. Therefore, a reclassification useful for pump-probe experiments is proposed, and the coherent anisotropy is discussed in terms of a more general transition dipole and molecular axis alignment instead of experiment-dependent ground- versus excited-state pathways. Although coherent excitation enhances alignment of the transition dipole, the molecular axes are less aligned than for a single dipole transition, lowering the initial anisotropy. As the splitting between excited states increases beyond the laser bandwidth and absorption line width, the initial anisotropy increases from 3/10 to 4/10. Asymmetric vibrational coordinates that lift the degeneracy control the electronic energy gap and off-diagonal coupling between electronic states. These vibrations dephase coherence and equilibrate the populations of the (nearly) degenerate states, causing the anisotropy to decay (possibly with oscillations) to 1/10. Small amounts of asymmetric inhomogeneity (2 cm(-1)) cause rapid (130 fs) suppression of both vibrational and electronic anisotropy beats on the excited state, but not vibrational beats on the ground electronic state. Recent measurements of conical intersection dynamics in a silicon napthalocyanine revealed anisotropic quantum beats that had to be assigned to asymmetric vibrations on the ground electronic state only [Farrow, D. A.; J. Chem. Phys. 2008, 128, 144510]. Small environmental asymmetries likely explain the observed absence

  18. Langmuir probe study of an inductively coupled magnetic-pole-enhanced helium plasma

    NASA Astrophysics Data System (ADS)

    Younus, Maria; Rehman, N. U.; Shafiq, M.; Naeem, M.; Zaka-ul-Islam, M.; Zakaullah, M.

    2017-03-01

    This study reports the effects of RF power and filling gas pressure variation on the plasma parameters, including the electron number density n e , electron temperature T e , plasma potential V p , skin depth δ, and electron energy probability functions (EEPFs) in a low-pressure inductively coupled helium plasma source with magnetic pole enhancement. An RF compensated Langmuir probe is used to measure these plasma parameters. It is observed that the electron number density increases with both the RF power and the filling gas pressure. Conversely, the electron temperature decreases with increasing RF power and gas pressure. It is also noted that, at low RF powers and gas pressures, the EEPFs are non-Maxwellian, while at RF powers of ≥50 W, they evolve into a Maxwellian distribution. The dependences of the skin depth and plasma potential on the RF power are also studied and show a decreasing trend.

  19. 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.

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

    SciTech Connect

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

    2016-03-09

    Here, we study angular observables in the $ {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.

  1. Probing Single Molecules with a Tunable Femtosecond Laser Coupled RF-STM

    NASA Astrophysics Data System (ADS)

    Cao, Weicai

    Scanning Tunneling Microscope (STM) has become a powerful tool in nanoscience for imaging, manipulation and electronic spectroscopy. STM inelastic electron tunneling spectroscopy (IETS) first achieved chemical identification of molecular species by characterizing vibrational energies. Recently, with the STM itProbe and H2 rotational spectromicroscopy, molecular structure and chemical bonds are observed with the STM. Despite these successes in spatial resolution, various efforts have been made to combine fs laser with STM to overcome the temporal resolution limitation of STM, there is so far no clear evidence of simultaneous fs and A resolution. Electronic properties of organic molecules are of central importance to applications such as molecular electronics, organic LEDs, and solar cells. Properties of these molecules can be probed by the scanning tunneling microscope (STM) at the single molecule level and with sub-A spatial resolution. The molecular orbital of 4, 7-Di ([2, 20-bithiophen]-5-yl) benzo[c] [1, 2, 5] thiadiazole (4T-BTD) with intramolecular donor-acceptor-donor sites is probed with the electronic state dI/dV imaging and H2 rotational and vibrational spectromicroscopy. 1, 4-Phenylene Diisocyanide (PDI) is probed by imaging with a CO-terminated tip and H2. PDI can self-assemble on noble metal surfaces to form nanostructures, which could have potential applications in molecular electronics and catalysis. Further combination of a RF-STM with a tunable femtosecond laser enables the investigation of light-molecule interactions. In this dissertation, efforts are spent to setup a new tunable fs laser (220 nm˜1040 nm) to couple with the RF-STM. The effects of the femtosecond laser are followed by detecting photo induced electron emission and photochemistry. A new double lock-in technique is applied to detect the weak laser-induced signal in the tunneling regime. To sharpen the energy width and increase the lifetime of the excited states of molecules, thin

  2. 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.

    PubMed

    Cappelletti, David; Falcinelli, Stefano; Pirani, Fernando

    2016-10-07

    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((2)P)-D2 and Cl((2)P)-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.

  3. 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.

  4. Comparison of various interpretation methods of the electric probe measurements in inductively coupled Ar and O{sub 2} plasmas

    SciTech Connect

    Woo Seo, Min; Keun Bae, Min; Chung, T. H.

    2014-02-15

    In low-pressure inductively coupled argon and oxygen discharges, the plasma density and electron temperature and the electron energy distribution function (EEDF) were obtained by using a cylindrical electric probe. The plasma densities were determined by various methods to interpret the probe current-voltage characteristic curve: the EEDF integration, the electron saturation current, the ion current at the floating potential, and the orbital-motion-limited (OML) ion current. Quite a good agreement exists between the plasma densities determined by various classical methods. Although the probe technique has some limitation in electronegative plasmas, the plasma densities determined from OML theory compare well with those measured by the ion saturation current at the floating potential in the oxygen discharges. In addition, the EEDFs of inductively coupled Ar and oxygen plasmas are observed to be nearly Maxwellian at the pressure range of 1-40 mTorr.

  5. 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.

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

    DOE PAGES

    Craig, Nathaniel; Gu, Jiayin; Liu, Zhen; ...

    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

  7. 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

  8. 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.

  9. A IR Diode Laser Spectroscopic Study of Adsorption and Intermolecular Interactions on Stepped Metal Surfaces: Carbon Monoxide on Vicinal COPPER(100)

    NASA Astrophysics Data System (ADS)

    Borguet, Eric Urbain

    The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique, Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority step-CO species accounting for a disproportionate fraction of the spectral intensity. A model has been elaborated which successfully accounts for, and simulates, the observed spectra. This enables site specific concentrations to be determined, even in the presence of strong dynamic-dipole coupling. These methods allow the spectroscopy, kinetics and intermolecular interactions of CO on a stepped Cu(100) surface to be probed. In particular, it has been possible to observe a dynamic equilibrium between CO adsorbed at step and terrace sites and to investigate the kinetics of site exchange on this surface. The IR spectra also reveal the nature and range of the intermolecular interactions and the local order which results. The CO/Cu(100) system is characterized by repulsive first and second nearest neighbor interactions. As a consequence, the adsorbates adopt a configuration which maximizes the intermolecular distance. Additionally, a non-resonant, broadband, adsorbate induced change in surface reflectivity is observed both in the IR and visible. This linear dependence of this signal with coverage provides a simple method of determining total adsorbed CO concentration.

  10. An IR diode laser spectroscopic study of adsorption and intermolecular interactions on stepped metal surfaces: CO on vicinal Cu(100). [IR (infrared)

    SciTech Connect

    Borguet, E.R.

    1993-01-01

    The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique. Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority step-CO species accounting for a disporportionate fraction of the spectral intensity. A model has been elaborated which successfully accounts for, and simulates, the observed spectra. This enables site specific concentrations to be determined, even in the presence of strong dynamic-dipole coupling. These methods allow the spectroscopy, kinetics and intermolecular interactions of CO on a stepped Cu(100) surface to be probed. In particular, it has been possible to observe a dynamic equilibrium between CO adsorbed at step and terrace sites and to investigate the kinetics of site exchanges on this surface. The IR spectra also reveal the nature and range of the intermolecular interactions and the local order which results. The CO/Cu(100) system is characterized by repulsive first and second nearest neighbor interactions. As a consequence, the adsorbates adopt a configuration which maximizes the intermolecular distance. Additionally, a non-resonant, broadband, adsorbate induced change in surface reflectivity is observed both in the IR and visible. This linear dependence of this signal with coverage provides a simple method of determining total absorbed CO concentration.

  11. Surface phonon coupling within boron nitride resolved by a novel near-field infrared pump-probe imaging technique

    NASA Astrophysics Data System (ADS)

    Gilburd, Leonid; Xu, Xiaoji G.; de Beer, Sissi; Bando, Yoshio; Golberg, Dmitri; Walker, Gilbert C.

    2016-09-01

    The excitation of surface phonon-polariton (SPhP) modes in polar materials using scattering type near-field optical microscopy (s-SNOM) has recently become an area of interest because of its potential for application as naturally occurring meta-materials and in low-loss energy transfer. Within this area, hexagonal boron nitride (h-BN) and boron nitride nanotubes (BNNTs) are the primary structures under investigation. Here we present pump-probe continuous wave (CW) scattering-type scanning near-field optical microscopy (s-SNOM) - a novel two color pump-probe infrared technique which uses two continuous wave tunable light sources and is based on s-SNOM. The technique allows us to spatially resolve coupling of the longitudinal optical and surface phonon polariton modes in BNNTs. However, no similar coupling is observed in two-dimensional h-BN crystals.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

    Kumar, A.; Graeves, R. A.

    1980-06-01

    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. A flow microslot NMR probe coupled with a capillary isotachophoresis system exhibits improved properties compared to solenoid designs.

    PubMed

    Gogiashvili, Mikheil; Telfah, Ahmad; Lambert, Jörg; Hergenröder, Roland

    2017-03-01

    We report on the hyphenation of capillary isotachophoresis (cITP) separations with online nuclear magnetic resonance (NMR) detection using a planar microslot waveguide probe design. While cITP is commonly coupled with a solenoidal microcoil NMR probe, the structural information provided is limited by broad resonances and poor spectral resolution due to the magnetic field created by the separation current. The microslot probe design described herein allows the separation capillary to be oriented parallel to the static magnetic field, B 0, eliminating the spectral broadening produced by the secondary magnetic field induced by the separation current. This allows high-resolution nuclear magnetic resonance spectra of the charged analytes to be obtained in online mode, whereas conventional solenoidal capillary NMR designs must resort to the stopped flow mode. The potential of the microslot probe for hyphenated electrophoretic separations is demonstrated by performing cITP focusing and online NMR detection of the (1)H NMR spectrum of a system containing spermine and aniline. Graphical Abstract High resolution NMR spectra in flow capillarelectrophoretic separations with microslot NMR probe.

  15. Preferences of rhodamine coupled (aminoalkyl)-piperazine probes towards Hg(II) ion and their FRET mediated signaling.

    PubMed

    Biswal, Biswonath; Bag, Bamaprasad

    2013-08-14

    The metal ion induced absorption and emission signaling pattern of rhodamine coupled bis-(aminopropyl)-piperazine (1-3) and (aminoethyl)-piperazine (4) based probes evaluated in MeCN as well as in an MeCN-H2O binary mixture medium revealed that these probes exhibit optical signaling perturbations to a varying extent in MeCN, however, their complexation induced signaling could be tuned selectively towards Hg(II) in the presence of an aqueous component in the solvent medium where competitive interactions such as metal-probe interactions and hydration of metal ions play the determining factor to induce aqueous promoted Hg(II) selectivity. Attachment of another fluorophore (anthracene and nitrobenzofurazan moieties in 2 and 3 respectively) at the other end of the rhodamine coupled bis-(aminopropyl)-piperazine receptor enabled these probes to facilitate a complexation induced fluorescence resonance energy transfer (FRET) from the excited fluorophore to the ring-opened rhodamine along with contributions through operative PET inhibition and rhodamine delactonization processes. The enhancement in absorption transition of these probes at ~557 nm upon selective Hg(II)-complexation and consequent colourless to pink colour change in the solution imply a chromogenic signaling pattern whereas simultaneous fluorescence amplification and/or FRET initiation lead to fluorogenic signaling to facilitate detection at lower concentration. The Hg(II)-selective photo-physical spectral modulation in the presence of other competitive metal ions, and their reversible dual channel signaling pattern under the action of counter anions or chelating agents such as EDTA or ethylenediamine establish the potential of these probes for highly selective, sensitive and reversible 'OFF-ON-OFF' detection of Hg(II). The complexation induced optical signaling pattern of probes with a propyl-linker in their receptor (1-3) in comparison with that of 4 consisting of an ethyl-spacer indicate that signaling

  16. Simulated imaging of intermolecular bonds using high throughput real-space density functional calculations

    NASA Astrophysics Data System (ADS)

    Lee, Alex; Kim, Minjung; Chelikowsky, James

    2015-03-01

    Recent experimental noncontact atomic force microscopy (AFM) studies on 8-hydroxyquinoline (8-hq) assemblies have imaged distinct lines between molecules that are thought to represent intermolecular bonding. To aid the interpretation of these images, we calculate simulated AFM images of an 8-hq dimer with a CO functionalized tip using a real-space pseudopotential formalism. We examine the effects of Pauli repulsion and tip probe relaxation as explanations for the enhanced resolution that resolves these intermolecular force lines. Our study aims to compute ab initio real-space images of intermolecular interactions.

  17. Franck—Condon breakdown as a probe of continuum coupling in molecular photoionization

    NASA Astrophysics Data System (ADS)

    Kakar, Sandeep; Choi, Heung Cheun; Poliakoff, E. D.

    1992-03-01

    We have measured vibrational branching ratios for 4σ -1 photoionization of CO in order to characterize continuum channel coupling. The results indicate that the shape resonance in the 5σ→ɛσ channel influences vibrational branching ratios of the 4σ -1 channel via continuum coupling, and the data illustrate how continuum channel coupling affects molecular photoionization dynamics.

  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. 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

  20. Probing subdiffraction limit separations with plasmon coupling microscopy: concepts and applications.

    PubMed

    Wu, Linxi; Reinhard, Björn M

    2014-06-07

    Due to their advantageous material properties, noble metal nanoparticles are versatile tools in biosensing and imaging. A characteristic feature of gold and silver nanoparticles is their ability to sustain localized surface plasmons that provide both large optical cross-sections and extraordinary photophysical stability. Plasmon coupling microscopy takes advantage of the beneficial optical properties and utilizes electromagnetic near-field coupling between individual noble metal nanoparticle labels to resolve subdiffraction limit separations in an all-optical fashion. This Tutorial provides an introduction into the physical concepts underlying distance dependent plasmon coupling, discusses potential experimental implementation of plasmon coupling microscopy, and reviews applications in the area of biosensing and imaging.

  1. Intermolecular potentials for hexafluoride gases

    SciTech Connect

    Aziz, R.A. . Dept. of Physics); Taylor, W.L. )

    1989-10-31

    Second virial coefficient and viscosity data were used to evaluate intermolecular potential functions proposed in the literature for SF{sub 6}, UF{sub 6}, and WF{sub 6}. It was found that none of the potentials could predict the properties simultaneously. By suitable adjustment of the repulsive wall, we constructed an inverse power (n{minus}7) potential which correlates second virial coefficient and viscosity data at the same time. The best integer repulsive exponent for SF{sub 6} was found to be n = 40, while that for UF{sub 6} and WF{sub 6} was n = 46. 41 refs., 10 figs., 11 tabs.

  2. Facile synthesis of diazido-functionalized biaryl compounds as radioisotope-free photoaffinity probes by Suzuki-Miyaura coupling.

    PubMed

    Hosoya, Takamitsu; Inoue, Atsushi; Hiramatsu, Toshiyuki; Aoyama, Hiroshi; Ikemoto, Takaaki; Suzuki, Masaaki

    2009-03-15

    Suzuki-Miyaura coupling of 3-azido-5-(azidomethyl)phenylboronic acid pinacol ester with various aryl bromides affords corresponding diazido-functionalized biaryl compounds in good yields. This approach provides an easy access to radioisotope-free photoaffinity probes possessing biaryl structure. By using this method, we prepared a novel diazido-functionalized dantrolene analog, which showed selective inhibitory effect on physiological Ca(2+) release (PCR) from sarcoplasmic reticulum (SR) in mouse skeletal muscle without affecting Ca(2+)-induced Ca(2+) release (CICR).

  3. Adsorption kinetics and intermolecular interactions of CO adsorbed on Cu(100) by transient laser reflection-absorption spectroscopy

    SciTech Connect

    Borguet, E.; Dai, H.L.

    1993-12-31

    IR and visible transient laser spectroscopic techniques have been developed to probe adsorption/desorption kinetics and intermolecular interactions of the CO/Cu(100) system. Vibrational spectroscopy, in general, can provide information about the nature of species adsorbed on surfaces e.g. chemical identity, site, orientation and concentration. In the presence of a few percent of CO adsorbed at step/defect sites, the spectra of the CO adsorbed on the terrace sites are greatly perturbed through dynamic-dipole coupling. This perturbation depends strongly on the intermolecular distance and the short-range order of the adsorbates. An analysis of this dynamic-dipole coupling reveals that the local arrangement of adsorbates is dominant by repulsive nearest-neighbor interactions. Successful modeling of the observed lineshapes allows the populations at each site to be determined at all coverages. The authors have also observed non-resonant adsorbate induced changes in both the IR and visible reflectance for a number of different adsorbates. This provides a simple and sensitive optical means of studying adsorption and desorption kinetics.

  4. 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.

  5. Probing the Higgs self coupling via single Higgs production at the LHC

    DOE PAGES

    Degrassi, G.; Giardino, P. P.; Maltoni, F.; ...

    2016-12-16

    Here, we propose a method to determine the trilinear Higgs self coupling that is alternative to the direct measurement of Higgs pair production total cross sections and differential distributions. Furthermore, the method relies on the effects that electroweak loops featuring an anomalous trilinear coupling would imprint on single Higgs production at the LHC. We first calculate these contributions to all the phenomenologically relevant Higgs production (ggF, VBF, WH, ZH, tmore » $$\\bar{t}$$ ) and decay (γγ,WW*/ZZ*→ 4f, b$$\\bar{b}$$,ττ) modes at the LHC and then estimate the sensitivity to the trilinear coupling via a one-parameter fit to the single Higgs measurements at the LHC 8 TeV. We also found that the bounds on the self coupling are already competitive with those from Higgs pair production and will be further improved in the current and next LHC runs.« less

  6. Probing the Higgs self coupling via single Higgs production at the LHC

    SciTech Connect

    Degrassi, G.; Giardino, P. P.; Maltoni, F.; Pagani, D.

    2016-12-16

    Here, we propose a method to determine the trilinear Higgs self coupling that is alternative to the direct measurement of Higgs pair production total cross sections and differential distributions. Furthermore, the method relies on the effects that electroweak loops featuring an anomalous trilinear coupling would imprint on single Higgs production at the LHC. We first calculate these contributions to all the phenomenologically relevant Higgs production (ggF, VBF, WH, ZH, t$\\bar{t}$ ) and decay (γγ,WW*/ZZ*→ 4f, b$\\bar{b}$,ττ) modes at the LHC and then estimate the sensitivity to the trilinear coupling via a one-parameter fit to the single Higgs measurements at the LHC 8 TeV. We also found that the bounds on the self coupling are already competitive with those from Higgs pair production and will be further improved in the current and next LHC runs.

  7. Probing the Higgs self coupling via single Higgs production at the LHC

    NASA Astrophysics Data System (ADS)

    Degrassi, G.; Giardino, P. P.; Maltoni, F.; Pagani, D.

    2016-12-01

    We propose a method to determine the trilinear Higgs self coupling that is alternative to the direct measurement of Higgs pair production total cross sections and differential distributions. The method relies on the effects that electroweak loops featuring an anomalous trilinear coupling would imprint on single Higgs production at the LHC. We first calculate these contributions to all the phenomenologically relevant Higgs production ( ggF, VBF, WH, ZH, toverline{t}H ) and decay (γ γ, W{W}^{ast }/Z{Z}^{ast}to 4f,boverline{b},τ τ ) modes at the LHC and then estimate the sensitivity to the trilinear coupling via a one-parameter fit to the single Higgs measurements at the LHC 8 TeV. We find that the bounds on the self coupling are already competitive with those from Higgs pair production and will be further improved in the current and next LHC runs.

  8. Probing crystal packing of uniformly (13)C-enriched powder samples using homonuclear dipolar coupling measurements.

    PubMed

    Mollica, Giulia; Dekhil, Myriam; Ziarelli, Fabio; Thureau, Pierre; Viel, Stéphane

    2015-02-01

    The relationship between the crystal packing of powder samples and long-range (13)C-(13)C homonuclear dipolar couplings is presented and illustrated for the case of uniformly (13)C-enriched L-alanine and L-histidine·HCl·H2O. Dipolar coupling measurement is based on the partial reintroduction of dipolar interactions by spinning the sample slightly off-magic-angle, while the coupling of interest for a given spin pair is isolated with a frequency-selective pulse. A cost function is used to correlate the so-derived dipolar couplings to trial crystal structures of the samples under study. This procedure allowed for the investigation of the l-alanine space group and L-histidine·HCl·H2O space group and unit-cell parameters.

  9. 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.

  10. Biocompatible magnetofluorescent probes: luminescent silicon quantum dots coupled with superparamagnetic iron(III) oxide.

    PubMed

    Erogbogbo, Folarin; Yong, Ken-Tye; Hu, Rui; Law, Wing-Cheung; Ding, Hong; Chang, Ching-Wen; Prasad, Paras N; Swihart, Mark T

    2010-09-28

    Luminescent silicon quantum dots (SiQDs) are gaining momentum in bioimaging applications, based on their unique combination of optical properties and biocompatibility. Here, we report the development of a multimodal probe that combines the optical properties of silicon quantum dots with the superparamagnetic properties of iron oxide nanoparticles to create biocompatible magnetofluorescent nanoprobes. Multiple nanoparticles of each type are coencapsulated within the hydrophobic core of biocompatible phospholipid-polyethyleneglycol (DSPE-PEG) micelles. The size distribution and composition of the magnetofluorescent nanoprobes were characterized by transmission electron microscopy (TEM) and energy-dispersive X-ray spectroscopy (EDS). Enhanced cellular uptake of these probes in the presence of a magnetic field was demonstrated in vitro. Their luminescence stability in a prostate cancer tumor model microenvironment was demonstrated in vivo. This paves the way for multimodal silicon quantum-dot-based nanoplatforms for a variety of imaging and delivery applications.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  12. 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

    2016-07-07

    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.

  13. Probing the CP nature of Higgs couplings in tth events at the LHC

    NASA Astrophysics Data System (ADS)

    Fiolhais, Miguel; Pease, Christopher; Onofre, Antonio

    2017-01-01

    The CP nature of the Higgs coupling to top quarks (tth) is studied in proton-proton collision events at a centre-of-mass energy of 13 TeV at the LHC. Pure scalar and pseudo-scalar Higgs boson signal events are generated with MadGraph5_aMC@NLO, and analysed in dileptonic final states with two oppositely charged leptons and four jets. These events are fully reconstructed by applying a kinematic fit. As a result, new angular distributions of the decay products as well as CP angular asymmetries are explored to separate the scalar from the pseudo-scalar components of the Higgs boson, which allows to reduce the contribution from the dominant irreducible background, ttbb. In addition, significant differences between the angular distributions and asymmetries are observed, providing new observables for a global fit of the Higgs couplings parameters.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Perturbation factors in the clinical handling of a fiber-coupled Raman probe for cutaneous in vivo diagnostic Raman spectroscopy.

    PubMed

    Schleusener, Johannes; Gluszczynska, Patrycja; Reble, Carina; Gersonde, Ingo; Helfmann, Jürgen; Cappius, Hans-Joachim; Fluhr, Joachim W; Meinke, Martina C

    2015-01-01

    The application of fiber-coupled Raman probes for the discrimination of cancerous and normal skin has the advantage of a non-invasive in vivo application, easy clinical handling, and access to the majority of body sites, which would otherwise be limited by stationary Raman microscopes. Nevertheless, including optical fibers and miniaturizing optical components, as well as measuring in vivo, involves the sensibility to external perturbation factors that could introduce artifacts to the acquired Raman spectra and thereby potentially reduce classification performance. In this study, typical perturbation factors of Raman measurements with a Raman fiber probe, optimized for clinical in vivo discrimination of skin cancer, were investigated experimentally. Measurements were performed under standardized conditions in clinical settings in vivo on human skin, as well as ex vivo on porcine ears. Raman spectra were analyzed in the fingerprint region between 1150 and 1730 cm(-1) using principal component analysis. The largest artifacts in the Raman spectra were found in measurements performed under the influence of strong ambient light conditions as well as after miscellaneous pre-treatments to the skin, such as use of a permanent marker or a sunscreen. Minor influences were also found in measurements using H2O immersion and when varying the probe contact force. The effect of reasonable variation of the fiber-bending radius was found to be of negligible impact. The influence of measurements on hairy or sun-exposed body sites, as well as inter-subject variation, was also investigated. The presented results may serve as a guide to avoid negative effects during the process of data acquisition and so avoid misclassification in tumor discrimination.

  19. A Dual Functional Electroactive and Fluorescent Probe for Coupled Measurements of Vesicular Exocytosis with High Spatial and Temporal Resolution.

    PubMed

    Liu, Xiaoqing; Savy, Alexandra; Maurin, Sylvie; Grimaud, Laurence; Darchen, François; Quinton, Damien; Labbé, Eric; Buriez, Olivier; Delacotte, Jérôme; Lemaître, Frédéric; Guille-Collignon, Manon

    2017-02-20

    In this work, Fluorescent False Neurotransmitter 102 (FFN102), a synthesized analogue of biogenic neurotransmitters, was demonstrated to show both pH-dependent fluorescence and electroactivity. To study secretory behaviors at the single-vesicle level, FFN102 was employed as a new fluorescent/electroactive dual probe in a coupled technique (amperometry and total internal reflection fluorescence microscopy (TIRFM)). We used N13 cells, a stable clone of BON cells, to specifically accumulate FFN102 into their secretory vesicles, and then optical and electrochemical measurements of vesicular exocytosis were experimentally achieved by using indium tin oxide (ITO) transparent electrodes. Upon stimulation, FFN102 started to diffuse out from the acidic intravesicular microenvironment to the neutral extracellular space, leading to fluorescent emissions and to the electrochemical oxidation signals that were simultaneously collected from the ITO electrode surface. The correlation of fluorescence and amperometric signals resulting from the FFN102 probe allows real-time monitoring of single exocytotic events with both high spatial and temporal resolution. This work opens new possibilities in the investigation of exocytotic mechanisms.

  20. Characterization of O2/Ar inductively coupled plasma studied by using a Langmuir probe and global model

    NASA Astrophysics Data System (ADS)

    Liu, Wei; Wen, De-Qi; Zhao, Shu-Xia; Gao, Fei; Wang, You-Nian

    2015-04-01

    An O2/Ar inductively coupled plasma is investigated by a Langmuir probe and a global model (volume averaged model). The electron density, electron temperature and electron energy distribution function (EEDF) are measured at different O2 contents, gas pressures and applied powers. At fixed pressure and power, the electron density first drops quickly with the O2 ratio and then tends to saturate in the high O2 ratio range. The effective electron temperature exhibits completely opposite behaviors at low and high pressures. This is caused by the different evolving behaviors of low and high energy electrons of the EEDFs with the O2 ratio. Both the Langmuir probe and the global model predict that the electron density of O2/Ar mixed plasma first increases, peaks and then drops constantly, upon increasing the pressure. An analysis based on the simulation reveals that the non-monotonic variation of electron density with the pressure is due to the non-monotonic variation of the ionizations from both ground state O and metastable O*. Due to the strong ionizations, the electron density increases linearly with the power. The effective electron temperature is unchanged because the EEDF shape that determines the electron temperature is not varied upon increasing the power. The calculated electron density and temperature when varying the power agree better with the experiments at high pressure, i.e. 45 mTorr. The quantitative deviation between the model and the experiment when varying the pressure and the O2 ratio can be explained by two aspects. (1) The electron energy probability function is assumed to have a Maxwellian distribution in the global model while the realistic EEDFs vary significantly with the pressure and/or the O2 ratio, as revealed by the experiment. (2) The power transfer efficiency (i.e. the fraction of the power coupled into plasma) increases with the pressure.

  1. 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.

  2. 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.

  3. 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

  4. Mode Coupling in Plasmonic Heterodimers Probed with Electron Energy Loss Spectroscopy.

    PubMed

    Flauraud, Valentin; Bernasconi, Gabriel D; Butet, Jérémy; Alexander, Duncan T L; Martin, Olivier J F; Brugger, Juergen

    2017-03-14

    While plasmonic antennas composed of building blocks made of the same material have been thoroughly studied, recent investigations have highlighted the unique opportunities enabled by making compositionally asymmetric plasmonic systems. So far, mainly heterostructures composed of nanospheres and nanodiscs have been investigated, revealing opportunities for the design of Fano resonant nanostructures, directional scattering, sensing and catalytic applications. In this article, an improved fabrication method is reported that enables precise tuning of the heterodimer geometry, with interparticle distances made down to a few nanometers between Au-Ag and Au-Al nanoparticles. A wide range of mode energy detuning and coupling conditions are observed by near field hyperspectral imaging performed with electron energy loss spectroscopy, supported by full wave analysis numerical simulations. These results provide direct insights into the mode hybridization of plasmonic heterodimers, pointing out the influence of each dimer constituent in the overall electromagnetic response. By relating the coupling of non-dipolar modes and plasmon-interband interaction with the dimer geometry, this work facilitates the development of plasmonic heterostructures with tailored responses, beyond the possibilities offered by homodimers.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. A microcoil NMR probe for coupling microscale HPLC with on-line NMR spectroscopy.

    PubMed

    Subramanian, R; Kelley, W P; Floyd, P D; Tan, Z J; Webb, A G; Sweedler, J V

    1999-12-01

    An HPLC NMR system is presented that integrates a commercial microbore HPLC system using a 0.5-mm column with a 500-MHz proton NMR spectrometer using a custom NMR probe with an observe volume of 1.1 microL and a coil fill factor of 68%. Careful attention to capillary connections and NMR flow cell design allows on-line NMR detection with no significant loss in separation efficiency when compared with a UV chromatogram. HPLC NMR is performed on mixtures of amino acids and small peptides with analyte injection amounts as small as 750 ng; the separations are accomplished in less than 10 min and individual NMR spectra are acquired with 12 s time resolution. Stopped-flow NMR is achieved by diversion of the chromatographic flow after observation of the beginning of the analyte band within the NMR flow cell. Isolation of the compound of interest within the NMR detection cell allows multidimensional experiments to be performed. A stopped-flow COSY spectrum of the peptide Phe-Ala is acquired in 3.5 h with an injected amount of 5 micrograms.

  10. Hydrated fractions of cellulosics probed by infrared spectroscopy coupled with dynamics of deuterium exchange.

    PubMed

    Driemeier, Carlos; Mendes, Fernanda M; Ling, Liu Yi

    2015-08-20

    This article presents a novel method to selectively probe the non-crystalline, hydrated fractions of cellulosic biomass. The method is based on time-resolved infrared spectra analyzed to provide information on spectral and dynamical features of deuterium exchange (OH → OD) in D2O atmosphere. We assign deuterium exchange spectral regions (700-3800 cm(-1)) and explore changes due to relative humidity, different cellulosic samples, and infrared polarization. Here, two results are highlighted. First, a wide range of celluloses isolated from plants show remarkable spectral similarities whatever the relative amounts of cellulose and xylan. This result supports an inherent type of hydrated disorder which is mostly insensitive to the molecular identities of the associated polysaccharides. Second, polarized infrared analysis of cotton reveals hydrated cellulose having chains preferentially aligned with those of crystals, while the hydroxyls of hydrated cellulose present much more randomized orientation. Our results provide new insights on molecular and group orientation and on hydrogen bonding in hydrated fractions of cellulosic biomass.

  11. Interrogation of the intersubunit interface of the open Hv1 proton channel with a probe of allosteric coupling

    PubMed Central

    Hong, Liang; Singh, Vikrant; Wulff, Heike; Tombola, Francesco

    2015-01-01

    The Hv1 voltage-gated proton channel is a dimeric complex consisting of two voltage-sensing domains (VSDs), each containing a gated proton permeation pathway. Dimerization is controlled by a cytoplasmic coiled-coil domain. The transitions from the closed to the open state in the two VSDs are known to occur cooperatively; however, the underlying mechanism is poorly understood. Intersubunit interfaces play a critical role in allosteric processes; but, such interfaces have not been determined in the open Hv1 channel. Here we show that 2-guanidinothiazole derivatives block the two Hv1 VSDs in a cooperative way, and use one of the compounds as a probe of allosteric coupling between open subunits. We find that the extracellular ends of the first transmembrane segments of the VSDs form the intersubunit interface that mediates coupling between binding sites, while the coiled-coil domain does not directly participate in the process. We also find strong evidence that the channel’s proton selectivity filter controls blocker binding cooperativity. PMID:26365828

  12. Probing the equilibrium dynamics of colloidal hard spheres above the mode-coupling glass transition.

    PubMed

    Brambilla, G; El Masri, D; Pierno, M; Berthier, L; Cipelletti, L; Petekidis, G; Schofield, A B

    2009-02-27

    We use dynamic light scattering and computer simulations to study equilibrium dynamics and dynamic heterogeneity in concentrated suspensions of colloidal hard spheres. Our study covers an unprecedented density range and spans seven decades in structural relaxation time, tau(alpha0, including equilibrium measurements above phi(c), the location of the glass transition deduced from fitting our data to mode-coupling theory. Instead of falling out of equilibrium, the system remains ergodic above phi(c) and enters a new dynamical regime where tau(alpha) increases with a functional form that was not anticipated by previous experiments, while the amplitude of dynamic heterogeneity grows slower than a power law with tau(alpha), as found in molecular glass formers close to the glass transition.

  13. 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.

  14. 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.

  15. Many-body effects in intermolecular forces.

    PubMed

    Elrod, M J; Saykally, R J

    1994-11-01

    The authors provide a review and literature survey of many-body effects in intermolecular forces. Topics include experimental methods, theoretical methods, many-body effects in atomic systems, and many-body effects in aqueous and nonaqueous molecular systems.

  16. 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.

  17. 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

  18. Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP).

    PubMed

    Morando, Michael; Capone, Douglas G

    2016-01-01

    Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, the roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake) with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a specific N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II. Alternatively, this may suggest the existence of tightly coupled metabolisms with primary assimilators, e.g., symbiosis, or the rapid and efficient scavenging of recently released products by highly active individuals. These results may be connected with global dominance often seen with these clades, likely conferring an advantage over other clades unable to access these resources. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e., different levels of nitrogen assimilation within clades, likely reflecting niche partitioning by ecotypes.

  19. Intraclade Heterogeneity in Nitrogen Utilization by Marine Prokaryotes Revealed Using Stable Isotope Probing Coupled with Tag Sequencing (Tag-SIP)

    PubMed Central

    Morando, Michael; Capone, Douglas G.

    2016-01-01

    Nitrogen can greatly influence the structure and productivity of microbial communities through its relative availability and form. However, the roles of specific organisms in the uptake of different nitrogen species remain poorly characterized. Most studies seeking to identify agents of assimilation have been correlative, indirectly linking activity measurements (e.g., nitrate uptake) with the presence or absence of biological markers, particularly functional genes and their transcripts. Evidence is accumulating of previously underappreciated functional diversity in major microbial subpopulations, which may confer physiological advantages under certain environmental conditions leading to ecotype divergence. This microdiversity further complicates our view of genetic variation in environmental samples requiring the development of more targeted approaches. Here, next-generation tag sequencing was successfully coupled with stable isotope probing (Tag-SIP) to assess the ability of individual phylotypes to assimilate a specific N source. Our results provide the first direct evidence of nitrate utilization by organisms thought to lack the genes required for this process including the heterotrophic clades SAR11 and the Archaeal Marine Group II. Alternatively, this may suggest the existence of tightly coupled metabolisms with primary assimilators, e.g., symbiosis, or the rapid and efficient scavenging of recently released products by highly active individuals. These results may be connected with global dominance often seen with these clades, likely conferring an advantage over other clades unable to access these resources. We also provide new direct evidence of in situ nitrate utilization by the cyanobacterium Prochlorococcus in support of recent findings. Furthermore, these results revealed widespread functional heterogeneity, i.e., different levels of nitrogen assimilation within clades, likely reflecting niche partitioning by ecotypes. PMID:27994576

  20. Probe tip heating assembly

    SciTech Connect

    Schmitz, Roger William; Oh, Yunje

    2016-10-25

    A heating assembly configured for use in mechanical testing at a scale of microns or less. The heating assembly includes a probe tip assembly configured for coupling with a transducer of the mechanical testing system. The probe tip assembly includes a probe tip heater system having a heating element, a probe tip coupled with the probe tip heater system, and a heater socket assembly. The heater socket assembly, in one example, includes a yoke and a heater interface that form a socket within the heater socket assembly. The probe tip heater system, coupled with the probe tip, is slidably received and clamped within the socket.

  1. Van Allen Probes observations of cross-scale coupling between electromagnetic ion cyclotron waves and higher-frequency wave modes

    NASA Astrophysics Data System (ADS)

    Colpitts, C. A.; Cattell, C. A.; Engebretson, M.; Broughton, M.; Tian, S.; Wygant, J.; Breneman, A.; Thaller, S.

    2016-11-01

    We present observations of higher-frequency ( 50-2500 Hz, 0.1-0.7 fce) wave modes modulated at the frequency of colocated lower frequency (0.5-2 Hz, on the order of fci) waves. These observations come from the Van Allen Probes Electric Field and Waves instrument's burst mode data and represent the first observations of coupling between waves in these frequency ranges. The higher-frequency wave modes, typically whistler mode hiss and chorus or magnetosonic waves, last for a few to a few tens of seconds but are in some cases observed repeatedly over several hours. The higher-frequency waves are observed to be unmodulated before and after the presence of the electromagnetic ion cyclotron (EMIC) waves, but when the EMIC waves are present, the amplitude of the higher-frequency waves drops to the instrument noise level once every EMIC wave cycle. Such modulation could significantly impact wave-particle interactions such as acceleration and pitch angle scattering, which are crucial in the formation and depletion of the radiation belts. We present one case study with broadband, high-frequency waves observed to be modulated by EMIC waves repeatedly over a 2 h time span on both spacecraft. Finally, we show two additional case studies where other high-frequency wave modes exhibit similar modulation.

  2. Probing the existence of G protein-coupled receptor dimers by positive and negative ligand-dependent cooperative binding.

    PubMed

    Albizu, Laura; Balestre, Marie-Noëlle; Breton, Christophe; Pin, Jean-Philippe; Manning, Maurice; Mouillac, Bernard; Barberis, Claude; Durroux, Thierry

    2006-11-01

    An increasing amount of ligand binding data on G protein-coupled receptors (GPCRs) is not compatible with the prediction of the simple mass action law. This may be related to the propensity of most GPCRs, if not all, to oligomerize. Indeed, one of the consequences of receptor oligomerization could be a possible cross-talk between the protomers, which in turn could lead to negative or positive cooperative ligand binding. We prove here that this can be demonstrated experimentally. Saturation, dissociation, and competition binding experiments were performed on vasopressin and oxytocin receptors expressed in Chinese hamster ovary or COS-7 cells. Linear, concave, and convex Scatchard plots were then obtained, depending on the ligand used. Moreover, some competition curves exhibited an increase of the radiotracer binding for low concentrations of competitors, suggesting a cooperative binding process. These data demonstrate that various vasopressin analogs display either positive or negative cooperative binding. Because positive cooperative binding cannot be explained without considering receptor as multivalent, these binding data support the concept of GPCR dimerization process. The results, which are in good accordance with the predictions of previous mathematical models, suggest that binding experiments can be used to probe the existence of receptor dimers.

  3. High Explosives Mixtures Detection Using Fiber Optics Coupled: Grazing Angle Probe/Fourier Transform Reflection Absorption Infrared Spectroscopy

    NASA Astrophysics Data System (ADS)

    Primera-Pedrozo, Oliva M.; Soto-Feliciano, Yadira M.; Pacheco-Londoño, Leonardo C.; Hernández-Rivera, Samuel P.

    2008-12-01

    Fourier Transform Infrared Spectroscopy operating in Reflection-Absorption mode has been demonstrated as a potential spectroscopic technique to develop new methodologies for detection of chemicals deposited on metallic surfaces. Mid-IR transmitting optical fiber bundle coupled to an external Grazing Angle Probe and an MCT detector together with a bench Michelson interferometer have been used to develop a highly sensitive and selective methodology for detecting traces of organic compounds on metal surfaces. The methodology is remote sensed, in situ and can detect surface loading concentrations of nanograms/cm2 of most target compounds. It is an environmentally friendly, solvent free technique that does not require sample preparation. In this work, the ever-important task of high explosives detection, present as traces of neat crystalline forms and in lab-made mixtures, equivalent to the important explosive formulation Pentolite, has been addressed. The sample set consisted of TNT, PETN (both pure samples) and the formulation based on them: Pentolite, present in various loading concentrations. The spectral data collected was subjected to a number of statistical pre-treatments, including first derivative and normalization transformations to make the data more suitable for the analysis. Principal Components Analysis combined with Linear Discriminant Analysis allowed the classification and discrimination of the target analytes contained in the sample set. Loading concentrations as 220 ng/cm2 were detected for each explosive in neat form and the in the simulated mixture of Pentolite.

  4. Hyperfine interaction, spin polarization, and spin delocalization as probes of donor-bridge-acceptor interactions in exchange-coupled biradicals.

    PubMed

    Kirk, Martin L; Shultz, David A; Habel-Rodriguez, Diana; Schmidt, Robert D; Sullivan, Ubie

    2010-11-18

    Computations and EPR spectroscopy are used to probe the spin distribution of donor-bridge-acceptor (D-B-A) biradical complexes: Tp(Cum,Me)Zn(SQ-NN) (1), Tp(Cum,Me)Zn(SQ-1,4-Ph-NN) (2), Tp(Cum,Me)Zn(SQ-2,5-TP-NN) (3), and Tp(Cum,Me)Zn(SQ-2,5-Xyl-NN) (4) (SQ = orthosemiquinone and NN = nitronylnitroxide). These complexes are ground-state analogs of the charge-separated excited states formed in photoinduced electron transfer reactions. The intraligand magnetic exchange interaction (J) in these complexes is mediated by the bridges and has been found to stabilize the triplet ground states of 1 and 2. Detailed spectroscopic and bonding calculations have been used to elucidate the role of the bridge fragment (B) and its conformation relative to donor (SQ) and acceptor (NN) on spin density distributions. The computed results correlate well with experimental nitrogen hyperfine coupling constants.

  5. 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.

  6. 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.

  7. 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

  8. 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).

  9. 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.

  10. Electroreductive Intermolecular Coupling of Coumarins with Benzophenones: Synthesis of 4-(2-Hydroxyphenyl)-5,5-diaryl-γ-butyrolactones, 2-(2,2-Diaryl-2,3-dihydrobenzofuran-3-yl)acetic Acids, and 4-(Diarylmethyl)coumarins.

    PubMed

    Kise, Naoki; Hamada, Yusuke; Sakurai, Toshihiko

    2016-11-18

    The electroreductive coupling of coumarins with benzophenones in the presence of TMSCl gave adducts reacted at the 4-position of coumarins as trimethylsilyl ethers. From 3-methylcoumarin, 3,4-cis-adducts were formed stereoselectively. The de-trimethylsilylation of the adducts with 1 M HCl aq or TBAF in THF at 25 °C produced 4-(2-hydroxyphenyl)-5,5-diaryl-γ-butyrolactones. The γ-butyrolactones were further transformed to 2-(2,2-diaryl-2,3-dihydrobenzofuran-3-yl)acetic acids by treatment with 1 M HCl aq at reflux temperature. The de-trimethylsilylation of the adducts with 1 M HCl in MeOH afforded 2-(2,2-diaryl-2,3-dihydrobenzofuran-3-yl)acetic acid methyl esters. The de-trimethylsiloxylation of the adducts or dehydration of the γ-butyrolactones brought about 4-(diarylmethyl)coumarins.

  11. Density functional calculation of intermolecular potentials.

    PubMed

    Nyeland, Carl

    2011-06-30

    Calculations of intermolecular potentials following the density functional theory (DFT) turn out to be very complicated without using some appropriate approximations. Most often the following three approximations have been considered. In one approximation the disturbed charge distributions during collisions are reduced to sums of undisturbed charge distributions from the colliding species. In another approximation, the so-called local density approximation (LDA), one neglects the fact that the intermolecular potentials that depend on charge densities also depend on gradients in the densities. In a third approximation one assumes that the intermolecular potential can be considered as a sum of two terms: a term for the long-range geometry and a term for the short-range geometry. In this Article the three approximations mentioned will be discussed for numerical accuracy for calculations of potentials between inert gas atoms and for calculations of potentials between surfaces and inert gas atoms. In the discussion a few other approximations will be mentioned too.

  12. Probing local structures of siliceous zeolite frameworks by solid-state NMR and first-principles calculations of 29Si-O-29Si scalar couplings.

    PubMed

    Cadars, Sylvian; Brouwer, Darren H; Chmelka, Bradley F

    2009-03-21

    Subtle structural details of siliceous zeolites are probed by using two-bond scalar (J) coupling constants to characterize covalently bonded 29Si-O-29Si site pairs and local framework order. Solid-state two-dimensional (2D) 29Si{29Si} NMR measurements and first-principles calculations of 2J(29Si-O-29Si) couplings shed insights on both the local structures of siliceous zeolites Sigma-2 and ZSM-12, as well as the sensitivity of J couplings for detailed characterization analyses. DFT calculations on a model linear silicate dimer show that 2J(Si-O-Si) couplings have complicated multiple angular dependencies that make semi-empirical treatments impractical, but which are amenable to cluster approaches for accurate J-coupling calculations in zeolites. DFT calculations of 2J(29Si-O-29Si) couplings of the siliceous zeolite Sigma-2, whose framework structure is known to high accuracy from single-crystal X-ray diffraction studies, yield excellent agreement between calculated and experimentally measured 2J(Si-O-Si) couplings. For the siliceous zeolite ZSM-12, calculated 2J(29Si-O-29Si) couplings based on less-certain powder X-ray diffraction analyses deviate significantly from experimental values, while a refined structure based on 29Si chemical-shift-tensor analyses shows substantially improved agreement. 29Si J-coupling interactions can be used as sensitive probes of local structures of zeolitic frameworks and offer new opportunities for refining and solving complicated structures, in combination with complementary scattering, modeling, and other nuclear spin interactions.

  13. 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.

  14. An improved intermolecular potential for sulfur hexafluoride

    SciTech Connect

    Aziz, R.A.; Slaman, M.J. ); Taylor, W.L.; Hurly, J.J. Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221 )

    1991-01-15

    Second virial coefficient data and viscosity were used to evaluate effective isotropic intermolecular potential functions proposed in the literature for sulfur hexafluoride. It was found that none of the potentials could predict the properties simultaneously. We have constructed a Morse--Morse--Spline--van der Waals (MMSV) potential which satisfactorily correlates second virial coefficient and viscosity data at the same time.

  15. Intermolecular Slip Mechanism in Tropocollagen Nanofibrils

    DTIC Science & Technology

    2009-01-01

    Imperfecta or Ehlers - Danlos Syndrome. REPORT DOCUMENTATION PAGE (SF298) (Continuation Sheet) Continuation for Block 13 ARO Report Number Intermolecular slip...our studies could advance our knowledge of mechan- isms underlying important collagen-related diseases like Osteogenesis Imperfecta or Ehlers - Danlos

  16. Mapping intermolecular bonding in C60

    PubMed Central

    Sundqvist, Bertil

    2014-01-01

    The formation of intermolecular bonds in C60 has been investigated in detail at pressures below 2.2 GPa and up to 750 K. Fullerene samples were heated in a temperature gradient to obtain data on the formation of dimers and low-dimensional polymers along isobars. Intermolecular bonding was analyzed ex situ by Raman scattering, using both intramolecular modes and intermolecular stretching modes. Semi-quantitative reaction maps are given for the formation of dimers and chains. The activation energy for dimer formation decreases by 0.2 meV pm−1 when intermolecular distances decrease and dimer formation is noticeably affected by the rotational state of molecules. Above 400–450 K larger oligomers are formed; below 1.4 GPa most of these are disordered, with small domains of linear chains, but above this the appearance of stretching modes indicates the existence of ordered one-dimensional polymers. At the highest pressures and temperatures two-dimensional polymers are also observed. PMID:25145952

  17. Mapping intermolecular bonding in C₆₀.

    PubMed

    Sundqvist, Bertil

    2014-08-22

    The formation of intermolecular bonds in C₆₀ has been investigated in detail at pressures below 2.2 GPa and up to 750 K. Fullerene samples were heated in a temperature gradient to obtain data on the formation of dimers and low-dimensional polymers along isobars. Intermolecular bonding was analyzed ex situ by Raman scattering, using both intramolecular modes and intermolecular stretching modes. Semi-quantitative reaction maps are given for the formation of dimers and chains. The activation energy for dimer formation decreases by 0.2 meV pm(-1) when intermolecular distances decrease and dimer formation is noticeably affected by the rotational state of molecules. Above 400-450 K larger oligomers are formed; below 1.4 GPa most of these are disordered, with small domains of linear chains, but above this the appearance of stretching modes indicates the existence of ordered one-dimensional polymers. At the highest pressures and temperatures two-dimensional polymers are also observed.

  18. Catalytic intermolecular alkene oxyamination with nitrenes.

    PubMed

    Dequirez, Geoffroy; Ciesielski, Jennifer; Retailleau, Pascal; Dauban, Philippe

    2014-07-14

    The Rh(II)-catalyzed intermolecular addition of nitrenes to aromatic and aliphatic alkenes provides vicinal amino alcohols with yields of up to 95 % and complete regioselectivity. This 1,2-oxyamination reaction involves the formation of an aziridine intermediate that undergoes in situ ring opening. The latter is induced by the Rh-bound nitrene that behaves as a Lewis acid.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  20. VSCF calculations for the intra- and intermolecular vibrational modes of the water dimer and its isotopologs

    NASA Astrophysics Data System (ADS)

    Monteiro, João G. S.; Barbosa, André G. H.

    2016-11-01

    In this work we show how the VSCF method may be successfully used to describe all fundamental vibrational transitions of several isotopologs of water dimer. By expressing the normal mode displacements in terms of appropriate delocalized internal coordinates we are able to minimize the mode-mode coupling in the PES and thus yield PT2-VSCF frequencies in good agreement with the experiment. The use of curvilinear normal modes is of paramount importance to describe vibrational transitions of the very soft intermolecular modes. Within our approach the maximum calculated error for the (H2O)2 intermolecular frequencies are reduced from 311 cm-1 (Cartesian normal modes) to just 56 cm-1 (curvilinear normal modes). Plots of the diagonal intermolecular potential and of the vibrational wave function illustrate the remarkable effect of different coordinate systems. In conclusion, our PT2-VSCF calculations provide a fair anharmonic description of the fundamental transitions of water dimers.

  1. High-resolution absorptive intermolecular multiple-quantum coherence NMR spectroscopy under inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Lin, Meijin; Lin, Yanqin; Chen, Xi; Cai, Shuhui; Chen, Zhong

    2012-01-01

    Intermolecular multiple-quantum coherence (iMQC) is capable of improving NMR spectral resolution using a 2D shearing manipulation method. A pulse sequence termed CT-iDH, which combines intermolecular double-quantum filter (iDQF) with a modified constant-time (CT) scheme, is designed to achieve fast acquisition of high-resolution intermolecular zero-quantum coherences (iZQCs) and intermolecular double-quantum coherences (iDQCs) spectra without strong coupling artifacts. Furthermore, double-absorption lineshapes are first realized in 2D intermolecular multi-quantum coherences (iMQCs) spectra under inhomogeneous fields through a combination of iZQC and iDQC signals to double the resolution without loss of sensitivity. Theoretically the spectral linewidth can be further reduced by half compared to original iMQC high-resolution spectra. Several experiments were performed to test the feasibility of the new method and the improvements are evaluated quantitatively. The study suggests potential applications for in vivo spectroscopy.

  2. 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

  3. Langmuir probe diagnostics of electron energy distributions with optical emission spectroscopy in capacitively coupled rf discharge in nitrogen

    SciTech Connect

    Abdel-Fattah, E.; Bazavan, M.; Sugai, H.

    2011-12-01

    Measurements with a rf compensated Langmuir probe and optical emission spectroscopy are carried out in capacitively coupled rf (13.56 MHz) pure nitrogen N{sub 2} discharges at fixed rf voltage over a wide range of pressure, 30 to 400 mTorr. The electron energy probability function (EEPF) measured below 100 mTorr resembles a bi-Maxwellian-type distribution. At pressure range of 100-200 mTorr, the EEPF has non-Maxwellian distribution with a ''dip'' near 4.5 eV. At the highest pressure of 400 mTorr, the EEPF evolves into a Druyvestein-like distribution and the ''dip'' disappears. The electron density significantly decreases with increase in the N{sub 2} pressure. On the other hand, the electron temperatures gradually decrease with an increase in N{sub 2} pressure, reaching minimum at 150 mTorr, beyond which it abruptly increases. Such evolution of the EEPFs shape with gas pressure has been discussed in terms of non-local electron kinetics and heating mode transition. The emission intensities of nitrogen (0-0) band of second positive system at 337.1 nm and (0-0) band of first negative systems at 391.4 nm are used to determine the dependence of their radiative states N{sub 2}(C{sup 3}{Pi}{sub u}) and N{sub 2}{sup +}(B{sup 2}{Sigma}{sub u}{sup +}) with nitrogen pressure. It is observed that the pressure influences the radiative states differently owing to their different populating mechanisms. The vibrational temperature T{sub {nu}ib} and rotational temperature T{sub rot} are measured for the sequence ({Delta}{nu}=-2) of N{sub 2} second positive system (C{sup 3}{Pi}{yields}B{sup 3}{Pi}{sub g}) using the method of comparing the measured and calculated spectra with a chi-squared minimization procedure. It was found that both T{sub {nu}ib} and T{sub rot} have similar dependences with N{sub 2} pressure; peaked at 100 mTorr beyond which it monotonically decreases with increase in the N{sub 2} pressure. The correlation between the observed maximum value of T{sub {nu}ib} around

  4. 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)

  5. Simultaneous Identification of 13 Foodborne Pathogens by Using Capillary Electrophoresis-Single Strand Conformation Polymorphism Coupled with Multiplex Ligation-Dependent Probe Amplification and Its Application in Foods.

    PubMed

    Kim, So-Young; Chung, Boram; Chang, Jin-Hee; Jung, Gyoo Yeol; Kim, Hyoun Wook; Park, Beom-Young; Oh, Sang Suk; Oh, Mi-Hwa

    2016-10-01

    Capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) coupled with stuffer-free multiplex ligation-dependent probe amplification (MLPA) was developed to identify 13 species of foodborne pathogens simultaneously. Species-specific MLPA probes were designed for nine of these species. These probes were targeted to the groEL, glyA, MMS, tuf, inv, ipaH, nuc, vvh, and 16S rRNA genes, which corresponded to Bacillus cereus, Campylobacter coli, Cronobacter sakazakii, Enterococcus spp., Salmonella spp., Shigella spp., Staphylococcus aureus, Vibrio vulnificus, and Yersinia enterocolitica, respectively. MLPA probes that had been previously developed by our laboratory were used for the other four species (Campylobacter jejuni, Clostridium perfringens, Escherichia coli O157:H7, and Listeria monocytogenes). The CE-SSCP method was optimized to identify all 13 foodborne microbes simultaneously in a single electrogram, in which 50-500 pg genomic DNA was detected per microbe. Twelve species were detected from animal-derived food samples (specifically, milk and sliced ham) that had been artificially inoculated with 12 of the foodborne pathogens, excluding V. vulnificus, which is not usually associated with animal foods. The method developed here could be used as an early warning system for outbreaks of foodborne diseases associated with animal-derived foods in the food industry.

  6. Intermolecular Michael reactions: a computational investigation.

    PubMed

    Kwan, Eugene E; Evans, David A

    2010-11-19

    Computational studies have suggested that η(3)-lithium enolates in which the cation is partially bound to both carbon and oxygen may be important reactive intermediates. DFT calculations are used to demonstrate that explicitly solvated acetone enolates are largely O-bound. With this premise in mind, the stereochemical course of intermolecular Michael additions is examined. The results are generally consistent with what is observed experimentally and the model advanced by Heathcock and co-workers.

  7. 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.

  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. A triterpene oleanolic acid conjugate with 3-hydroxyflavone derivative as a new membrane probe with two-color ratiometric response.

    PubMed

    Turkmen, Zeynep; Klymchenko, Andrey S; Oncul, Sule; Duportail, Guy; Topcu, Gulacti; Demchenko, Alexander P

    2005-07-29

    We report on the synthesis by coupling of a triterpenoid oleanolic acid with 4'-diethylamino-3-hydroxyflavone (FE) to produce an environment-sensitive biomembrane probe with two-band ratiometric response in fluorescence emission. The synthesized compound (probe FOT) was tested in a series of model solvents and demonstrated the response to solvent polarity and intermolecular hydrogen bonding very similar to that of parent probe FE. Meantime when incorporated into lipid bilayer membranes, it showed new features differing in response between lipids of different surface charges as well as between glycerophospholipids and sphingomyelin. We observed that in the conditions of coexistence of rafts and non-raft structures the probe is excluded from the rafts.

  10. NMR detection of intermolecular interaction sites in the dimeric 5'-leader of the HIV-1 genome.

    PubMed

    Keane, Sarah C; Van, Verna; Frank, Heather M; Sciandra, Carly A; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F

    2016-11-15

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5'-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a (2)H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5'-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5' (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a (2)H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones.

  11. 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.

  12. Temperature Dependence of the Surface Resistance of a Bi-Sr-Ca-Cu-O Whisker Measured by the Probe-Coupled Microstrip Resonator Method

    NASA Astrophysics Data System (ADS)

    Okai, Daisuke; Ohshima, Shigetoshi; Kishida, Satoru; Hatano, Takeshi

    2001-07-01

    The temperature dependence of the surface resistance of Bi-Sr-Ca-Cu-O whiskers measured by the probe-coupled microstrip resonator method was examined. Two kinds of whiskers were measured: plate-like and wire-like. The surface resistances of the plate-like and wire-like whiskers were 0.65 mΩ and 1.6 mΩ at 53 K and 6.9 GHz, respectively. These values were approximately 4 ˜ 10 times larger than that of a high-quality Bi2Sr2CaCu2Ox (Bi-2212) single crystal.

  13. Time-averaging approximation in the interaction picture: Anisotropy of vibrational pump-probe experiments for coupled chromophores with application to liquid water

    NASA Astrophysics Data System (ADS)

    Yang, Mino

    2012-10-01

    A time-averaging approximation method developed to efficiently calculate the short-time dynamics of coupled vibrational chromophores using mixed quantum/classical theories is extended in order to be applicable to the study of vibrational dynamics at longer time scales. A quantum mechanical time propagator for long times is decomposed into the product of short-time propagators, and a time-averaging approximation is then applied to each of the latter. Using the extended time-averaging approximation, we calculate the anisotropy decay of the data obtained from impulsive vibrational pump-probe experiments on the OH stretching modes of water, which is in excellent agreement with numerically exact results.

  14. 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.

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

    PubMed

    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 = 10(20) 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.

  16. 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.

  17. 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.

  18. Determination of the 14N quadrupole coupling constant of nitroxide spin probes by W-band ELDOR-detected NMR.

    PubMed

    Florent, Marc; Kaminker, Ilia; Nagarajan, Vijayasarathi; Goldfarb, Daniella

    2011-06-01

    Nitroxide spin probe electron paramagnetic resonance (EPR) has proven to be a very successful method to probe local polarity and solvent hydrogen bonding properties at the molecular level. The g(xx) and the (14)N hyperfine A(zz) principal values are the EPR parameters of the nitroxide spin probe that are sensitive to these properties and are therefore monitored experimentally. Recently, the (14)N quadrupole interaction of nitroxides has been shown to be also highly sensitive to polarity and H-bonding (A. Savitsky et al., J. Phys. Chem. B 112 (2008) 9079). High-field electron spin echo envelope modulation (ESEEM) was used successfully to determine the P(xx) and P(yy) principal components of the (14)N quadrupole tensor. The P(zz) value was calculated from the traceless character of the quadrupole tensor. We introduce here high-field (W-band, 95 GHz, 3.5 T) electron-electron double resonance (ELDOR)-detected NMR as a method to obtain the (14)N P(zz) value directly, together with A(zz). This is complemented by W-band hyperfine sublevel correlation (HYSCORE) measurements carried out along the g(xx) direction to determine the principal P(xx) and P(yy) components. Through measurements of TEMPOL dissolved in solvents of different polarities, we show that A(zz) increases, while |P(zz)| decreases with polarity, as predicted by Savitsky et al.

  19. Determination of the 14N quadrupole coupling constant of nitroxide spin probes by W-band ELDOR-detected NMR

    NASA Astrophysics Data System (ADS)

    Florent, Marc; Kaminker, Ilia; Nagarajan, Vijayasarathi; Goldfarb, Daniella

    2011-06-01

    Nitroxide spin probe electron paramagnetic resonance (EPR) has proven to be a very successful method to probe local polarity and solvent hydrogen bonding properties at the molecular level. The g xx and the 14N hyperfine A zz principal values are the EPR parameters of the nitroxide spin probe that are sensitive to these properties and are therefore monitored experimentally. Recently, the 14N quadrupole interaction of nitroxides has been shown to be also highly sensitive to polarity and H-bonding (A. Savitsky et al., J. Phys. Chem. B 112 (2008) 9079). High-field electron spin echo envelope modulation (ESEEM) was used successfully to determine the P xx and P yy principal components of the 14N quadrupole tensor. The P zz value was calculated from the traceless character of the quadrupole tensor. We introduce here high-field (W-band, 95 GHz, 3.5 T) electron-electron double resonance (ELDOR)-detected NMR as a method to obtain the 14N P zz value directly, together with A zz. This is complemented by W-band hyperfine sublevel correlation (HYSCORE) measurements carried out along the g xx direction to determine the principal P xx and P yy components. Through measurements of TEMPOL dissolved in solvents of different polarities, we show that A zz increases, while | P zz| decreases with polarity, as predicted by Savitsky et al.

  20. 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.

  1. Tip relaxation in atomic force microscopy imaging simulations to resolve intermolecular bonds

    NASA Astrophysics Data System (ADS)

    Lee, Alex; Sakai, Yuki; Chelikowsky, Jim

    Experimental noncontact atomic force microscopy (AFM) studies have reported distinct lines in regions with no electron density for a variety of systems. The appearance of these lines is unexpected because Pauli repulsion is thought to be the dominant factor in the AFM imaging mechanism. These lines have been proposed to represent intermolecular bonding. Recent theoretical studies have shown that accounting for tip probe relaxation can sharpen images and highlight features that make simulations more comparable to experiment. We will apply a similar tip relaxation scheme to our computational method-which uses an ab initio real-space pseudopotential formalism with frozen density embedding theory added-to the study of dibenzo[a,h]thianthrene and an 8-hydroxyquinoline dimer to develop our interpretation of imaged intermolecular bonds. Work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

  2. Investigation of intermolecular double-quantum off-resonance longitudinal relaxation in the tilted rotating frame

    NASA Astrophysics Data System (ADS)

    Cai, Honghao; Zheng, Bingwen; Ke, Hanping; Chen, Zhong

    2015-11-01

    A modified correlation spectroscopy revamped by asymmetric z-gradients echo detection (CRAZED) sequence was applied to investigate the behavior of intermolecular double-quantum longitudinal relaxation processes in the tilted rotating frame. Theoretical formalism based on dipolar field theory was presented in detail. Spectroscopic measurements and quantitative analysis demonstrated that the signal intensities and intermolecular double-quantum off-resonance longitudinal relaxation time in the rotating frame (T1ρ, DQC eff) are inversely correlated with the tilt angle (θ), while positively correlated with the effective frequency of spin-locking field (ωe). Magnetic resonance imaging experiments of an agarose phantom also prove the validity of the theoretical analysis and demonstrated the feasibility of imaging based on T1ρ, DQC eff . The rotating-frame double-quantum relaxation measurements are useful for probing slow-motion molecules and this study provides the guidance for optimization of the spin-lock experiments.

  3. Intermolecular potential energy surface for CS2 dimer.

    PubMed

    Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface.

  4. 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.

  5. 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.

    PubMed

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

    2012-11-28

    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.

  6. 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.

  7. Interpreting the widespread nonlinear force spectra of intermolecular bonds

    PubMed Central

    Friddle, Raymond W.; Noy, Aleksandr; De Yoreo, James J.

    2012-01-01

    Single molecule force spectroscopy probes the strength, lifetime, and energetic details of intermolecular interactions in a simple experiment. A growing number of these studies have reported distinctly nonlinear trends in rupture force with loading rate that are typically explained in conventional models by invoking complex escape pathways. Recent analyses suggested that these trends should be expected even for simple barriers based on the basic assumptions of bond rupture dynamics and thus may represent the norm rather than the exception. Here we explore how these nonlinear trends reflect the two fundamental regimes of bond rupture: (i) a near-equilibrium regime, produced either by bond reforming in the case of a single bond or by asynchronized rupture of multiple individual bonds, and (ii) a kinetic regime produced by fast, non-equilibrium bond rupture. We analyze both single- and multi-bonded cases, describe the full evolution of the system as it transitions between near- and far-from-equilibrium loading regimes, and show that both interpretations produce essentially identical force spectra. Data from 10 different molecular systems show that this model provides a comprehensive description of force spectra for a diverse suite of bonds over experimentally relevant loading rates, removes the inconsistencies of previous interpretations of transition state distances, and gives ready access to both kinetic and thermodynamic information about the interaction. These results imply that single-molecule binding free energies for a vast number of bonds have already been measured. PMID:22869712

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

    PubMed

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

    2016-01-05

    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.

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

    PubMed

    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; Pasa-Tolić, Ljiljana; Smith, Richard D; Lipton, Mary S

    2010-05-07

    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 (18)O 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 (16)O and (18)O 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 Delta gspD mutant cells of many outer membrane proteins including the outer membrane c-type cytochromes OmcA and MtrC, in agreement with a previous report that these proteins are substrates of the type II secretion system.

  10. 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

  11. Coherent coupling of two dopants in a silicon nanowire probed by Landau-Zener-Stückelberg interferometry.

    PubMed

    Dupont-Ferrier, E; Roche, B; Voisin, B; Jehl, X; Wacquez, R; Vinet, M; Sanquer, M; De Franceschi, S

    2013-03-29

    We report on microwave-driven coherent electron transfer between two coupled donors embedded in a silicon nanowire. By increasing the microwave frequency we observe a transition from incoherent to coherent driving revealed by the emergence of a Landau-Zener-Stückelberg quantum interference pattern of the measured current through the donors. This interference pattern is fitted to extract characteristic parameters of the double-donor system. In particular we estimate a charge dephasing time of 0.3±0.1  ns, comparable to other types of charge-based two-level systems. The demonstrated coherent coupling between two dopants is an important step towards donor-based quantum computing devices in silicon.

  12. Ultrafast quenching of the antiferromagnetic order in FeBO3: direct optical probing of the phonon-magnon coupling.

    PubMed

    Kimel, A V; Pisarev, R V; Hohlfeld, J; Rasing, Th

    2002-12-31

    The dynamics of the optically induced phase transition from the antiferromagnetic to the paramagnetic state in FeBO3 is observed using a pump-probe magneto-optical Faraday technique employing 100 fs laser pulses. At the pump energy of 1.55 eV phonon-assisted transitions dominate in the absorption of light and ultrafast heating of the lattice occurs. The quenching of the magnetic order is caused by an increase of the magnon temperature due to energy transfer from the heated lattice. The heating time of the magnon system is around 700 ps, which is a factor of 20 faster than previously reported phonon-magnon interaction times.

  13. Human leukocyte antigen typing using a knowledge base coupled with a high-throughput oligonucleotide probe array analysis.

    PubMed

    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.

  14. Intermolecular interaction approach for TADF (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wong, Ken-Tsung

    2016-09-01

    Materials with thermally activated delayed fluorescence (TADF) have recently emerged as new fluorescent emitters for highly efficient organic light-emitting diodes (OLEDs). Molecule with TADF behavior needs to have a small singlet-triplet energy difference (ΔES-T) that allows the up-conversion from nonradiative triplet state (T1) to radiative singlet state (S1) via reverse intersystem crossing (RISC) process. Generally, molecules with small ΔES-T can be obtained via carefully manipulate the degree of "intramolecular" charge transfer (ICT) between electron-donating and -accepting components, such that the electron exchange energy that contributes to ΔES-T, can be minimized. Alternatively, excited state with small ΔES-T can be feasibly realized via "intermolecular" charge transfer occurring at the interface between spatially separating donor (D) and acceptor (A) molecules. Because the exchange energy decreases as the HOMO-LUMO separation distance increases, theoretically, the intermolecular D/A charge transfer state (or exciplex) should have rather small ΔES-T, leading to efficient TADF. However, it is still a challenge to access highly efficient exciplex systems. This is mainly because exciplex formation is commonly accompanied with a large red shift of emission spectra and long radiative lifetime, which tend to diminish photoluminescence quantum yield (PLQY) as well as electroluminescence (EL) performance. Until now, exciplex-based OLEDs with external quantum efficiency (EQE) above 10% are still limited. By judicious selection of donor and acceptor, the formation of efficient exciplex can be feasibly achieved. In this conference, our recent efforts on highly efficient exciplexes using C3-symmetry triazine acceptors and various donors, and their device characteristics will be presented.

  15. Some mathematical models of intermolecular autophosphorylation.

    PubMed

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

    2015-04-07

    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.

  16. Jupiter probe heatshield configuration optimization

    NASA Technical Reports Server (NTRS)

    Dirling, R. B., Jr.; Binder, J. D.

    1978-01-01

    The effect of initial probe heatshield shape on the total probe mass loss during Jovian entry is considered. Modification of the aerothermal environment and probe entry trajectory due to changing probe heatshield shape is included in a computerized technique designed for rapid assessment of the effect of probe initial shape on heatshield mass loss. Results obtained indicate the importance of trajectory and heating distribution coupling with probe shape and mass change.

  17. 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.

  18. Time-resolved ion flux, electron temperature and plasma density measurements in a pulsed Ar plasma using a capacitively coupled planar probe

    NASA Astrophysics Data System (ADS)

    Darnon, Maxime; Cunge, Gilles; Braithwaite, Nicholas St. J.

    2014-04-01

    The resurgence of industrial interest in pulsed radiofrequency plasmas for etching applications highlights the fact that these plasmas are much less well characterized than their continuous wave counterparts. A capacitively coupled planar probe is used to determine the time variations of the ion flux, electron temperature (of the high-energy tail of the electron energy distribution function) and plasma density. For a pulsing frequency of 1 kHz or higher, the plasma never reaches a steady state during the on-time and is not fully extinguished during the off-time. The drop of plasma density during the off-time leads to an overshoot in the electron temperature at the beginning of each pulse, particularly at low frequencies, in good agreement with modeling results from the literature.

  19. 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

  20. Studies on the radical species in inductively coupled Ar/CH4 plasma using improved single Langmuir probe diagnostic methods and fluid simulation

    NASA Astrophysics Data System (ADS)

    Cha, Ju-Hong; Seo, Kwon-Sang; Lee, Jung Yeol; Lee, Hae June; Lee, Ho-Jun

    2016-09-01

    An inductively coupled plasma source driven by 13.56MHz was prepared for the deposition of a-C:H thin film. Properties of the plasma source are investigated by fluid simulation including Navier-Stokes equation 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. Numerical methods including fitting, digital smoothing, digital filter with window function were used to calculate the electron energy distribution accurately. Dependencies of plasma parameters on process were well agreed with simulation results. It was found that RF power, inlet pressure and composition ratio significantly affect to the electron density, temperature and energy distribution. Electron density and plasma potential profile were changed along the input power and gas pressure. Below the input power density of 0.1W/cm3 , higher plasma potential was observed at higher pressure. However, over the 0.1W/cm3 , lower plasma potential was observed along the higher pressure. This result was occurred owing to the change of electron energy distribution. And from the simulation results, the specific chemical reaction channel, not CxHy but CHx, affect to the radical density profile.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Probing triple-W production and anomalous WWWW coupling at the CERN LHC and future TeV proton-proton collider

    NASA Astrophysics Data System (ADS)

    Wen, Yiwen; Qu, Huilin; Yang, Daneng; Yan, Qi-shu; Li, Qiang; Mao, Yajun

    2015-03-01

    Triple gauge boson production at the LHC can be used to test the robustness of the Standard Model and provide useful information for VBF di-boson scattering measurement. Especially, any derivations from SM prediction will indicate possible new physics. In this paper we present a detailed Monte Carlo study on measuring W ± W ± W ∓ production in pure leptonic and semileptonic decays, and probing anomalous quartic gauge WWWW couplings at the CERN LHC and future hadron collider, with parton shower and detector simulation effects taken into account. Apart from cut-based method, multivariate boosted decision tree method has been exploited for possible improvement. For the leptonic decay channel, our results show that at the TeV pp collider with integrated luminosity of 20(100)[3000] fb-1, one can reach a significance of 0.4(1.2)[10] σ to observe the SM W ± W ± W ∓ production. For the semileptonic decay channel, one can have 0.5(2)[14] σ to observe the SM W ± W ± W ∓ production. We also give constraints on relevant Dim-8 anomalous WWWW coupling parameters.

  7. Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil.

    PubMed

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

    2011-05-01

    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 (13)C-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-(13)C]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 (13)C-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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. Intermolecular hydrogen bonding in chlorine dioxide photochemistry: A time-resolved resonance Raman study

    NASA Astrophysics Data System (ADS)

    Philpott, Matthew P.; Hayes, Sophia C.; Thomsen, Carsten L.; Reid, Philip J.

    2001-01-01

    The geminate-recombination and vibrational-relaxation dynamics of chlorine dioxide (OClO) dissolved in ethanol and 2,2,2-trifluoroethanol (TFE) are investigated using time-resolved resonance Raman spectroscopy. Stokes spectra are measured as a function of time following photoexcitation using degenerate pump and probe wavelengths of 398 nm. For OClO dissolved in ethanol, subpicosecond geminate recombination occurs resulting in the reformation of ground-state OClO with a quantum yield of 0.5±0.1. Following recombination, intermolecular-vibrational relaxation of OClO occurs with a time constant of 31±10 ps. For OClO dissolved in TFE, recombination occurs with a time constant of 1.8±0.8 ps and a quantum yield of only 0.3±0.1. The intermolecular-vibrational-relaxation time constant of OClO in TFE is 79±27 ps. The reduced geminate-recombination quantum yield, delayed recombination, and slower vibrational relaxation for OClO in TFE is interpreted in terms of greater self-association of the solvent. Degenerate pump-probe experiments are also presented that demonstrate decay of the Cl-solvent charge-transfer complex on the ˜1-ns time scale in ethanol and TFE. This time is significantly longer than the abstraction times observed for other systems demonstrating that Cl hydrogen abstraction from alcohols occurs in the presence of a significant energy barrier.

  13. NMR detection of intermolecular interaction sites in the dimeric 5′-leader of the HIV-1 genome

    PubMed Central

    Keane, Sarah C.; Van, Verna; Frank, Heather M.; Sciandra, Carly A.; McCowin, Sayo; Santos, Justin; Heng, Xiao; Summers, Michael F.

    2016-01-01

    HIV type-1 (HIV-1) contains a pseudodiploid RNA genome that is selected for packaging and maintained in virions as a noncovalently linked dimer. Genome dimerization is mediated by conserved elements within the 5′-leader of the RNA, including a palindromic dimer initiation signal (DIS) that has been proposed to form kissing hairpin and/or extended duplex intermolecular contacts. Here, we have applied a 2H-edited NMR approach to directly probe for intermolecular interactions in the full-length, dimeric HIV-1 5′-leader (688 nucleotides; 230 kDa). The interface is extensive and includes DIS:DIS base pairing in an extended duplex state as well as intermolecular pairing between elements of the upstream Unique-5′ (U5) sequence and those near the gag start site (AUG). Other pseudopalindromic regions of the leader, including the transcription activation (TAR), polyadenylation (PolyA), and primer binding (PBS) elements, do not participate in intermolecular base pairing. Using a 2H-edited one-dimensional NMR approach, we also show that the extended interface structure forms on a time scale similar to that of overall RNA dimerization. Our studies indicate that a kissing dimer-mediated structure, if formed, exists only transiently and readily converts to the extended interface structure, even in the absence of the HIV-1 nucleocapsid protein or other RNA chaperones. PMID:27791166

  14. Synthesis and intermolecular interactions of N-benzylidenetyramines

    NASA Astrophysics Data System (ADS)

    Maldonado, Mauricio; Pérez-Redondo, Adrián; Quevedo, Rodolfo

    2017-01-01

    In this paper, the synthesis and intermolecular interactions between N-benzylidenetyramine molecules were investigated. The crystal structure of N-(4-nitrobenzylidene)tyramine shows a molecular organization in zigzag chains with intermolecular O-H⋯N hydrogen bonds between the azomethine and phenolic hydroxyl groups. Those chains are held together by C-H⋯O hydrogen bonds to generate layers, which are connected by C-H⋯O, π⋯π and NO2⋯π interactions.

  15. Synthesis and Characterization of Tricarbonyl-Re/Tc(I) Chelate Probes Targeting the G Protein-Coupled Estrogen Receptor GPER/GPR30

    PubMed Central

    Burai, Ritwik; Ramesh, Chinnasamy; Nayak, Tapan K.; Dennis, Megan K.; Bryant, Bj K.; Prossnitz, Eric R.; Arterburn, Jeffrey B.

    2012-01-01

    The discovery of the G protein-coupled estrogen receptor GPER (also GPR30) and the resulting development of selective chemical probes have revealed new aspects of estrogen receptor biology. The potential clinical relevance of this receptor has been suggested from numerous studies that have identified GPER expression in breast, endometrial, ovarian and other cancers. Thus GPER can be considered a candidate biomarker and target for non-invasive imaging and therapy. We have designed and synthesized a series of organometallic tricarbonyl-rhenium complexes conjugated to a GPER-selective small molecule derived from tetrahydro-3H-cyclopenta[c]quinoline. The activity and selectivity of these chelates in GPER-mediated signaling pathways were evaluated. These results demonstrate that GPER targeting characteristics depend strongly on the structure of the chelate and linkage. Ethanone conjugates functioned as agonists, a 1,2,3-triazole spacer yielded an antagonist, and derivatives with increased steric volume exhibited decreased activities. Promising GPER selectivity was observed, as none of the complexes interacted with the nuclear estrogen receptors. Radiolabeling with technetium-99m in aqueous media was efficient and gave radioligands with high radiochemical yields and purity. These chelates have favorable physicochemical properties, show excellent stability in biologically relevant media, exhibit receptor specificity and are promising candidates for continuing development as diagnostic imaging agents targeting GPER expression in cancer. PMID:23077529

  16. Design of a scanning probe microscope with advanced sample treatment capabilities: An atomic force microscope combined with a miniaturized inductively coupled plasma source.

    PubMed

    Hund, Markus; Herold, Hans

    2007-06-01

    We describe the design and performance of an atomic force microscope (AFM) combined with a miniaturized inductively coupled plasma source working at a radio frequency of 27.12 MHz. State-of-the-art scanning probe microscopes (SPMs) have limited in situ sample treatment capabilities. Aggressive treatments such as plasma etching or harsh treatments such as etching in aggressive liquids typically require the removal of the sample from the microscope. Consequently, time consuming procedures are required if the same sample spot has to be imaged after successive processing steps. We have developed a first prototype of a SPM which features a quasi in situ sample treatment using a modified commercial atomic force microscope. A sample holder is positioned in a special reactor chamber; the AFM tip can be retracted by several millimeters so that the chamber can be closed for a treatment procedure. Most importantly, after the treatment, the tip is moved back to the sample with a lateral drift per process step in the 20 nm regime. The performance of the prototype is characterized by consecutive plasma etching of a nanostructured polymer film.

  17. 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.

  18. Intermolecular Singlet and Triplet Exciton Transfer Integrals from Many-Body Green's Functions Theory.

    PubMed

    Wehner, Jens; Baumeier, Björn

    2017-03-08

    A general approach to determine orientation and distance-dependent effective intermolecular exciton transfer integrals from many-body Green's functions theory is presented. On the basis of the GW approximation and the Bethe-Salpeter equation (BSE), a projection technique is employed to obtain the excitonic coupling by forming the expectation value of a supramolecular BSE Hamiltonian with electron-hole wave functions for excitations localized on two separated chromophores. Within this approach, accounting for the effects of coupling mediated by intermolecular charge transfer (CT) excitations is possible via perturbation theory or a reduction technique. Application to model configurations of pyrene dimers shows an accurate description of short-range exchange and long-range Coulomb interactions for the coupling of singlet and triplet excitons. Computational parameters, such as the choice of the exchange-correlation functional in the density-functional theory (DFT) calculations that underly the GW-BSE steps and the convergence with the number of included CT excitations, are scrutinized. Finally, an optimal strategy is derived for simulations of full large-scale morphologies by benchmarking various approximations using pairs of dicyanovinyl end-capped oligothiophenes (DCV5T), which are used as donor material in state-of-the-art organic solar cells.

  19. 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

  20. Probing Spin and Spin-Orbit Coupling effects in Narrow-gap Semiconductor Nano-structures by THz Magneto-photoresponse Spectroscopy and Magneto-transport Measurements

    NASA Astrophysics Data System (ADS)

    Pakmehr, Mehdi

    Using the spin degree of freedom in a emergent field Known as Spintronics has motivated scientist in different disciplines including physicist within last 10 years. Due to different interaction mechanisms which affects the physical behavior of spin (eg its state and transport properties) within solid medium (Semiconductors in our case), one needs to distinguish these mechanisms and their importance for making any practical spin based devices. For example the idea of making spin based transistors with electrons being transported within InGaAs and their spin state is being controlled by Rashba type field has been around for around 25 years but injection of spin polarized currents from a source into the channel has not been solved yet. Spin orbit coupling (SOC) is one of the mechanisms which changes the spin state of electrons and avoid the existence of pure spin state as a favorable one from device point of view. SOC could have a different origin depending on material type or structure of device. One method of measuring and quantifying this mechanisms within semiconductor nanostructures is through measuring the parameters known as Lande g-factor. This parameters turns out to be a promising one to probe different effects on electronic band structure including quantum confinement, strain, electric filed, etc. We probe a combination of these effects (SOC, Strain, band mixing, etc) by measuring different g-factor tensor components of narrow gap Zinc blend semiconductor nanostructures which we hope finally serve to the purpose of making reliable spin based devices* (Spintronics). To reach this goal we have developed and implemented THz magneto-Photoresponse spectroscopy in conjunction with magneto-transport measurements at cryogenic temperatures. The samples include InAs and HgTe based Quantum wells as well as InAs based quantum point contact. Our findings clarify the situation where the combination of SOC, Strain, quantum confinements as well as many body electron effect

  1. Exciton dynamics reveal aggregates with intermolecular order at hidden interfaces in solution-cast organic semiconducting films.

    PubMed

    Wong, Cathy Y; Cotts, Benjamin L; Wu, Hao; Ginsberg, Naomi S

    2015-01-12

    Large-scale organic electronics manufacturing requires solution processing. For small-molecule organic semiconductors, solution processing results in crystalline domains with high charge mobility, but the interfaces between these domains impede charge transport, degrading device performance. Although understanding these interfaces is essential to improve device performance, their intermolecular and electronic structure is unknown: they are smaller than the diffraction limit, are hidden from surface probe techniques, and their nanoscale heterogeneity is not typically resolved using X-ray methods. Here we use transient absorption microscopy to isolate a unique signature of a hidden interface in a TIPS-pentacene thin film, exposing its exciton dynamics and intermolecular structure. Surprisingly, instead of finding an abrupt grain boundary, we reveal that the interface can be composed of nanoscale crystallites interleaved by a web of interfaces that compound decreases in charge mobility. Our novel approach provides critical missing information on interface morphology necessary to correlate solution-processing methods to optimal device performance.

  2. Exciton dynamics reveal aggregates with intermolecular order at hidden interfaces in solution-cast organic semiconducting films

    NASA Astrophysics Data System (ADS)

    Wong, Cathy Y.; Cotts, Benjamin L.; Wu, Hao; Ginsberg, Naomi S.

    2015-01-01

    Large-scale organic electronics manufacturing requires solution processing. For small-molecule organic semiconductors, solution processing results in crystalline domains with high charge mobility, but the interfaces between these domains impede charge transport, degrading device performance. Although understanding these interfaces is essential to improve device performance, their intermolecular and electronic structure is unknown: they are smaller than the diffraction limit, are hidden from surface probe techniques, and their nanoscale heterogeneity is not typically resolved using X-ray methods. Here we use transient absorption microscopy to isolate a unique signature of a hidden interface in a TIPS-pentacene thin film, exposing its exciton dynamics and intermolecular structure. Surprisingly, instead of finding an abrupt grain boundary, we reveal that the interface can be composed of nanoscale crystallites interleaved by a web of interfaces that compound decreases in charge mobility. Our novel approach provides critical missing information on interface morphology necessary to correlate solution-processing methods to optimal device performance.

  3. 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.

  4. Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands.

    PubMed

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

    2016-11-07

    The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm(-1)), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm(-1)); the out-of-plane torsion (23.24 cm(-1)); twice the disrotatory bend (31.51 cm(-1)); and the in-plane conrotatory bend (92.25 cm(-1)). The disrotatory bend and torsion, separated by only 0.98 cm(-1), are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm(-1) below the conrotatory bend, remains unassigned.

  5. Energy relaxation of intermolecular motions in supercooled water and ice: A molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yagasaki, Takuma; Saito, Shinji

    2011-12-01

    We investigate the energy relaxation of intermolecular motions in liquid water at temperatures ranging from 220 K to 300 K and in ice at 220 K using molecular dynamics simulations. We employ the recently developed frequency resolved transient kinetic energy analysis, which provides detailed information on energy relaxation in condensed phases like two-color pump-probe spectroscopy. It is shown that the energy cascading in liquid water is characterized by four processes. The temperature dependences of the earlier three processes, the rotational-rotational, rotational-translational, and translational-translational energy transfers, are explained in terms of the density of states of the intermolecular motions. The last process is the slow energy transfer arising from the transitions between potential energy basins caused by the excitation of the low frequency translational motion. This process is absent in ice because the hydrogen bond network rearrangement, which accompanies the interbasin transitions in liquid water, cannot take place in the solid phase. We find that the last process in supercooled water is well approximated by a stretched exponential function. The stretching parameter, β, decreases from 1 to 0.72 with decreasing temperature. This result indicates that the dynamics of liquid water becomes heterogeneous at lower temperatures.

  6. Five intermolecular vibrations of the CO2 dimer observed via infrared combination bands

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

    The weakly bound van der Waals dimer (CO2)2 has long been of considerable theoretical and experimental interest. Here, we study its low frequency intermolecular vibrations by means of combination bands in the region of the CO2 monomer ν3 fundamental (≈2350 cm-1), which are observed using a tunable infrared laser to probe a pulsed supersonic slit jet expansion. With the help of a recent high level ab initio calculation by Wang, Carrington, and Dawes, four intermolecular frequencies are assigned: the in-plane disrotatory bend (22.26 cm-1); the out-of-plane torsion (23.24 cm-1); twice the disrotatory bend (31.51 cm-1); and the in-plane conrotatory bend (92.25 cm-1). The disrotatory bend and torsion, separated by only 0.98 cm-1, are strongly mixed by Coriolis interactions. The disrotatory bend overtone is well behaved, but the conrotatory bend is highly perturbed and could not be well fitted. The latter perturbations could be due to tunneling effects, which have not previously been observed experimentally for CO2 dimer. A fifth combination band, located 1.3 cm-1 below the conrotatory bend, remains unassigned.

  7. Intermolecular Vibrational Modes Speed Up Singlet Fission in Perylenediimide Crystals.

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-05

    We report numerical simulations based on a non-Markovian density matrix propagation scheme of singlet fission (SF) in molecular crystals. Ab initio electronic structure calculations were used to parametrize the exciton and phonon Hamiltonian as well as the interactions between the exciton and the intramolecular and intermolecular vibrational modes. We demonstrate that the interactions of the exciton with intermolecular vibrational modes are highly sensitive to the stacking geometry of the crystal and can, in certain cases, significantly accelerate SF. This result may help in understanding the fast SF experimentally observed in a broad range of molecular crystals and offers a new direction for the engineering of efficient SF sensitizers.

  8. 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.

  9. 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

    2015-10-05

    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.

  10. 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…

  11. 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.

  12. Intermolecular potentials from shock structure experiments. [for monatomic gases

    NASA Technical Reports Server (NTRS)

    Sturtevant, B.; Steinhilper, E. A.

    1974-01-01

    Ground-state intermolecular interaction potentials determined from shock structure experiments with four monatomic gases are reported. These potentials are assessed for self-consistency, using the law of corresponding states, and their suitability for engineering applications in rarefied gas dynamics is discussed.

  13. 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…

  14. 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…

  15. 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…

  16. 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.

  17. 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.

  18. Intermolecular vibrations of the CO2-CS2 complex: Experiment and theory agree, but understanding remains challenging

    NASA Astrophysics Data System (ADS)

    Dehghany, M.; Rezaei, Mojtaba; Moazzen-Ahmadi, N.; McKellar, A. R. W.; Brown, James; Wang, Xiao-Gang; Carrington, Tucker

    2016-12-01

    The infrared spectrum of the cross-shaped van der Waals complex CO2-CS2 is observed in the region of the CO2 ν3 fundamental band (≈2350 cm-1) using a tuneable diode laser to probe a pulsed supersonic slit jet expansion. Two combination bands are assigned, corresponding to the intermolecular torsion and CO2 bend modes, and their positions and rotational structure agree extremely well (<0.1 cm-1) with calculations based on a recent ab initio intermolecular potential. The b-type torsional band is well-behaved, but the a-type CO2 bending band is highly unusual, with large shifts between the subband origins for Ka = 0, 2, and 4. The shifts may be rationalized as due to tunnelling effects and Ka-dependent perturbations from other intermolecular modes. But even though they are well predicted by our calculations, there is no simple qualitative explanation. The predicted low-lying planar slipped parallel isomer of CO2-CS2 is not observed.

  19. 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.

  20. 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.

  1. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors.

    PubMed

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  2. Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors

    NASA Astrophysics Data System (ADS)

    Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

    2010-12-01

    Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular π-π interaction by increasing the conjugated dimension of the compounds.

  3. Intermolecular Hydrogen Bonding in Peptide and Modified Jeffamine Organogels

    NASA Astrophysics Data System (ADS)

    Savin, Daniel; Richardson, Adam

    2011-03-01

    In these studies, we present two systems whereby supramolecular assembly results in rigid organogels. First, a series of AB diblock copolymers consisting of poly(Lysine(Z)) (P(Lys(Z)) blocks were synthesized and found to form stable, rigid organogels in THF (ca. 1 - 1.5 wt.% solutions) and chloroform at room temperature. In these systems, the protecting group on the P(Lys) side-chains remains intact and gel formation results from the assembly of the solventphobic P(Lys(Z)) chains through intermolecular beta-sheet formation. The non-peptide block was found to have an effect on organogel properties due to interfacial frustration, which disrupts H-bonding. Second, Jeffamine polymers were modified in a facile way to incorporate intermolecular H-bonding groups to yield networks able to gel various solvents as well as mineral and canola oil. We present the physical and rheological properties of the organogels produced.

  4. Energetics of Intermolecular Hydrogen Bonds in a Hydrophobic Protein Cavity

    NASA Astrophysics Data System (ADS)

    Liu, Lan; Baergen, Alyson; Michelsen, Klaus; Kitova, Elena N.; Schnier, Paul D.; Klassen, John S.

    2014-05-01

    This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine β-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)7- ions, compared with that of the (Lg + PA)7- ion, it is concluded that the -OH groups of the X-OHPA ligands participate in strong (5 - 11 kcal mol-1) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the -OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the -OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 ± 0.2) × 105 M-1] is similar to the value for the PA [(3.8 ± 0.1) × 105 M-1]; Ka for 3-OHPA [(1.1 ± 0.3) × 106 M-1] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 ± 0.2) × 104 M-1] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand -OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds.

  5. 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

  6. Highly Stereoselective Intermolecular Haloetherification and Haloesterification of Allyl Amides

    PubMed Central

    Soltanzadeh, Bardia; Jaganathan, Arvind; Staples, Richard J.

    2016-01-01

    An organocatalytic and highly regio-, diastereo-, and enantioselective intermolecular haloetherification and haloesterification reaction of allyl amides is reported. A variety of alkene substituents and substitution patterns are compatible with this chemistry. Notably, electronically unbiased alkene substrates exhibit exquisite regio- and diastereoselectivity for the title transformation. We also demonstrate that the same catalytic system can be used in both chlorination and bromination reactions of allyl amides with a variety of nucleophiles with little or no modification. PMID:26110812

  7. Calciate-mediated intermolecular hydroamination of diphenylbutadiyne with secondary anilines.

    PubMed

    Glock, Carsten; Görls, Helmar; Westerhausen, Matthias

    2012-07-18

    Calciate-mediated intermolecular hydroamination of diphenylbutadiyne with N-phenyl and N-isopropyl-substituted anilines yields E- and Z-isomers of the corresponding 1-anilino-1,4-diphenylbut-1-ene-3-yne. In the case of HNPh(2) solely heterobimetallic K(2)Ca(NPh(2))(4) is able to effectively catalyze this hydroamination reaction in tetrahydrofuran at elevated temperatures.

  8. 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.

  9. Direction-dependent intermolecular interactions: catechol on TiO2(110)-1×1

    NASA Astrophysics Data System (ADS)

    Li, Shao-Chun; Diebold, Ulrike

    2009-08-01

    The adsorption of a submonolayer of catechol (C6H6O2) on the rutile TiO2(110)-1×1 surface has been investigated by Scanning Tunneling Microscopy (STM). The catechol molecules are preferentially adsorbed on the surface 5-fold coordinated Ti4+ sites, and occupy two neighboring lattice Ti sites. No preference for adsorption at surface step edges is observed at room temperature. A statistical analysis of intermolecular distances demonstrates that the interaction between the molecules strongly depends on the surface crystallographic direction: catechol molecules exhibit attractive interaction along [1-1 0], while they repel each other along the [001] direction. The attractive interaction is proposed to be caused by the coupling of π bonding electrons and the repulsive interaction is possibly mediated by substrate.

  10. Raman Q-branch line shapes as a test of the H2-Ar intermolecular potential

    NASA Technical Reports Server (NTRS)

    Green, Sheldon

    1990-01-01

    The line-shape cross sections of vibrational Raman Q-branch spectra are determined theoretically for D2 and H2 in Ar. The calculations are based on accurate close-coupling matrices and the intermolecular potential obtained by Le Roy and Hutson (1987) from spectra of van der Waals complexes. The calculation techniques applied are explained, and the results are presented in tables and graphs and discussed in detail with reference to published experimental data. Agreement to within about 25 percent is obtained for the line widths, but the line shifts are found to be a factor of two smaller than the measured values, and a temperature dependence of line-width cross sections is predicted which is not observed experimentally.

  11. Intermolecular interactions in AST zeolites through (14)N NMR and DFT calculations.

    PubMed

    Dib, Eddy; Freire, Mélanie; Pralong, Valérie; Mineva, Tzonka; Alonso, Bruno

    2017-03-01

    The structure of the silica AST zeolites (octadecasil) synthesized in fluoride medium using tetramethylammonium (TMA) as the organic structure-directing agent has been reinvestigated using (14)N NMR quadrupolar parameters and DFT calculations. The value of the experimental (14)N quadrupolar coupling constant (CQ = 27 kHz) is larger than expected for a TMA cation possessing a high degree of motion. The analysis of a DFT-optimized octadecasil cluster along with the comparison between measured and calculated (14)N NMR parameters demonstrate the presence of weak C-H...O hydrogen bonds between the TMA in the [4(6)6(12)] cages and the silica skeleton. These intermolecular interactions can be related to the presence of Si...F tetrel bonds within the [4(6)] cages. These new results provide additional information with regard to the formation mechanisms and structure of the octadecasil zeolites.

  12. 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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-01

    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(N6) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N5) computational cost.

  15. 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.

  16. 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.

  17. Second law considerations in Fourier heat conduction of a lattice chain in relation to intermolecular potentials

    NASA Astrophysics Data System (ADS)

    Jesudason, Christopher G.

    2017-01-01

    Two aspects of conductive heat are focused here (i) the nature of conductive heat, defined as that form of energy that is transferred as a result of a temperature difference and (ii) the nature of the intermolecular potentials that induces both thermal energy flow and the temperature profile at the steady state for a 1-D lattice chain. It is found that the standard presuppositions of people like Benofy and Quay (BQ) following Joseph Fourier do not obtain for at least a certain specified regime of intermolecular potential parameters related to harmonic (quadratic) potentials for nearest neighbor interactions. For these harmonic potentials, it appears from the simulation results that steady state solutions exist utilizing non-synthetic thermostats that couple not just the two particles at the extreme ends of the lattice chain, but to a control volume of N particles located at either ends of the chain that does not accord with the unique analytical solutions that obtains for single particle thermostatting at the ends of the lattice with a different thermostatting algorithm that utilizes coupling coefficients. If the method used here is considered a more "realistic" or feasible model of the physical reality, then a re-evaluation of some aspects of the standard theoretical methodology is warranted since the standard model solution profile does not accord with the simulation temperature profile determined here for this related model. We also note that the sinusoidal temperature profile generated suggests that thermal integrated circuits with several thermal P-N junctions may be constructed, opening a way to create more complex thermal transistor circuits. A stationary principle is proposed for regions that violate the Fourier principle Jq.∇T ≤ 0, where Jq is the heat current vector and T the temperature.

  18. Intermolecular vibrations of fluorobenzene-Ar up to 130 cm(-1) in the ground electronic state.

    PubMed

    Gascooke, Jason R; Alexander, Ula N; Lawrance, Warren D

    2012-08-28

    Sixteen intermolecular vibrational levels of the S(0) state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ~130 cm(-1) in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm(-1). The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70-75 cm(-1). There are small differences in energy, particularly above 60 cm(-1), however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar(2) trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ~35 cm(-1) displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend

  19. Small-angle X-ray scattering probe of intermolecular interaction in red blood cells

    NASA Astrophysics Data System (ADS)

    Liu, Guan-Fen; Wang, We-Jia; Xu, Jia-Hua; Dong, Yu-Hui

    2015-03-01

    With high concentrations of hemoglobin (Hb) in red blood cells, self-interactions among these molecules could increase the propensities of their polymerization and aggregation. In the present work, high concentration Hb in solution and red blood cells were analyzed by small-angle X-ray scattering. Calculation of the effective structure factor indicates that the interaction of Hb molecules is the same when they are crowded together in both the cell and physiological saline. The Hb molecules stay individual without the formation of aggregates and clusters in cells. Supported by National Basic Research Program of China (2009CB918600) and National Natural Science Foundation of China (10979005)

  20. 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.

  1. 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

    2014-11-04

    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.

  2. In vivo absolute quantification for mouse muscle metabolites using an inductively coupled synthetic signal injection method and newly developed 1H/31P dual tuned probe

    PubMed Central

    Lee, Donghoon; Marro, Kenneth; Mathis, Mark; Shankland, Eric; Hayes, Cecil

    2013-01-01

    Purpose To obtain robust estimates of 31P metabolite content in mouse skeletal muscles using our recently developed MR absolute quantification method and a custom-built 1H/31P dual tuned radiofrequency (RF) coil optimized for mouse leg. Materials and Methods We designed and fabricated a probe consisting of two dual tuned 1H/31P solenoid coils: one leg was inserted to each solenoid. The mouse leg volume coil was incorporated with injector coils for MR absolute quantification. The absolute quantification method uses a synthetic reference signal injection approach and solves several challenges in MR absolute quantification including changes of coil loading and receiver gains. Results The 1H/31P dual tuned probe was composed of two separate solenoid coils, one for each leg, to increase coil filling factors and signal-to-noise ratio. Each solenoid was equipped with a second coil to allow injection of reference signals. 31P metabolite concentrations determined for normal mice were well within the expected range reported in the literature. Conclusion We developed an RF probe and an absolute quantification approach adapted for mouse skeletal muscle. PMID:24464912

  3. Measurement of W+W- production in pp collisions at √s = 8 TeV and probing anomalous triple-gauge-boson couplings with the ATLAS detector

    NASA Astrophysics Data System (ADS)

    Feng, Haolu

    This thesis presents the measurement of the vector boson pair W+W- production cross section in proton-proton collisions at the center-of-mass energy sqrt(s) = 8 TeV. The leptonic decay channels of the W+W- →ℓ +nuℓℓ-nu ℓor ℓ=(e,mu) are analyzed using data corresponding to 20.3 fb -1 of integrated luminosity collected by the ATLAS detector in 2012 at the Large Hadron Collider at CERN (in Geneva, Switzerland). The experimental signature of this measurement is two energetic isolated leptons ( e+e-, mu+mu-, e+mu-, e+/-mu∓) and associated large missing transverse energy (due to neutrinos in final states). A total of 6636 WW+ℓℓ candidate events is selected in ATLAS data with an estimation of 1547+/-28 background events from non-W+W- production processes. The measured total production cross section is 71+1.1 -1.1(stat)+5.7-5.0(syst)+2.1 -2.0)(lumi) pb, which is comparable with the theoretical prediction of 63.2+2.0-1.8 pb calculated with NNLO QCD and NLO EW corrections. The anomalous triple-gauge-boson couplings (WWZ and WWgamma) could signal new physics beyond the Standard Model at much higher energy scales compared to the directly detectable mass scale at the LHC. An effective Lagrangian is used to generalize the anomalous triple-gauge-boson couplings to describe the W ++W- productions at the LHC. These anomalous couplings can be experimentally probed by comparing the leading lepton transverse momentum spectrum with the theoretical predictions in different triple-gauge-boson coupling space. No observation of deviations from the Standard Model predicted couplings is found by a maximum likelihood fitting of the leading lepton transverse momentum. Therefore, the most stringent limits to date on the anomalous triple-gauge-boson couplings are set from this analysis.

  4. Novel electronic ferroelectricity in an organic charge-order insulator investigated with terahertz-pump optical-probe spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamakawa, H.; Miyamoto, T.; Morimoto, T.; Yada, H.; Kinoshita, Y.; Sotome, M.; Kida, N.; Yamamoto, K.; Iwano, K.; Matsumoto, Y.; Watanabe, S.; Shimoi, Y.; Suda, M.; Yamamoto, H. M.; Mori, H.; Okamoto, H.

    2016-02-01

    In electronic-type ferroelectrics, where dipole moments produced by the variations of electron configurations are aligned, the polarization is expected to be rapidly controlled by electric fields. Such a feature can be used for high-speed electric-switching and memory devices. Electronic-type ferroelectrics include charge degrees of freedom, so that they are sometimes conductive, complicating dielectric measurements. This makes difficult the exploration of electronic-type ferroelectrics and the understanding of their ferroelectric nature. Here, we show unambiguous evidence for electronic ferroelectricity in the charge-order (CO) phase of a prototypical ET-based molecular compound, α-(ET)2I3 (ET:bis(ethylenedithio)tetrathiafulvalene), using a terahertz pulse as an external electric field. Terahertz-pump second-harmonic-generation(SHG)-probe and optical-reflectivity-probe spectroscopy reveal that the ferroelectric polarization originates from intermolecular charge transfers and is inclined 27° from the horizontal CO stripe. These features are qualitatively reproduced by the density-functional-theory calculation. After sub-picosecond polarization modulation by terahertz fields, prominent oscillations appear in the reflectivity but not in the SHG-probe results, suggesting that the CO is coupled with molecular displacements, while the ferroelectricity is electronic in nature. The results presented here demonstrate that terahertz-pump optical-probe spectroscopy is a powerful tool not only for rapidly controlling polarizations, but also for clarifying the mechanisms of ferroelectricity.

  5. Characterization of structure and properties of thin film crystals and ferroelectric BiFeO3: A coupled TEM, SPM, and optical probe approach

    NASA Astrophysics Data System (ADS)

    Jokisaari, Jacob Ragnar

    Correlating advanced microscopy methods including transmission electron microscopy, scanning probe microscopy, and optical spectroscopy on the same materials and even the same specimens allows complimentary measurements to be obtained, revealing new details about structure-property relationships measured on a nanometer scale. Combining measurements not only corroborates the information obtained from any particular method, but also compensates for deficiencies of any single technique. An array of microscopy techniques including high resolution transmission electron microscopy, scanning probe microscopy, and Raman spectroscopy were applied to address scientific and engineering questions concerning the structure and properties of domain patterns in BiFeO3 ferroelectric thin films and to examine novel TiO2(B) thin films suitable for Li-ion battery applications. In BiFeO3, application of these combined techniques allowed a relationship between epitaxial strain and domain width to be established, two cases of strained films with unique domain structures to be identified, transformation of domain structures from all 109° to mixed to all 71° based on differing film thicknesses of 100 and 200 nm to be observed, and to identify growth-induced defects that control domain structure over very long range, 100 nm or more, compared to many studies. In TiO2(B) films, a combination of advanced microscopy and first principals calculations were applied with Raman spectroscopy to produce a definitive reference for further investigation of the crystallinity, structure, composition, and properties of TiO2(B) materials with Raman spectroscopy. Finally to extend these studies of nanostructures and allow direct measurement of electronic and optical properties, the design, development, and construction of proof-of-concept prototypes of specimen rods for in-situ transmission electron microcopy combining electrical probe, scanning tunneling measurements, and optical excitation and

  6. Effects of intermolecular interaction on inelastic electron tunneling spectra

    NASA Astrophysics Data System (ADS)

    Kula, Mathias; Luo, Yi

    2008-02-01

    We have examined the effects of intermolecular interactions on the inelastic electron tunneling spectroscopy (IETS) of model systems: a pair of benzenethiol or a pair of benzenedithiol sandwiched between gold electrodes. The dependence of the IETS on the mutual position of and distance between the paired molecules has been predicted and discussed in detailed. It is shown that, although in most cases, there are clear spectral fingerprints present which allow identification of the actual structures of the molecules inside the junction. Caution must be exercised since some characteristic lines can disappear at certain symmetries. The importance of theoretical simulation is emphasized.

  7. 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

  8. INTERMOLECULAR FORCES IN ASSOCIATION OF PURINES WITH POLYBENZENOID HYDROCARBONS.

    PubMed

    PULLMAN, B; CLAVERIE, P; CAILLET, J

    1965-03-12

    The interactions in solution between purine or pyrimidine bases and polybenzenoid aromatic hydrocarbons probably consist in a vertical, stacking-type physical association. By molecular orbital calculations the role of the Van der Waals-London intermolecular forces in these interactions is determined. The electrostatic dipole-dipole forces are negligible, the polarization (or induction) dipole-induced dipole forces are contributory, but most important are the dispersion (or fluctuation) forces. This loose, physical type of interaction should not show any specificity with respect to the carcinogenic activity of the hydrocarbons.

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

    NASA Astrophysics Data System (ADS)

    Ye, ChuanXiang; Zhao, Yi; Liang, WanZhen

    2015-10-01

    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.

  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. Intermolecular potential and rovibrational states of the H2O-D2 complex

    NASA Astrophysics Data System (ADS)

    van der Avoird, Ad; Scribano, Yohann; Faure, Alexandre; Weida, Miles J.; Fair, Joanna R.; Nesbitt, David J.

    2012-05-01

    A five-dimensional intermolecular potential for H2O-D2 was obtained from the full nine-dimensional ab initio potential surface of Valiron et al. [P. Valiron, M. Wernli, A. Faure, L. Wiesenfeld, C. Rist, S. Kedžuch, J. Noga, J. Chem. Phys. 129 (2008) 134306] by averaging over the ground state vibrational wave functions of H2O and D2. On this five-dimensional potential with a well depth De of 232.12 cm-1 we calculated the bound rovibrational levels of H2O-D2 for total angular momentum J = 0-3. The method used to compute the rovibrational levels is similar to a scattering approach—it involves a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer—while it uses a discrete variable representation of the intermolecular distance coordinate R. The basis was adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H2O and D2, as well as to inversion symmetry. As expected, the H2O-D2 dimer is more strongly bound than its H2O-H2 isotopologue [cf. A. van der Avoird, D.J. Nesbitt, J. Chem. Phys. 134 (2011) 044314], with dissociation energies D0 of 46.10, 50.59, 67.43, and 73.53 cm-1 for pH2O-oD2, oH2O-oD2, pH2O-pD2, and oH2O-pD2. A rotationally resolved infrared spectrum of H2O-D2 was measured in the frequency region of the H2O bend mode. The ab initio calculated values of the rotational and distortion constants agree well with the values extracted from this spectrum.

  12. The rotational spectrum, geometry, and intermolecular force constant of the heterodimer of hydrogen cyanide and fluoroform

    NASA Astrophysics Data System (ADS)

    Goodwin, Elizabeth J.; Legon, A. C.

    1986-02-01

    The ground-state rotational spectra of six isotopic species of an intermolecular complex formed by hydrogen cyanide and fluoroform have been measured using the pulsed-nozzle, Fourier-transform microwave technique. The rotational constant B0, the centrifugal distortion constants DJ,DJK,HJ, HJK, and HKJ, and, where appropriate, the nuclear quadrupole coupling constants χ(14N) and χ(D) have been determined for each of the species HC14NṡṡṡHCF3, DC14NṡṡṡHCF3, HC14ṡṡṡDCF3, HC15NṡṡṡHCF3, HC15NṡṡṡDCF3, and DC15NṡṡṡHCF3. For HC14NṡṡṡHCF3 the values are as follows: B0=1151.2991(4) MHz, DJ=1.91(1) kHz, DJK=282.75(6) kHz, HJ=-0.1(1) Hz, HJK=44.3(5) Hz, HKJ=53(5) Hz, and χ(14N)=3.948(8) MHz. The form of the spectra and magnitudes of the rotational constants allow the conclusion that the geometry of the complex is of C3V symmetry with the nuclei in the order HCNṡṡṡHCF3 and lead to r(NṡṡṡC)=3.489(2) Å for HCF3 species but 3.483(1) Å for DCF3 species. The intermolecular stretching force constant determined from DJ is kσ=3.52 N m-1.

  13. 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.

  14. Intermolecular interactions and the thermodynamic properties of supercritical fluids

    NASA Astrophysics Data System (ADS)

    Yigzawe, Tesfaye M.; Sadus, Richard J.

    2013-05-01

    The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids.

  15. Hybrid materials from intermolecular associations between cationic lipid and polymers.

    PubMed

    Pereira, Edla M A; Kosaka, Priscila M; Rosa, Heloísa; Vieira, Débora B; Kawano, Yoshio; Petri, Denise F S; Carmona-Ribeiro, Ana M

    2008-08-07

    Intermolecular associations between a cationic lipid and two model polymers were evaluated from preparation and characterization of hybrid thin films cast on silicon wafers. The novel materials were prepared by spin-coating of a chloroformic solution of lipid and polymer on silicon wafer. Polymers tested for miscibility with the cationic lipid dioctadecyldimethylammonium bromide (DODAB) were polystyrene (PS) and poly(methyl methacrylate) (PMMA). The films thus obtained were characterized by ellipsometry, wettability, optical and atomic force microscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and activity against Escherichia coli. Whereas intermolecular ion-dipole interactions were available for the PMMA-DODAB interacting pair producing smooth PMMA-DODAB films, the absence of such interactions for PS-DODAB films caused lipid segregation, poor film stability (detachment from the silicon wafer) and large rugosity. In addition, the well-established but still remarkable antimicrobial DODAB properties were transferred to the novel hybrid PMMA/DODAB coating, which is demonstrated to be highly effective against E. coli.

  16. 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

  17. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGES

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

    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

  18. Photon counting as a probe of superfluidity in a two-band Bose-Hubbard system coupled to a cavity field.

    PubMed

    Rajaram, Sara; Trivedi, Nandini

    2013-12-13

    We show that photon number measurement can be used to detect superfluidity for a two-band Bose-Hubbard model coupled to a cavity field. The atom-photon coupling induces transitions between the two internal atomic levels and results in entangled polaritonic states. In the presence of a cavity field, we find different photon numbers in the Mott-insulating versus superfluid phases, providing a method of distinguishing the atomic phases by photon counting. Furthermore, we examine the dynamics of the photon field after a rapid quench to zero atomic hopping by increasing the well depth. We find a robust correlation between the field's quench dynamics and the initial superfluid order parameter, thereby providing a novel and accurate method of determining the order parameter.

  19. Hybridization and electron-phonon coupling in ferroelectric BaTiO3 probed by resonant inelastic x-ray scattering

    NASA Astrophysics Data System (ADS)

    Fatale, S.; Moser, S.; Miyawaki, J.; Harada, Y.; Grioni, M.

    2016-11-01

    We investigated the ferroelectric perovskite material BaTiO3 by resonant inelastic x-ray scattering (RIXS) at the Ti L3 edge. We observe with decreasing temperature a transfer of spectral weight from the elastic to the charge-transfer spectral features, indicative of increasing Ti 3 d -O 2 p hybridization. When the incident photon energy selects transitions to the Ti 3 d eg manifold, the quasielastic RIXS response exhibits a tail indicative of phonon excitations. A fit of the spectral line shape by a theoretical model allows us to estimate the electron-phonon coupling strength M ˜0.25 eV, which places BaTiO3 in the intermediate coupling regime.

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

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2006-01-01

    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.

  1. 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.

  2. Probing Higgs width and top quark Yukawa coupling from t t¯ and t t¯ t¯ productions

    NASA Astrophysics Data System (ADS)

    Cao, Qing-Hong; Chen, Shao-Long; Liu, Yandong

    2017-03-01

    We demonstrate that four top-quark production is a powerful tool to constrain the top Yukawa coupling. The constraint is robust in the sense that it does not rely on the Higgs boson decay. Taking into account the projection of the t t ¯H production by the ATLAS Collaboration, we obtained a bound on the Higgs boson width, ΓH≤2.57 ΓHSM, at the 14 TeV Large Hadron Collider with an integrated luminosity of 300 fb-1.

  3. 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.

  4. Electromechanical method coupling non-invasive skin impedance probing and in vivo subcutaneous liquid microinjection: controlling the diffusion pattern of nanoparticles within living soft tissues.

    PubMed

    Sung, Baeckkyoung; Kim, Se Hoon; Lee, Jin-Kyu; Lee, Byung-Cheon; Soh, Kwang-Sup

    2014-08-01

    Transdermal drug delivery is the way to transport drug carriers, such as nanoparticles, across the skin barrier to the dermal and/or subcutaneous layer. In order to control the transdermal drug delivery process, based on the heterogeneous and nonlinear structures of the skin tissues, we developed a novel electromechanical method combining in vivo local skin impedance probing, subcutaneous micro-injection of colloidal nanoparticles, and transcutaneous electrical stimulation. Experiments on the nude mice using in vivo fluorescence imaging exhibited significantly different apparent diffusion patterns of the nanoparticles depending on the skin impedance: Anisotropic and isotropic patterns were observed upon injection into low and high impedance points, respectively. This result implies that the physical complexity in living tissues may cause anisotropic diffusion of drug carriers, and can be used as a parameter for controlling drug delivery process. This method also can be combined with microneedle-based drug release systems, micro-fabricated needle-electrodes, and/or advanced in vivo targeting/imaging technologies using nanoparticles.

  5. Intermolecular vibrations of (CH2)2O-HF and -DF hydrogen bonded complexes investigated by Fourier transform infrared spectroscopy and ab initio calculations.

    PubMed

    Cirtog, M; Asselin, P; Soulard, P; Madebène, B; Alikhani, M E

    2010-10-14

    A series of Fourier transform infrared spectra (FTIR) of the hydrogen bonded complexes (CH(2))(2)O-HF and -DF have been recorded in the 50-750 cm(-1) range up to 0.1 cm(-1) resolution in a static cell maintained at near room temperature. The direct observation of three intermolecular transitions enabled us to perform band contour analysis of congested cell spectra and to determine reliable rovibrational parameters such as intermolecular frequencies, rovibrational and anharmonic coupling constants involving two l(1) and l(2) librations and one σ stretching intermolecular motion. Inter-inter anharmonic couplings could be identified between ν(l(1)), ν(l(2)), ν(σ) and the two lowest frequency bending modes. The positive sign of coupling constants (opposite with respect to acid stretching intra-inter ones) reveals a weakening of the hydrogen bond upon intermolecular excitation. The four rovibrational parameters ν(σ) and x(σj) (j = σ, δ(1), δ(2)) derived in the present far-infrared study and also in a previous mid-infrared one [Phys. Chem. Chem. Phys. 2005, 1, 592] make deviations appear smaller than 1% for frequencies and 12% for coupling constants which gives confidence to the reliability of the data obtained. Anharmonic frequencies obtained at the MP2 level with Aug-cc-pvTZ basis set agree well with experimental values over a large set of frequencies and coupling constants. An estimated anharmonic corrected value of the dissociation energy D for both oxirane-HF (2424 cm(-1)) and -DF (2566 cm(-1)) has been derived using a level of theory as high as CCSD(T)/Aug-cc-pvQZ, refining the harmonic value previously calculated for oxirane-HF with the MP2 method and a smaller basis set. Finally, contrary to short predissociation lifetimes evidenced for acid stretching excited states, any homogeneous broadening related to vibrational dynamics of (CH(2))(2)O-HF and -DF has been observed within the three highest frequency intermolecular states, as expected with low

  6. 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

  7. 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.

  8. Intermolecular forces and energies between ligands and receptors.

    PubMed

    Moy, V T; Florin, E L; Gaub, H E

    1994-10-14

    The recognition mechanisms and dissociation pathways of the avidin-biotin complex and of actin monomers in actin filaments were investigated. The unbinding forces of discrete complexes of avidin or streptavidin with biotin analogs are proportional to the enthalpy change of the complex formation but independent of changes in the free energy. This result indicates that the unbinding process is adiabatic and that entropic changes occur after unbinding. On the basis of the measured forces and binding energies, an effective rupture length of 9.5 +/- 1 angstroms was calculated for all biotin-avidin pairs and approximately 1 to 3 angstroms for the actin monomer-monomer interaction. A model for the correlation among binding forces, intermolecular potential, and molecular function is proposed.

  9. 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.

  10. Intermolecular vibrations and fast relaxations in supercooled ionic liquids

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.

    2011-06-01

    Short-time dynamics of ionic liquids has been investigated by low-frequency Raman spectroscopy (4 < ω < 100 cm-1) within the supercooled liquid range. Raman spectra are reported for ionic liquids with the same anion, bis(trifluoromethylsulfonyl)imide, and different cations: 1-butyl-3-methylimidazolium, 1-hexyl-3-methylimidazolium, 1-butyl-1-methylpiperidinium, trimethylbutylammonium, and tributylmethylammonium. It is shown that low-frequency Raman spectroscopy provides similar results as optical Kerr effect (OKE) spectroscopy, which has been used to study intermolecular vibrations in ionic liquids. The comparison of ionic liquids containing aromatic and non-aromatic cations identifies the characteristic feature in Raman spectra usually assigned to librational motion of the imidazolium ring. The strength of the fast relaxations (quasi-elastic scattering, QES) and the intermolecular vibrational contribution (boson peak) of ionic liquids with non-aromatic cations are significantly lower than imidazolium ionic liquids. A correlation length assigned to the boson peak vibrations was estimated from the frequency of the maximum of the boson peak and experimental data of sound velocity. The correlation length related to the boson peak (˜19 Å) does not change with the length of the alkyl chain in imidazolium cations, in contrast to the position of the first-sharp diffraction peak observed in neutron and X-ray scattering measurements of ionic liquids. The rate of change of the QES intensity in the supercooled liquid range is compared with data of excess entropy, free volume, and mean-squared displacement recently reported for ionic liquids. The temperature dependence of the QES intensity in ionic liquids illustrates relationships between short-time dynamics and long-time structural relaxation that have been proposed for glass-forming liquids.

  11. 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)

  12. 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.

  13. General, mild, and intermolecular Ullmann-type synthesis of diaryl and alkyl aryl ethers catalyzed by diol-copper(I) complex.

    PubMed

    Naidu, Ajay B; Jaseer, E A; Sekar, Govindasamy

    2009-05-15

    A wide range of diaryl ethers and alkyl aryl ethers are synthesized through intermolecular C(aryl)-O bond formation from the corresponding aryl iodides/aryl bromides and phenols/alcohols through Ullmann-type coupling reaction in the presence of a catalytic amount of easily available (+/-)-diol L3-CuI complex under very mild reaction conditions. Less reactive aryl bromides can also be used for O-arylation of phenols under the same reaction conditions without increasing the reaction temperature, catalyst loading, and time. The catalytic system not only is capable of coupling hindered substrate but also tolerates a broad range of a series of functional groups.

  14. Visualized detection of single-base difference in multiplexed loop-mediated isothermal amplification amplicons by invasive reaction coupled with oligonucleotide probe-modified gold nanoparticles.

    PubMed

    Lu, Yan; Ma, Xueping; Wang, Jianping; Sheng, Nan; Dong, Tianhui; Song, Qinxin; Rui, Jianzhong; Zou, Bingjie; Zhou, Guohua

    2017-04-15

    Loop-mediated isothermal amplification (LAMP) is a well-developed DNA amplification method with an ultra-high sensitivity, but it is difficult to recognize a single-base difference (like genotyping) in target-specific amplicons by conventional detection ways, such as the intercalation of dyes into dsDNA amplicons or the increase of solution turbidity along with the polymerization process. To allow genotyping based on LAMP suitable for POCT (point-of-care testing) or on-site testing, here we proposed a highly specific and cost-effective method for detecting a single-base difference in LAMP amplicons. The method includes three key steps, sequence amplifier to amplify multiple fragments containing the single nucleotide polymorphisms (SNPs) of interest, allele identifier to recognize a targeted base in the amplicons by invasive reaction, and signal generator to yield signals by hybridization-induced assembly of oligonucleotide probe-modified gold nanoparticles. Because the allele identifier is sensitive to one base difference, it is possible to use multiplexed LAMP (mLAMP) to generate amplicon mixtures for multiple SNP typing. Genotyping of 3 different SNPs (CYP2C19*2, CYP2C19*3 and MDR1-C3435T) for guiding the dosage of clopidogrel is successfully carried out in a 3-plex LAMP on real clinical samples. As our method relies on the naked-eye detection and constant-temperature reaction, no expensive instrument is required for both target amplification and sequence identification, thus much suitable for inexpensive gene-guided personalized medicine in source-limited regions.

  15. Coupling of laser excitation and inelastic neutron scattering: attempt to probe the dynamics of light-induced C-phycocyanin dynamics.

    PubMed

    Combet, Sophie; Pieper, Jörg; Coneggo, Frédéric; Ambroise, Jean-Pierre; Bellissent-Funel, Marie-Claire; Zanotti, Jean-Marc

    2008-06-01

    Excitation energy transfer (EET) in light-harvesting antennae is a highly efficient key event in photosynthesis, where light-induced dynamics of the antenna pigment-protein complexes may play a functional role. So far, however, the relationship between EET and protein dynamics remains unknown. C-phycocyanin (C-PC) is the main pigment/protein complex present in the cyanobacterial antenna, called "phycobilisome". The aim of the present study was to investigate light-induced C-PC internal thermal motions (ps timescale) measured by inelastic neutron scattering. To synchronize the beginning of the laser flash (6 ns duration) with that of the neutron test pulse ( approximately 87 micros duration), we developed a novel type of "time-resolved" experimental setup on MIBEMOL time-of-flight neutron spectrometer (LLB, France). Data acquisition has been modified to get quasi-simultaneously "light" and "dark" measurements (with and without laser, respectively) and eliminate many spurious effects that could occur on the sample during the experiment. The study was carried out on concentrated C-PC ( approximately 135 g/L protein in D(2)O phosphate buffer), contained in an aluminium/sapphire sample holder (almost "transparent" for neutrons) and homogeneously illuminated inside an "integrating sphere". We observed very similar incoherent dynamical structure factors of C-PC with or without light. The vibrational density of states showed two very slightly increased vibrational modes with light, at approximately 30 and approximately 50 meV ( approximately 240 and approximately 400 cm(-1), respectively). These effects have to be verified by further experiments before probing any temporal evolution, by introducing a time delay between the laser flash and the neutron test pulse.

  16. 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.

  17. Highly sensitive determination of nitric oxide in biologic samples by a near-infrared BODIPY-based fluorescent probe coupled with high-performance liquid chromatography.

    PubMed

    Zhang, Hui-Xian; Chen, Jian-Bo; Guo, Xiao-Feng; Wang, Hong; Zhang, Hua-Shan

    2013-11-15

    Nitric oxide (NO) acts as an important regulator and mediator in numerous processes of biological systems. In this work, the analytical potential of a novel near-infrared (NIR, >600 nm) BODIPY-based fluorescent probe for NO, 8-(3,4-diaminophenyl)-4,4-difluoro-4-bora-3a,4a-diaza-di(1,2-dihydro) naphtho[b, g]s-indacene (DANPBO-H) has been evaluated in high performance liquid chromatography (HPLC). In 25 mM pH 6.50 borate buffer, DANPBO-H reacted with NO to give the corresponding triazole, DANPBO-H-T, at 35 °C for 20 min. DANPBO-H-T was eluted using a mobile phase of methanol/tetrahydrofuran/50mM pH 7.00 H3Cit-NaOH buffer (81:7:12, v/v/v) in 4 min on a C8 column and detected with fluorescence detection at excitation and emission wavelengths of 621 and 631 nm, respectively. The limit of detection (LOD) (signal-to-noise=3) reached to 5.50×10(-10) M. Excellent selectivity was observed against other reactive oxygen/nitrogen species. Various representative biological matrixes including the whole blood and organs of mice, the pangen and radical of rice, human vascular endothelial (ECV-304) cells and mouse macrophage (RAW 264.7) cells were used to verify the feasibility and resistance to interfering effects from complex biological sample matrixes of the developed DANPBO-H-based HPLC method. Compared to the existing derivatization-based HPLC methods for NO, the proposed method eliminates interfering effects from complex biological sample matrixes efficiently owing to the fluorescence detection in the NIR region, and is more advantageous and robust for the sensitive and selective determination of NO in complex biological samples.

  18. Intermolecular interactions in rifabutin—2-hydroxypropyl-β-cyclodextrin—water solutions

    NASA Astrophysics Data System (ADS)

    Anshakova, A. V.; Yermolenko, Yu. V.; Konyukhov, V. Yu.; Polshakov, V. I.; Maksimenko, O. O.; Gelperina, S. E.

    2015-05-01

    The possibility of a intermolecular complex rifabutin (RB)-2-hydroxypropyl-β-cyclodextrin (HP-β-CD) formed as a result of the interaction of the piperidine fragment of the RB molecule and the hydrophobic cavity of the HP-β-CD molecule was found. The stability constant of the intermolecular complex was determined.

  19. The use of intermolecular potential functions in fitting pressure induced spectra

    NASA Technical Reports Server (NTRS)

    Goorvitch, D.; Silvaggio, P. M.; Boese, R. W.

    1981-01-01

    An example is presented which demonstrates the importance of using physically realistic derivatives of the intermolecular potential when fitting pressure-induced spectra. The use of nonrealistic derivatives may mask second-order temperature effects in the theory. As the temperature decreases, the intermolecular potential may have an important angular dependence.

  20. 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

  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. Structural variability and the nature of intermolecular interactions in Watson-Crick B-DNA base pairs.

    PubMed

    Czyznikowska, Z; Góra, R W; Zaleśny, R; Lipkowski, P; Jarzembska, K N; Dominiak, P M; Leszczynski, J

    2010-07-29

    A set of nearly 100 crystallographic structures was analyzed using ab initio methods in order to verify the effect of the conformational variability of Watson-Crick guanine-cytosine and adenine-thymine base pairs on the intermolecular interaction energy and its components. Furthermore, for the representative structures, a potential energy scan of the structural parameters describing mutual orientation of the base pairs was carried out. The results were obtained using the hybrid variational-perturbational interaction energy decomposition scheme. The electron correlation effects were estimated by means of the second-order Møller-Plesset perturbation theory and coupled clusters with singles and doubles method adopting AUG-cc-pVDZ basis set. Moreover, the characteristics of hydrogen bonds in complexes, mimicking those appearing in B-DNA, were evaluated using topological analysis of the electron density. Although the first-order electrostatic energy is usually the largest stabilizing component, it is canceled out by the associated exchange repulsion in majority of the studied crystallographic structures. Therefore, the analyzed complexes of the nucleic acid bases appeared to be stabilized mainly by the delocalization component of the intermolecular interaction energy which, in terms of symmetry adapted perturbation theory, encompasses the second- and higher-order induction and exchange-induction terms. Furthermore, it was found that the dispersion contribution, albeit much smaller in terms of magnitude, is also a vital stabilizing factor. It was also revealed that the intermolecular interaction energy and its components are strongly influenced by four (out of six) structural parameters describing mutual orientation of bases in Watson-Crick pairs, namely shear, stagger, stretch, and opening. Finally, as a part of a model study, much of the effort was devoted to an extensive testing of the UBDB databank. It was shown that the databank quite successfully reproduces the

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Gold Nanoparticle Internal Structure and Symmetry Probed by Unified Small-Angle X-ray Scattering and X-ray Diffraction Coupled with Molecular Dynamics Analysis.

    PubMed

    Fleury, Blaise; Cortes-Huerto, Robinson; Taché, Olivier; Testard, Fabienne; Menguy, Nicolas; Spalla, Olivier

    2015-09-09

    Shape and size are known to determine a nanoparticle's properties. Hardly ever studied in synthesis, the internal crystal structure (i.e., particle defects, crystallinity, and symmetry) is just as critical as shape and size since it directly impacts catalytic efficiency, plasmon resonance, and orients anisotropic growth of metallic nanoparticles. Hence, its control cannot be ignored any longer in today's research and applications in nanotechnology. This study implemented an unprecedented reliable measurement combining these three structural aspects. The unified small-angle X-ray scattering and diffraction measurement (SAXS/XRD) was coupled with molecular dynamics to allow simultaneous determination of nanoparticles' shape, size, and crystallinity at the atomic scale. Symmetry distribution (icosahedra-Ih, decahedra-Dh, and truncated octahedra-TOh) of 2-6 nm colloidal gold nanoparticles synthesized in organic solvents was quantified. Nanoparticle number density showed the predominance of Ih, followed by Dh, and little, if any, TOh. This result contradicts some theoretical predictions and highlights the strong effect of the synthesis environment on structure stability. We foresee that this unified SAXS/XRD analysis, yielding both statistical and quantitative counts of nanoparticles' symmetry distribution, will provide new insights into nanoparticle formation, growth, and assembly.

  8. Isotope Probing of the UDP‐Apiose/UDP‐Xylose Synthase Reaction: Evidence of a Mechanism via a Coupled Oxidation and Aldol Cleavage

    PubMed Central

    Eixelsberger, Thomas; Horvat, Doroteja; Gutmann, Alexander; Weber, Hansjörg

    2017-01-01

    Abstract The C‐branched sugar d‐apiose (Api) is essential for plant cell‐wall development. An enzyme‐catalyzed decarboxylation/pyranoside ring‐contraction reaction leads from UDP‐α‐d‐glucuronic acid (UDP‐GlcA) to the Api precursor UDP‐α‐d‐apiose (UDP‐Api). We examined the mechanism of UDP‐Api/UDP‐α‐d‐xylose synthase (UAXS) with site‐selectively 2H‐labeled and deoxygenated substrates. The analogue UDP‐2‐deoxy‐GlcA, which prevents C‐2/C‐3 aldol cleavage as the plausible initiating step of pyranoside‐to‐furanoside conversion, did not give the corresponding Api product. Kinetic isotope effects (KIEs) support an UAXS mechanism in which substrate oxidation by enzyme‐NAD+ and retro‐aldol sugar ring‐opening occur coupled in a single rate‐limiting step leading to decarboxylation. Rearrangement and ring‐contracting aldol addition in an open‐chain intermediate then give the UDP‐Api aldehyde, which is intercepted via reduction by enzyme‐NADH. PMID:28102965

  9. Diffusion and molecular interactions in a methanol/polyimide system probed by coupling time-resolved FTIR spectroscopy with gravimetric measurements

    PubMed Central

    Musto, Pellegrino; Galizia, Michele; La Manna, Pietro; Pannico, Marianna; Mensitieri, Giuseppe

    2013-01-01

    In this contribution the diffusion of methanol in a commercial polyimide (PMDA-ODA) is studied by coupling gravimetric measurements with in-situ, time-resolved FTIR spectroscopy. The spectroscopic data have been treated with two complementary techniques, i.e., difference spectroscopy (DS) and least-squares curve fitting (LSCF). These approaches provided information about the overall diffusivity, the nature of the molecular interactions among the system components and the dynamics of the various molecular species. Additional spectroscopic measurements on thin film samples (about 2 μm) allowed us to identify the interaction site on the polymer backbone and to propose likely structures for the H-bonding aggregates. Molar absorptivity values from a previous literature report allowed us to estimate the population of first-shell and second-shell layers of methanol in the polymer matrix. In terms of diffusion kinetics, the gravimetric and spectroscopic estimates of the diffusion coefficients were found to be in good agreement with each other and with previous literature reports. A Fickian behavior was observed throughout, with diffusivity values markedly affected by the total concentration of sorbed methanol. PMID:24809042

  10. Probing the photoexcited states of rhodium corroles by time-resolved Q-band EPR. Observation of strong spin-orbit coupling effects.

    PubMed

    Rozenshtein, V; Wagnert, L; Berg, A; Stavitski, E; Berthold, T; Kothe, G; Saltsman, I; Gross, Z; Levanon, H

    2008-06-19

    The photoexcited states of two 5,10,15-tris(pentafluorophenyl)corroles (tpfc), hosting Rh(III) in their core, namely Rh(pyr)(PPh 3)(tpfc) and Rh(PPh 3)(tpfc), have been studied by time-resolved electron paramagnetic resonance (TREPR) combined with pulsed laser excitation. Using the transient nutation technique, the spin polarized spectra are assigned to photoexcited triplet states. The spectral widths observed for the two Rh(III) corroles crucially depend on the axial ligands at the Rh(III) metal ion. In case of Rh(PPh 3)(tpfc), the TREPR spectra are found to extend over 200 mT, which exceeds the spectral width of non-transition-metal corroles by more than a factor of 3. Moreover, the EPR lines of the Rh(III) corroles are less symmetric than those of the non-transition-metal corrroles. The peculiarities in the TREPR spectra of the Rh(III) corroles can be rationalized in terms of strong spin-orbit coupling (SOC) associated with the transition-metal character of the Rh(III) ion. It is assumed that SOC in the photoexcited Rh(III) corroles effectively admixes metal centered (3)dd-states to the corrole centered (3)pipi*-states detected in the TREPR experiments. This admixture leads to an increased zero-field splitting and a large g-tensor anisotropy as manifested by the excited Rh(III) corroles.

  11. 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.; ...

    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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. PROBING THE CARBON–PHOSPHORUS BOND COUPLING IN LOW-TEMPERATURE PHOSPHINE (PH{sub 3})–METHANE (CH{sub 4}) INTERSTELLAR ICE ANALOGUES

    SciTech Connect

    Turner, Andrew M.; Abplanalp, Matthew J.; Kaiser, Ralf I.

    2016-03-10

    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 P{sub 8}H{sub 10} and CH{sub 3}P{sub 8}H{sub 9}, 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 CH{sub 3}PH{sub 2} and CH{sub 6}P{sub 2} can form via insertion of carbene and phosphinidene and that the methylenediphosphine (PH{sub 2}CH{sub 2}PH{sub 2}) isomer forms in the ices, although methylphosphine (CH{sub 3}P{sub 2}H{sub 3}) 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.

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

    PubMed Central

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

    2013-01-01

    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 force measurements of the formation of a peptide bond catalyzed by 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 1µm/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 non-polar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski’s equality and demonstrated, as expected, that non-equilibrium 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. PMID:23679912

  18. Astrophysical probes of fundamental physics

    NASA Astrophysics Data System (ADS)

    Martins, C. J. A. P.

    2009-10-01

    I review the motivation for varying fundamental couplings and discuss how these measurements can be used to constrain fundamental physics scenarios that would otherwise be inaccessible to experiment. I highlight the current controversial evidence for varying couplings and present some new results. Finally I focus on the relation between varying couplings and dark energy, and explain how varying coupling measurements might be used to probe the nature of dark energy, with some advantages over standard methods. In particular I discuss what can be achieved with future spectrographs such as ESPRESSO and CODEX.

  19. Role of Amino Acid Insertions on Intermolecular Forces between Arginine Peptide Condensed DNA Helices

    PubMed Central

    DeRouchey, Jason E.; Rau, Donald C.

    2011-01-01

    In spermatogenesis, chromatin histones are replaced by arginine-rich protamines to densely compact DNA in sperm heads. Tight packaging is considered necessary to protect the DNA from damage. To better understand the nature of the forces condensing protamine-DNA assemblies and their dependence on amino acid content, the effect of neutral and negatively charged amino acids on DNA-DNA intermolecular forces was studied using model peptides containing six arginines. We have previously observed that the neutral amino acids in salmon protamine decrease the net attraction between protamine-DNA helices compared with the equivalent homo-arginine peptide. Using osmotic stress coupled with x-ray scattering, we have investigated the component attractive and repulsive forces that determine the net attraction and equilibrium interhelical distance as a function of the chemistry, position, and number of the amino acid inserted. Neutral amino acids inserted into hexa-arginine increase the short range repulsion while only slightly affecting longer range attraction. The amino acid content alone of salmon protamine is enough to rationalize the forces that package DNA in sperm heads. Inserting a negatively charged amino acid into hexa-arginine dramatically weakens the net attraction. Both of these observations have biological implications for protamine-DNA packaging in sperm heads. PMID:21994948

  20. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    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.

  2. 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.

  3. Ab initio intermolecular potential energy surfaces for the Ar-NCCN van der Waals complexes

    NASA Astrophysics Data System (ADS)

    Solimannejad, Mohammad; Jouypazadeh, Hamidreza; Farrokhpour, Hossein

    2014-11-01

    The intermolecular potential energy surface of complex pairing argon with cyanogen molecule (NCCN) was calculated using the coupled cluster with single and double and perturbative triple excitations (CCSD(T)) with aug-cc-pvdz basis set extended with a set of mid-bond (3s3p2d1f1g) functions. The interaction energies were calculated by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The calculated potential energies were fitted to an analytical expression. The calculated Ar-NCCN potential energy surface shows a global minimum at 3.35 Å, the distance between argon and centre of mass of cyanogen, for the T-shaped geometry and two local minimum at distance of 5.54 Å for the linear geometry on one side of cyanogen. Finally, the interaction second virial coefficients were calculated using the fitted potential energy surface and were compared with those obtained by the parameters of the Beattie-Bridgeman equation of states of pure argon and cyanogens fluids, approximately.

  4. 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.

  5. 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

  6. 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.

  7. Effect of donor orientation on ultrafast intermolecular electron transfer in coumarin-amine systems

    SciTech Connect

    Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H.

    2008-09-21

    Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component ({tau}{sub 1}) is the measure of the fastest ET rate ({tau}{sub 1}={tau}{sub ET}{sup fast}=(k{sub ET}{sup fast}){sup -1}), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V{sub el}). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the {tau}{sub 1} remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x{sub A}) is found to be {approx}0.4 for aromatic amines and {approx}0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the {tau}{sub 1} values are seen to increase very sharply. The large difference in the critical x{sub A} values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic ({pi}-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of {pi}-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869

  8. Noncovalent Intermolecular Forces in Phycobilisomes of Porphyridium cruentum.

    PubMed

    Zilinskas, B A; Glick, R E

    1981-08-01

    Using sensitized fluorescence as a measure of intactness of phycobilisomes isolated from Porphyridium cruentum, the effects of various environmental perturbations on phycobilisome integrity were investigated. The rate of phycobilisome dissociation in 0.75 ionic strength sodium salts proceeds in the order: SCN(-) > NO(3) (-) > Cl(-) > C(6)H(5)O(7) (3-) > SO(4) (2-) > PO(4) (3-), as predicted from the lyotropic series of anions and their effects on hydrophobic interactions in proteins. Similarly, increasing temperature (to 30 C) and pH values approaching the isoelectric points of the biliproteins stabilize phycobilisomes. Deuterium substitution at exchangeable sites on the phycobiliproteins decreases the rate of phycobilisome dissociation, while substitution at nonexchangeable sites increases rates of dissociation. It is concluded that hydrophobic intermolecular interactions are the most important forces in maintaining the phycobilisome structure. Dispersion forces also seem to contribute to phycobilisome stabilization. The adverse effects of electrostatic repulsion must not be ignored; however, it seems that the requirement of phycobilisomes of high salt concentrations is not simply countershielding of charges on the proteins.

  9. Intermolecular forces between the motor protein and the filament.

    PubMed

    Suda, H; Taylor, T W

    1993-03-07

    Intermolecular forces between motor proteins and filaments were evaluated on the basis of the experimental data of an in vitro motility assay by considering the molecular friction in the movement system. The molecular friction was caused by a different mechanism from that of the hydrodynamic drag. However, the molecular frictional forces apparently gave the same expression as the hydrodynamic frictional forces. The resulting equation was very effective in examining the physical properties of the weak interaction in the dynein-microtubules system from basic experiments carried out by Vale et al. (1989). From careful analysis of their experimental data, it was concluded that the hydrodynamic friction was not dominant, even in the weak binding state. The electrostatic interaction between dynein-heads and microtubules in the weak binding state was analyzed by applying the DLVO (Derjaguin-Landau-Verway-Overbeek) theory in colloid science through the ionic dependence of one-dimensional diffusion. The interacting distance between charges which took part in the weak adhesion was estimated to be 3 nm. In the present study, the molecular mechanism of the sliding velocity was also investigated for the myosin-actin filaments and the kinesin-microtubules systems by fitting the ATP-dependence and the ionic dependence in ATP-driven active sliding.

  10. 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).

  11. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    NASA Astrophysics Data System (ADS)

    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

    2016-03-01

    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.

  12. Phosphite-oxazole/imidazole ligands in asymmetric intermolecular Heck reaction.

    PubMed

    Mazuela, Javier; Tolstoy, Paivi; Pàmies, Oscar; Andersson, Pher G; Diéguez, Montserrat

    2011-02-07

    We describe the application of a new class of ligands--the phosphite-oxazole/imidazole (L1-L5a-g)--in asymmetric intermolecular Pd-catalyzed Heck reactions under thermal and microwave conditions. These ligands combine the advantages of the oxazole/imidazole moiety with those of the phosphite moiety: they are more stable than their oxazoline counterparts, less sensitive to air and other oxidizing agents than phosphines and phosphinites, and easy to synthesize from readily available alcohols. The results indicate that activities, regio- and enantioselectivities, are highly influenced by the type of nitrogen donor group (oxazole or imidazole), the oxazole and biaryl-phosphite substituents and the axial chirality of the biaryl moiety of the ligand. By carefully selecting the ligand components, we achieved high activities, regio- (up to 99%) and enantioselectivities (up to 99%) using several triflate sources. Under microwave-irradiation conditions, reaction times were considerably shorter (from 24 h to 30 min) and regio- and enantioselectivities were still excellent.

  13. 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

    2016-03-11

    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.

  14. 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

  15. Determination of stepsize parameters for intermolecular vibrational energy transfer

    SciTech Connect

    Tardy, D.C.

    1992-03-01

    Intermolecular energy transfer of highly excited polyatomic molecules plays an important role in many complex chemical systems: combustion, high temperature and atmospheric chemistry. By monitoring the relaxation of internal energy we have observed trends in the collisional efficiency ({beta}) for energy transfer as a function of the substrate's excitation energy and the complexities of substrate and deactivator. For a given substrate {beta} increases as the deactivator's mass increase to {approximately}30 amu and then exhibits a nearly constant value; this is due to a mass mismatch between the atoms of the colliders. In a homologous series of substrate molecules (C{sub 3}{minus}C{sub 8}) {beta} decreases as the number of atoms in the substrate increases; replacing F with H increases {beta}. All substrates, except for CF{sub 2}Cl{sub 2} and CF{sub 2}HCl below 10,000 cm{sup {minus}1}, exhibited that {beta} is independent of energy, i.e. <{Delta}E>{sub all} is linear with energy. The results are interpreted with a simple model which considers that {beta} is a function of the ocillators energy and its vibrational frequency. Limitations of current approximations used in high temperature unimolecular reactions were evaluated and better approximations were developed. The importance of energy transfer in product yields was observed for the photoactivation of perfluorocyclopropene and the photoproduction of difluoroethyne. 3 refs., 18 figs., 4 tabs.

  16. 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.

  17. Cobalt complex of cinchonine: intermolecular interactions in two crystalline modifications.

    PubMed

    Skórska, Agnieszka; Oleksyn, Barbara J; Sliwiński, Jan

    2002-01-01

    Two crystalline modifications of cinchonine cobalt complex, C19H23Cl3CoN2O, were obtained from mixture of saturated alcohol solutions of CoCl3 x 6H2O and cinchonine. The X-ray structure analysis revealed that the asymmetric unit of one modification, CoCn1, contains only zwitterionic molecules of the complex. In the asymmetric unit of the other, CoCn2, there are two molecules of the title compound and two molecules of ethanol. The influence of the absolute configuration, the CoCl3 coordination with quinoline, and the presence of alcohol molecules on the studied structures was established by comparison of the crystal and molecular structures of both cobalt complexes with the analogous quinine complex and zinc complex of cinchonine. The interactions that dominate in the packing of the molecules in both structures are intermolecular hydrogen bonds. They form characteristic ring systems, depending on the presence of the alcohol molecules. The ring features are also related to the absolute configuration of the alkaloid.

  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. 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

    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.

  1. Cantilevered probe detector with piezoelectric element

    DOEpatents

    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.

  2. Cantilevered probe detector with piezoelectric element

    DOEpatents

    Adams, Jesse D [Reno, NV; Sulchek, Todd A [Oakland, CA; Feigin, Stuart C [Reno, NV

    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. 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,…

  4. A surface enhanced Raman scattering quantitative analytical platform for detection of trace Cu coupled the catalytic reaction and gold nanoparticle aggregation with label-free Victoria blue B molecular probe.

    PubMed

    Li, Chongning; Ouyang, Huixiang; Tang, Xueping; Wen, Guiqing; Liang, Aihui; Jiang, Zhiliang

    2017-01-15

    With development of economy and society, there is an urgent need to develop convenient and sensitive methods for detection of Cu(2+) pollution in water. In this article, a simple and sensitive SERS sensor was proposed to quantitative analysis of trace Cu(2+) in water. The SERS sensor platform was prepared a common gold nanoparticle (AuNP)-SiO2 sol substrate platform by adsorbing HSA, coupling with the catalytic reaction of Cu(2+)-ascorbic acid (H2A)-dissolved oxygen, and using label-free Victoria blue B (VBB) as SERS molecular probes. The SERS sensor platform response to the AuNP aggregations by hydroxyl radicals (•OH) oxidizing from the Cu(2+) catalytic reaction, which caused the SERS signal enhancement. Therefore, by monitoring the increase of SERS signal, Cu(2+) in water can be determined accurately. The results show that the SERS sensor platforms owns a linear response with a range from 0.025 to 25μmol/L Cu(2+), and with a detection limit of 0.008μmol/L. In addition, the SERS method demonstrated good specificity for Cu(2+), which can determined accurately trace Cu(2+) in water samples, and good recovery and accuracy are obtained for the water samples. With its high selectivity and good accuracy, the sensitive SERS quantitative analysis method is expected to be a promising candidate for determining copper ions in environmental monitoring and food safety.

  5. Scanning probe microscopy of biomedical interfaces

    NASA Astrophysics Data System (ADS)

    Vansteenkiste, S. O.; Davies, M. C.; Roberts, C. J.; Tendler, S. J. B.; Williams, P. M.

    1998-02-01

    The development of the scanning probe microscopes over the past decade has provided a number of exciting new surface analytical techniques making a significant progress in the characterisation of biomedical interfaces. In this review, several examples are presented to illustrate that SPM is a powerful and promising tool for surface investigations including biomolecules, cell membranes, polymers and even living cells. The ability of the SPM instrument to monitor adhesion phenomena and provide quantitative information about intermolecular interactions is also described. Moreover, the huge potential of the scanning probe microscopes to study dynamic processes at interfaces under nearly physiological conditions is highlighted. Novel applications in the field of biochemistry, microbiology, biomaterial engineering, drug delivery and even medicine are discussed.

  6. Temperature averaging thermal probe

    NASA Technical Reports Server (NTRS)

    Kalil, L. F.; Reinhardt, V. (Inventor)

    1985-01-01

    A thermal probe to average temperature fluctuations over a prolonged period was formed with a temperature sensor embedded inside a solid object of a thermally conducting material. The solid object is held in a position equidistantly spaced apart from the interior surfaces of a closed housing by a mount made of a thermally insulating material. The housing is sealed to trap a vacuum or mass of air inside and thereby prevent transfer of heat directly between the environment outside of the housing and the solid object. Electrical leads couple the temperature sensor with a connector on the outside of the housing. Other solid objects of different sizes and materials may be substituted for the cylindrically-shaped object to vary the time constant of the probe.

  7. Temperature averaging thermal probe

    NASA Astrophysics Data System (ADS)

    Kalil, L. F.; Reinhardt, V.

    1985-12-01

    A thermal probe to average temperature fluctuations over a prolonged period was formed with a temperature sensor embedded inside a solid object of a thermally conducting material. The solid object is held in a position equidistantly spaced apart from the interior surfaces of a closed housing by a mount made of a thermally insulating material. The housing is sealed to trap a vacuum or mass of air inside and thereby prevent transfer of heat directly between the environment outside of the housing and the solid object. Electrical leads couple the temperature sensor with a connector on the outside of the housing. Other solid objects of different sizes and materials may be substituted for the cylindrically-shaped object to vary the time constant of the probe.

  8. Interplay between intramolecular and intermolecular structures of 1,1,2,2-tetrachloro-1,2-difluoroethane

    NASA Astrophysics Data System (ADS)

    Rovira-Esteva, M.; Murugan, N. A.; Pardo, L. C.; Busch, S.; Tamarit, J. Ll.; Pothoczki, Sz.; Cuello, G. J.; Bermejo, F. J.

    2011-08-01

    We report on the interplay between the short-range order of molecules in the liquid phase of 1,1,2,2-tetrachloro-1,2-difluoroethane and the possible molecular conformations, trans and gauche. Two complementary approaches have been used to get a comprehensive picture: analysis of neutron-diffraction data by a Bayesian fit algorithm and a molecular dynamics simulation. The results of both show that the population of trans and gauche conformers in the liquid state can only correspond to the gauche conformer being more stable than the trans conformer. Distinct conformer geometries induce distinct molecular short-range orders around them, suggesting that a deep intra- and intermolecular interaction coupling is energetically favoring one of the conformers by reducing the total molecular free energy.

  9. Intermolecular vibrations and vibrational dynamics of a phenol⋯methanol binary complex studied by LIF spectroscopy

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Deb Pratim; Biswas, Souvick; Chakraborty, Tapas

    2017-04-01

    Low-frequency intermolecular vibrations in S0 and S1 states of p-fluorophenol (pFP) methanol binary complex have been studied using laser induced fluorescence (LIF) spectroscopy in a supersonic jet expansion. Vibrational fundamentals of five such modes show up in fluorescence excitation (FE) spectrum, and corresponding ground state frequencies are obtained measuring disperse fluorescence (DF) spectra. Signatures of strong coupling between the hydrogen bond stretching fundamental (σ01) and a ring mode of pFP moiety in S1 state are revealed. In comparison with the analogous pFP-water complex, the present system displays very low threshold (∼170 cm-1) for vibrational energy relaxation in S1 state.

  10. 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.

  11. The effect of the intermolecular potential formulation on the state-selected energy exchange rate coefficients in N2-N2 collisions.

    PubMed

    Kurnosov, Alexander; Cacciatore, Mario; Laganà, Antonio; Pirani, Fernando; Bartolomei, Massimiliano; Garcia, Ernesto

    2014-04-05

    The rate coefficients for N2-N2 collision-induced vibrational energy exchange (important for the enhancement of several modern innovative technologies) have been computed over a wide range of temperature. Potential energy surfaces based on different formulations of the intramolecular and intermolecular components of the interaction have been used to compute quasiclassically and semiclassically some vibrational to vibrational energy transfer rate coefficients. Related outcomes have been rationalized in terms of state-to-state probabilities and cross sections for quasi-resonant transitions and deexcitations from the first excited vibrational level (for which experimental information are available). On this ground, it has been possible to spot critical differences on the vibrational energy exchange mechanisms supported by the different surfaces (mainly by their intermolecular components) in the low collision energy regime, though still effective for temperatures as high as 10,000 K. It was found, in particular, that the most recently proposed intermolecular potential becomes the most effective in promoting vibrational energy exchange near threshold temperatures and has a behavior opposite to the previously proposed one when varying the coupling of vibration with the other degrees of freedom.

  12. 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.

  13. Competing intermolecular interactions in some 'bridge-flipped' isomeric phenylhydrazones.

    PubMed

    Ojala, William H; Arola, Trina M; Brigino, Ann M; Leavell, Jeremy D; Ojala, Charles R

    2012-07-01

    To examine the roles of competing intermolecular interactions in differentiating the molecular packing arrangements of some isomeric phenylhydrazones from each other, the crystal structures of five nitrile-halogen substituted phenylhydrazones and two nitro-halogen substituted phenylhydrazones have been determined and are described here: (E)-4-cyanobenzaldehyde 4-chlorophenylhydrazone, C(14)H(10)ClN(3), (Ia); (E)-4-cyanobenzaldehyde 4-bromophenylhydrazone, C(14)H(10)BrN(3), (Ib); (E)-4-cyanobenzaldehyde 4-iodophenylhydrazone, C(14)H(10)IN(3), (Ic); (E)-4-bromobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)BrN(3), (IIb); (E)-4-iodobenzaldehyde 4-cyanophenylhydrazone, C(14)H(10)IN(3), (IIc); (E)-4-chlorobenzaldehyde 4-nitrophenylhydrazone, C(13)H(10)ClN(3)O(2), (III); and (E)-4-nitrobenzaldehyde 4-chlorophenylhydrazone, C(13)H(10)ClN(3)O(2), (IV). Both (Ia) and (Ib) are disordered (less than 7% of the molecules have the minor orientation in each structure). Pairs (Ia)/(Ib) and (IIb)/(IIc), related by a halogen exchange, are isomorphous, but none of the 'bridge-flipped' isomeric pairs, viz. (Ib)/(IIb), (Ic)/(IIc) or (III)/(IV), is isomorphous. In the nitrile-halogen structures (Ia)-(Ic) and (IIb)-(IIc), only the bridge N-H group and not the bridge C-H group acts as a hydrogen-bond donor to the nitrile group, but in the nitro-halogen structures (III) (with Z' = 2) and (IV), both the bridge N-H group and the bridge C-H group interact with the nitro group as hydrogen-bond donors, albeit via different motifs. The occurrence here of the bridge C-H contact with a hydrogen-bond acceptor suggests the possibility that other pairs of `bridge-flipped' isomeric phenylhydrazones may prove to be isomorphous, regardless of the change from isomer to isomer in the position of the N-H group within the bridge.

  14. Hydrogen-Bonding Polarizable Intermolecular Potential Model for Water.

    PubMed

    Jiang, Hao; Moultos, Othonas A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2016-12-08

    A polarizable intermolecular potential model with short-range directional hydrogen-bonding interactions was developed for water. The model has a rigid geometry, with bond lengths and angles set to experimental gas-phase values. Dispersion interactions are represented by the Buckingham potential assigned to the oxygen atom, whereas electrostatic interactions are modeled by Gaussian charges. Polarization is handled by a Drude oscillator site, using a negative Gaussian charge attached to the oxygen atom by a harmonic spring. An explicit hydrogen-bonding term is included in the model to account for the effects of charge transfer. The model parameters were optimized to density, configurational energy, pair correlation function, and the dielectric constant of water under ambient conditions, as well as the minimum gas-phase dimer energy. Molecular dynamics and Gibbs ensemble Monte Carlo simulations were performed to evaluate the new model with respect to the thermodynamic and transport properties over a wide range of temperature and pressure conditions. Good agreement between model predictions and experimental data was found for most of the properties studied. The new model yields better performance relative to the majority of existing models and outperforms the BK3 model, which is one of the best polarizable models, for vapor-liquid equilibrium properties, whereas the new model is not better than the BK3 model for representation of other properties. The model can be efficiently simulated with the thermalized Drude oscillator algorithm, resulting in computational costs only 3 times higher than those of the nonpolarizable TIP4P/2005 model, whereas having significantly improved properties. Because it involves only a single Drude oscillator site, the new model is significantly faster than polarizable models with multiple sites. With the explicit inclusion of hydrogen-bond interactions, the model may provide a better description of the phase behavior of aqueous mixtures.

  15. Intermolecular Forces in Introductory Chemistry Studied by Gas Chromatography, Computer Models, and Viscometry

    NASA Astrophysics Data System (ADS)

    Wedvik, Jonathan C.; McManaman, Charity; Anderson, Janet S.; Carroll, Mary K.

    1998-07-01

    An experiment on intermolecular forces for first-term introductory college chemistry is presented. The experiment integrates traditional viscometry-based measurements with modern chromatographic analysis and use of computer-based molecular models. Students performing gas chromatographic (GC) analyses of mixtures of n-alkanes and samples that simulate crime scene evidence discover that liquid mixtures can be separated rapidly into their components based upon intermolecular forces. Each group of students is given a liquid sample that simulates one collected at an arson scene, and the group is required to determine the identity of the accelerant. Students also examine computer models to better visualize how molecular structure affects intermolecular forces: London forces, dipole-dipole interactions, and hydrogen bonding. The relative viscosities of organic liquids are also measured to relate physical properties to intermolecular forces.

  16. The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding: phosphorylated azoles.

    PubMed

    Chernyshev, Kirill A; Larina, Ludmila I; Chirkina, Elena A; Krivdin, Leonid B

    2012-02-01

    The effects of intramolecular and intermolecular coordination on (31)P nuclear shielding have been investigated in the series of tetracoordinated, pentacoordinated and hexacoordinated N-vinylpyrazoles and intermolecular complexes of N-vinylimidazole and 1-allyl-3,5-dimethylpyrazole with phosphorous pentachloride both experimentally and theoretically. It was shown that either intramolecular or intermolecular coordination involving phosphorous results in a dramatic (31)P nuclear shielding amounting to approximately 150 ppm on changing the phosphorous coordination number by one. A major importance of solvent effects on (31)P nuclear shielding of intramolecular and intermolecular complexes involving N → P coordination bond has been demonstrated. It was found that the zeroth-order regular approximation-gauge-including atomic orbital-B1PW91/DZP method was sufficiently accurate for the calculation of (31)P NMR chemical shifts, provided relativistic corrections are taken into account, the latter being of crucial importance in the description of (31)P nuclear shielding.

  17. 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)....

  18. 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)

  19. 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.

  20. 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.

  1. 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.

  2. Intermolecular forces and scaling relations between heterogeneous macromolecular surfaces

    NASA Astrophysics Data System (ADS)

    Rosenberg, Kenneth J.

    Most theories regarding the behavior of intermolecular forces assume perfectly smooth surfaces with well-defined chemical and material properties. In this thesis, three separate systems are studied to explore the accuracy of this assumption in very different situations. In the first system, the effects of milli-molar amounts of dissolved gas (the amount typically present in normal atmospheric conditions) have been studied at a pristine oil/water interface. It was found that the removal of the dissolved gas significantly increased the lifetime of the oil droplets, effectively reducing the long-range hydrophobic attractive force present under standard conditions. In the second system, the effect of varying normal and lateral roughness of solid surfaces in understanding the long-range steric forces and shorter-range adhesive (van der Waals) forces are studied. Various techniques to reproducibly control and vary the roughness were developed for a number of different types of polymeric surfaces. A strong correlation between the roughness and the repulsive steric force was observed for randomly rough surfaces. Similar scaling relations between the roughness and the magnitude of the adhesive force were measured. Friction measurements between these surfaces show that even a few nanometers of roughness significantly reduces the critical shear stress required to initiate sliding. However, the coefficient of friction was relatively unaffected by the range of roughness considered, in agreement with the macroscopic Amontons' law. The third and final system dealt with the properties of adsorbed layers of polyampholytes (containing both positively and negatively charged groups), as opposed to the more common classes of neutral polymers or polyelectrolytes. These measurements took advantage of a naturally occurring family of proteins (a class of polyampholytes), known as tau, which exist in six different well-defined lengths and charge densities. Force measurements were made with

  3. Interatomic and intermolecular Coulombic decay: the coming of age story

    NASA Astrophysics Data System (ADS)

    Jahnke, T.

    2015-04-01

    In pioneering work by Cederbaum et al an excitation mechanism was proposed that occurs only in loosely bound matter (Cederbaum et al 1997 Phys. Rev. Lett. 79 4778): it turned out, that (in particular) in cases where a local Auger decay is energetically forbidden, an excited atom or molecule is able to decay in a scheme which was termed ‘interatomic Coulombic decay’ (or ‘intermolecular Coulombic decay’) (ICD). As ICD occurs, the excitation energy is released by transferring it to an atomic or molecular neighbor of the initially excited particle. As a consequence the neighboring atom or molecule is ionized as it receives the energy. A few years later the existence of ICD was confirmed experimentally (Marburger et al 2003 Phys. Rev. Lett. 90 203401; Jahnke et al 2004 Phys. Rev. Lett. 93 163401; Öhrwall et al 2004 Phys. Rev. Lett. 93 173401) by different techniques. Since this time it has been found that ICD is not (as initially suspected) an exotic feature of van der Waals or hydrogen bonded systems, but that ICD is a very general and common feature occurring after a manifold of excitation schemes and in numerous weakly bound systems, as revealed by more than 200 publications. It was even demonstrated, that ICD can become more efficient than a local Auger decay in some system. This review will concentrate on recent experimental investigations on ICD. It will briefly introduce the phenomenon and give a short summary of the ‘early years’ of ICD (a detailed view on this episode of investigations can be found in the review article by U Hergenhahn with the same title (Hergenhahn 2011 J. Electron Spectrosc. Relat. Phenom. 184 78)). More recent articles will be presented that investigate the relevance of ICD in biological systems and possible radiation damage of such systems due to ICD. The occurrence of ICD and ICD-like processes after different excitation schemes and in different systems is covered in the middle section: in that context the helium dimer (He2

  4. 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.

  5. Palladium-catalyzed Heck-type cross-couplings of unactivated alkyl iodides.

    PubMed

    McMahon, Caitlin M; Alexanian, Erik J

    2014-06-02

    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.

  6. Theoretical analysis of anharmonic coupling and cascading Raman signals observed with femtosecond stimulated Raman spectroscopy.

    PubMed

    Mehlenbacher, Randy D; Lyons, Brendon; Wilson, Kristina C; Du, Yong; McCamant, David W

    2009-12-28

    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 approximately 10(-4) DeltaOD (change in the optical density). The cascading signals, however, will produce stimulated Raman signal of approximately 10(-2) DeltaOD, as has been observed experimentally. Experiments probing deuterochloroform find significant sidebands of the CCl(3) bend, which has an E type symmetry, shifted from the A(1) 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 CDCl(3) modes as sidebands shifted from both the C

  7. Generalized spin-ratio scaled MP2 method for accurate prediction of intermolecular interactions for neutral and ionic species

    NASA Astrophysics Data System (ADS)

    Tan, Samuel; Barrera Acevedo, Santiago; Izgorodina, Ekaterina I.

    2017-02-01

    The accurate calculation of intermolecular interactions is important to our understanding of properties in large molecular systems. The high computational cost of the current "gold standard" method, coupled cluster with singles and doubles and perturbative triples (CCSD(T), limits its application to small- to medium-sized systems. Second-order Møller-Plesset perturbation (MP2) theory is a cheaper alternative for larger systems, although at the expense of its decreased accuracy, especially when treating van der Waals complexes. In this study, a new modification of the spin-component scaled MP2 method was proposed for a wide range of intermolecular complexes including two well-known datasets, S22 and S66, and a large dataset of ionic liquids consisting of 174 single ion pairs, IL174. It was found that the spin ratio, ɛΔ s=E/INT O SEIN T S S , calculated as the ratio of the opposite-spin component to the same-spin component of the interaction correlation energy fell in the range of 0.1 and 1.6, in contrast to the range of 3-4 usually observed for the ratio of absolute correlation energy, ɛs=E/OSES S , in individual molecules. Scaled coefficients were found to become negative when the spin ratio fell in close proximity to 1.0, and therefore, the studied intermolecular complexes were divided into two groups: (1) complexes with ɛΔ s< 1 and (2) complexes with ɛΔ s≥ 1 . A separate set of coefficients was obtained for both groups. Exclusion of counterpoise correction during scaling was found to produce superior results due to decreased error. Among a series of Dunning's basis sets, cc-pVTZ and cc-pVQZ were found to be the best performing ones, with a mean absolute error of 1.4 kJ mol-1 and maximum errors below 6.2 kJ mol-1. The new modification, spin-ratio scaled second-order Møller-Plesset perturbation, treats both dispersion-driven and hydrogen-bonded complexes equally well, thus validating its robustness with respect to the interaction type ranging from ionic

  8. Intermolecular interactions of oligothienoacenes: Do S⋯S interactions positively contribute to crystal structures of sulfur-containing aromatic molecules?

    PubMed

    Tsuzuki, Seiji; Orita, Hideo; Sato, Naoki

    2016-11-07

    Intermolecular interactions in the crystals of tetra- and penta-thienoacene were studied using ab initio molecular orbital calculations for evaluating the magnitude of characteristic S⋯S interactions with great attention paid to their origin. The interactions between the π-stacked neighboring molecules are significantly greater than those between the neighboring molecules exhibiting the S⋯S contact, although it has sometimes been claimed that the S⋯S interactions play important roles in adjusting the molecular arrangement of sulfur-containing polycyclic aromatic molecules in the crystals owing to short S⋯S contacts. The coupled cluster calculations with single and double substitutions with noniterative triple excitation interaction energies at the basis set limit estimated for the π-stacked and S⋯S contacted neighboring molecules in the tetrathienoacene crystal are -11.17 and -4.27 kcal/mol, respectively. Those for π-stacked molecules in the pentathienoacene crystal is -14.38 kcal/mol, while those for S⋯S contacted molecules are -7.02 and -6.74 kcal/mol. The dispersion interaction is the major source of the attraction between the π-stacked and S⋯S contacted molecules, while the orbital-orbital interactions are repulsive: The orbital-orbital interactions, which are significant for charge carrier transport properties, are not much more than the results of the short S⋯S contact caused by the strong dispersion interactions. Besides, the intermolecular interaction energy calculated for a trithienoacene dimer has strong orientation dependence.

  9. 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.

  10. Asymmetric Palladium-Catalyzed Directed Intermolecular Fluoroarylation of Styrenes

    PubMed Central

    2015-01-01

    A mild catalytic asymmetric direct fluoro-arylation of styrenes has been developed. The palladium-catalyzed three-component coupling of Selectfluor, a styrene and a boronic acid, provides chiral monofluorinated compounds in good yield and in high enantiomeric excess. A mechanism proceeding through a Pd(IV)-fluoride intermediate is proposed for the transformation and synthesis of an sp3 C–F bond. PMID:24617344

  11. Localization of the dominant non-enzymatic intermolecular cross-linking sites on fibrous collagen.

    PubMed

    Chiue, Hiroko; Yamazoye, Tsutako; Matsumura, Sueo

    2015-06-05

    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.

  12. Definition and computation of intermolecular contact in liquids using additively weighted Voronoi tessellation.

    PubMed

    Isele-Holder, Rolf E; Rabideau, Brooks D; Ismail, Ahmed E

    2012-05-10

    We present a definition of intermolecular surface contact by applying weighted Voronoi tessellations to configurations of various organic liquids and water obtained from molecular dynamics simulations. This definition of surface contact is used to link the COSMO-RS model and molecular dynamics simulations. We demonstrate that additively weighted tessellation is the superior tessellation type to define intermolecular surface contact. Furthermore, we fit a set of weights for the elements C, H, O, N, F, and S for this tessellation type to obtain optimal agreement between the models. We use these radii to successfully predict contact statistics for compounds that were excluded from the fit and mixtures. The observed agreement between contact statistics from COSMO-RS and molecular dynamics simulations confirms the capability of the presented method to describe intermolecular contact. Furthermore, we observe that increasing polarity of the surfaces of the examined molecules leads to weaker agreement in the contact statistics. This is especially pronounced for pure water.

  13. Analysis of hypersonic nozzles including vibrational nonequilibrium and intermolecular force effects

    NASA Technical Reports Server (NTRS)

    Canupp, Patrick W.; Candler, Graham V.; Perkins, John N.; Erickson, Wayne D.

    1992-01-01

    A computational fluid dynamics algorithm is developed for the study of high-pressure axisymmetric hypersonic nozzle flows. The effects of intermolecular forces and vibrational nonequilibrium are included in the analysis. The numerical simulation of gases with an arbitrary equation of state is discussed. Simulations for a high pressure nozzle (p(0) = 138 MPa) demonstrate that both intermolecular forces and vibrational nonequilibrium have a significant affect on the flow. These nonideal effects tend to increase the Mach number at the nozzle exit plane. Thus, they must be included in the design and analysis of high pressure hypersonic nozzles.

  14. Experimental and computational investigation of intermolecular interactions in cyclopentanone with methanol mixture

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Feng; Huang, Rong-Yi; Wang, Jun-Wei; Geng, Tong-Mou; Zhao, Shun-Ping; Wu, Gen-Hua

    2014-09-01

    In this Letter, excess molar volumes, refractive index deviations, Raman spectra and quantum-chemical calculations have been used to explore the underlying intermolecular interactions in the binary mixture containing cyclopentanone (CPN) and methanol. The experimental data reveal that the 1:1 (Ia) and 1:2 (Ib) cross-associations between CPN and methanol are formed in the studied binary mixture. This result has been further corroborated via theoretical calculations. In addition, the observed 1747 and 1732 cm-1 bands can be assigned to the Cdbnd O stretching vibrations of the intermolecular cross-associations Ia and Ib, respectively, in distinct contradiction with the previous explanations.

  15. Intermolecular associations in an equimolar formamide-water solution based on neutron scattering and DFT calculations.

    PubMed

    Abdelmoulahi, Hafedh; Ghalla, Houcine; Nasr, Salah; Darpentigny, Jacques; Bellissent-Funel, Marie-Claire

    2016-10-07

    In the present work, we have investigated the intermolecular associations of formamide with water in an equimolar formamide-water solution (FA-Water) by means of neutron scattering in combination with density functional theory calculations. The neutron scattering data were analyzed to deduce the structure factor SM(q) and the intermolecular pair correlation function gL(r). By considering different hydrogen bonded FA-Water associations, it has been shown that some of them describe well the local order in the solution. Natural bond orbital and atoms in molecules analyses have been performed to give more insight into the properties of hydrogen bonds involved in the more probable models.

  16. 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.

  17. Virtual photon exchange, intermolecular interactions and optical response functions

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2015-11-01

    According to molecular quantum electrodynamics, coupling between material particles occurs due to an exchange of one or more virtual photons. In this work, the relationship between polarisability and hyperpolarisability tensors of atoms and molecules that feature in linear and nonlinear optical processes, and their analytically continued form in the complex frequency domain that appear in formulae describing fundamental inter-particle interactions, is studied. Examples involving a single virtual photon exchange, which are linearly proportional to electric dipole moments at each centre, include the electrostatic energy and the resonant transfer of excitation energy. The Casimir-Polder dispersion potential, and its discriminatory counterpart applicable to coupled chiral molecules, are used to illustrate response properties depending on the exchange of two virtual photons. Meanwhile, the energy shift between two hyperpolarisable species, a higher order discriminatory contribution to the dispersion potential, is employed to represent forces arising from the three virtual photon exchange. It is shown that for energy shifts that are quadratic or bilinear or cubic in the transition dipole moment, it is necessary to account for all two- and three-photon optical processes, such as absorption, emission and linear and nonlinear scattering of light in order to arrive at the correct form of the molecular response tensor.

  18. Two-dimensional infrared spectroscopy of intermolecular hydrogen bonds in the condensed phase.

    PubMed

    Elsaesser, Thomas

    2009-09-15

    Hydrogen bonding plays a key role in the structural, physical, and chemical properties of liquids such as water and in macromolecular structures such as proteins. Vibrational spectroscopy is an important tool for understanding hydrogen bonding because it provides a way to observe local molecular geometries and their interaction with the environment. Linear vibrational spectroscopy has mapped characteristic changes of vibrational spectra and the occurrence of new bands that form upon hydrogen bonding. However, linear vibrational spectroscopy gives very limited insight into ultrafast dynamics of the underlying molecular interactions, such as the motions of hydrogen-bonded groups, energy dissipation and delocalization, and the fluctuations within hydrogen-bonded structures that occur in the ultrafast time domain. Nonlinear vibrational spectroscopy with its femtosecond time resolution can discern these dynamic processes in real time and has emerged as an important tool for unraveling molecular dynamics and for quantifying interactions that govern the vibrational and structural dynamics of hydrogen bonds. This Account reviews recent progress originating from third-order nonlinear methods of coherent multidimensional vibrational spectroscopy. Ultrafast dynamics of intermolecular hydrogen bonds are addressed for a number of prototype systems: hydrogen-bonded carboxylic acid dimers in an aprotic liquid environment, the disordered fluctuating hydrogen-bond network of liquid water, and DNA oligomers interacting with water. Cyclic carboxylic acid dimers display a rich scheme of vibrational couplings, resulting in OH stretching absorption bands with highly complex spectral envelopes. Two-dimensional spectroscopy of acetic acid dimers in a nonpolar liquid environment demonstrates that multiple Fermi resonances of the OH stretching mode with overtones and combination tones of fingerprint vibrations dominate both the 2D and linear absorption spectra. The coupling of the OH

  19. Microfluidic multifunctional probe array dielectrophoretic force spectroscopy with wide loading rates.

    PubMed

    Park, In Soo; Eom, Kilho; Son, Jongsang; Chang, Woo-Jin; Park, Kidong; Kwon, Taeyun; Yoon, Dae Sung; Bashir, Rashid; Lee, Sang Woo

    2012-10-23

    The simultaneous investigation of a large number of events with different types of intermolecular interactions, from nonequilibrium high-force pulling assays to quasi-equilibrium unbinding events in the same environment, can be very important for fully understanding intermolecular bond-rupture mechanisms. Here, we describe a novel dielectrophoretic force spectroscopy technique that utilizes microsized beads as multifunctional probes for parallel measurement of intermolecular forces with an extremely wide range of force rate (10(-4) to 10(4) pN/s) inside a microfluidic device. In our experiments, various forces, which broadly form the basis of all molecular interactions, were measured across a range of force loading rates by multifunctional probes of various diameters with a throughput of over 600 events per mm(2), simultaneously and in the same environment. Furthermore, the individual bond-rupture forces, the parameters for the characterization of entire energy landscapes, and the effective stiffness of the force spectroscopy were determined on the basis of the measured results. This method of determining intermolecular forces could be very useful for the precise and simultaneous examination of various molecular interactions, as it can be easily and cost-effectively implemented within a microfluidic device for a range of applications including immunoassays, molecular mechanics, chemical and biological screening, and mechanobiology.

  20. 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.

  1. 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.

  2. 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.

  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 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.

  5. Intermolecular electronic interactions in the primary charge separation in bacterial photosynthesis

    SciTech Connect

    Plato, M.; Moebius, K.; Michel-Beyerle, M.E.; Bixon, M.; Jortner, J. )

    1988-10-26

    In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state ({sup 1}P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B{sup {minus}} and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer integrals for B{sub L}{sup {minus}}H{sub L}{sup {minus}}B{sub L}H{sub L}{minus} and for B{sub M}{sup {minus}}H{sub M}{minus}B{sub M}H{sub M}{sup {minus}} was calculated to be 2.1 {plus minus} 0.5, which together with the value of 2.8 {plus minus} 0.7 for the ratio of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for {sup 1}P*B{sub M}-P{sup +}B{sub M}- results in the electronic contribution of 33 {plus minus} 16 to the ratio k{sub L}/k{sub m} of the rate constants k{sub L} and k{sub M} for the primary charge separation across the L and M branches of the RC, respectively. The asymmetry of the electronic coupling terms, which originates from the combination of the asymmetry in the charge distribution of {sup 1}P* and of structural asymmetry of the P-M and B-H arrangements across the L and M subunits, provides a major contribution to the unidirectionality of the charge separation in bacterial photosynthesis. A significant contribution to the transfer integrals between adjacent pigments originates from nearby methyl groups through hyperconjugation. The ratio 6 {plus minus} 2 of the transfer integrals for {sup 1}P*B{sub L}-P{sup +}B{sub L}- and for B{sub L}-H{sub L}-B{sub L}H{sub L}- was utilized to estimate the energetic parameters required to ensure the dominance of the superexchange mediated unistep electron transfer {sup 1}P*BH {yields} P{sup +}BH{sup {minus}} over the thermally activated {sup 1}P*B {yields} P{sup +}B{sup {minus}} process. 31 refs., 6 figs., 2 tabs.

  6. Selective intermolecular amination of C-H bonds at tertiary carbon centers.

    PubMed

    Roizen, Jennifer L; Zalatan, David N; Du Bois, J

    2013-10-18

    C-H insertion: A method for intermolecular amination of tertiary CH bonds is described that uses limiting amounts of substrate and a convenient phenol-derived nitrogen source. Structure-selectivity and mechanistic studies suggest that steric interaction between the substrate and active oxidant is the principal determinant of product selectivity.

  7. 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…

  8. The B-box module of CYLD is responsible for its intermolecular interaction and cytoplasmic localization.

    PubMed

    Xie, Songbo; Chen, Miao; Gao, Siqi; Zhong, Tao; Zhou, Peng; Li, Dengwen; Zhou, Jun; Gao, Jinmin; Liu, Min

    2017-02-07

    The tumor suppressor protein cylindromatosis (CYLD), as a microtubule-associated deubiquitinase, plays a pivotal role in a wide range of cellular activities, including innate immunity, cell division, and ciliogenesis. Structural characterization reveals a small zinc-binding B-box inserted within the ubiquitin specific protease (USP) domain of CYLD; however, the exact role for this module remains yet to be elucidated. Here we identify a critical role for the B-box in facilitating the intermolecular interaction and subcellular localization of CYLD. By co-immunoprecipitation assays we uncover that CYLD has the ability to form an intermolecular complex. Native gel electrophoresis analysis and pull down assays show that the USP domain of CYLD is essential for its intermolecular interaction. Further investigation reveals that deletion of the B-box from the USP domain disrupts the intermolecular interaction of CYLD. Importantly, although loss of the B-box has no obvious effect on the deubiquitinase activity of CYLD, it abolishes the USP domain-mediated retention of CYLD in the cytoplasm. Collectively, these data demonstrate an important role for the B-box module of CYLD in mediating its assembly and subcellular distribution, which might be related to the functions of CYLD in various biological processes.

  9. 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.

  10. 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…

  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. Head-to-tail intermolecular hydrogen bonding of OH and NH groups with fluoride.

    PubMed

    Ashokkumar, Pichandi; Ramakrishnan, Vayalakkavoor T; Ramamurthy, Perumal

    2011-02-07

    To explore the anion-recognition ability of the phenolic hydroxyl group and the amino hydrogen, we synthesized three different acridinedione (ADD) based anion receptors, 1, 2 and 3, having OH, NH, and combination of OH and NH groups, respectively. Absorption, emission and (1)H NMR spectral studies revealed that receptor 1, having only a phenolic OH group, shows selective deprotonation of the hydroxyl proton towards F(-), which results in an "ON-OFF"-type signal in the fluorescence spectral studies. Receptor 2, which only has an amino hydrogen, also shows deprotonation of the amino hydrogen with F(-), whereas receptor 3 (having both OH and NH groups) shows head-to-tail intermolecular hydrogen bonding of OH and NH groups with F(-) prior to deprotonation. The observation of hydrogen bonding of the OH and NH groups in a combined solution of 1 and 2 with F(-) in a head-to-tail hetero-intermolecular fashion, and the absence of head-to-head and tail-to-tail intermolecular hydrogen bonding in 1 and 2 with F(-), prove that the difference in the acidity of the OH and NH protons leads to the formation of an intermolecular hydrogen-bonding complex with F(-) prior to deprotonation. The presence of this hydrogen-bonding complex was confirmed by absorption spectroscopy, 3D emission contour studies, and (1)H NMR titration.

  13. Investigation of intermolecular interactions between fluorene-based conjugated polymers using the dispersion-corrected DFT

    NASA Astrophysics Data System (ADS)

    Ayoub, Sarah; Lagowski, Jolanta B.

    2015-03-01

    Alternating triphenylamine-fluorene, TPAFn (n=1-3), and fluorene-oxadiazole OxFn (n=1-3) conjugated copolymers are important components of novel high-efficiency multi-layer organic light-emitting diodes (OLEDs). In this work, we investigate the intermolecular interactions between the various combinations of monomers of OxFn-TPAFn (n=1-3) copolymers using the dispersion-corrected density functional theory (B97D) method. The monomer combinations are taken with and without the presence of long alkyl chains in order to study the effect of side-chains on the polymer backbone intermolecular interactions. The dispersion effect is studied by comparing the structures of the interacting monomers with those in vacuum. In addition, we calculate intermolecular distances, energy gaps and binding energies of monomer dimers corresponding to different pairings of OxFn-TPAFn (n=1-3) monomers. Our results show that the combination of OxF3-TPAF2 monomers exhibites the highest binding energy, closest intermolecular distance, and the best matching of chain lengths amongst all of the combinations of OxFn-TPAFn (n=1-3) monomers. Experiments have shown that OxF3-TPAF2 combination gives the best performance for OLEDS made of OxF-TPAF polymer layers.

  14. High-frequency intermolecular homologous recombination during herpes simplex virus-mediated plasmid DNA replication.

    PubMed

    Fu, Xinping; Wang, Hua; Zhang, Xiaoliu

    2002-06-01

    Homologous recombination is a prominent feature of herpes simplex virus (HSV) type 1 DNA replication. This has been demonstrated and traditionally studied in experimental settings where repeated sequences are present or are being introduced into a single molecule for subsequent genome isomerization. In the present study, we have designed a pair of unique HSV amplicon plasmids to examine in detail intermolecular homologous recombination (IM-HR) between these amplicon plasmids during HSV-mediated DNA replication. Our data show that IM-HR occurred at a very high frequency: up to 60% of the amplicon concatemers retrieved from virion particles underwent intermolecular homologous recombination. Such a high frequency of IM-HR required that both plasmids be replicated by HSV-mediated replication, as IM-HR events were not detected when either one or both plasmids were replicated by simian virus 40-mediated DNA replication, even with the presence of HSV infection. In addition, the majority of the homologous recombination events resulted in sequence replacement or targeted gene repair, while the minority resulted in sequence insertion. These findings imply that frequent intermolecular homologous recombination may contribute directly to HSV genome isomerization. In addition, HSV-mediated amplicon replication may be an attractive model for studying intermolecular homologous recombination mechanisms in general in a mammalian system. In this regard, the knowledge obtained from such a study may facilitate the development of better strategies for targeted gene correction for gene therapy purposes.

  15. Intermolecular Sulfur···Oxygen Interactions: Theoretical and Statistical Investigations.

    PubMed

    Zhang, Xuejin; Gong, Zhen; Li, Jian; Lu, Tao

    2015-10-26

    Intermolecular S···O interactions are very common and are important in biological systems, but until recently, the presence of these contacts in protein-ligand systems largely depended on serendipitous discovery instead of rational design. Here we provide insight into the phenomenon of intermolecular S···O contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the S···O interactions and to determine their energy dependence on their geometric parameters. Protein Data Bank mining is performed to systematically determine the occurrence and geometry of intermolecular S···O interactions, and several representative examples are discussed. Three typical cases are investigated using a combined quantum mechanics/molecular mechanics approach to demonstrate the potential of these interactions in improving binding affinities and physiochemical properties. Overall, our work elucidates the structures and energy features of intermolecular S···O interactions and addresses their use in molecular design.

  16. Ultrasonic and IR study of intermolecular association through hydrogen bonding in ternary liquid mixtures.

    PubMed

    Awasthi, Aashees; Shukla, J P

    2003-08-01

    Complex formation in ternary liquid mixtures of dimethylsulfoxide (DMSO) with phenol and o-cresol in carbontetrachloride has been studied by measuring ultrasonic velocity at 2 MHz, in the concentration range of 0.019-0.162 (in mole fraction of DMSO) at varying temperatures of 20, 30 and 40 degrees C. Using measured values of ultrasonic velocity, other parameters such as adiabatic compressibility, intermolecular free length, molar sound velocity, molar compressibility, specific acoustic impedance and molar volume have been evaluated. These parameters have been utilized to study the solute-solute interactions in these systems. The ultrasonic velocity shows a maxima and adiabatic compressibility a corresponding minima as a function of concentration for these mixtures. The results indicate the occurrence of complex formation between unlike molecules through intermolecular hydrogen bonding between oxygen atom of DMSO molecule and hydrogen atom of phenol and o-cresol molecules. The excess values of adiabatic compressibility and intermolecular free length have also been evaluated. The variation of both these parameters with concentration also indicates the possibility of the complex formation in these systems. Further, to investigate the presence of O-HO bond complexes and the strength of molecular association with concentrations, the infrared spectra of both the systems, DMSO-phenol and DMSO-o-cresol, have been recorded for various concentrations at room temperature (20 degrees C). The results obtained using infrared spectroscopy for both the systems also support the occurrence of complex formation through intermolecular hydrogen bonding in these ternary liquid mixtures.

  17. 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…

  18. 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

  19. 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.

  20. Characterization of qubit chains by Feynman probes

    NASA Astrophysics Data System (ADS)

    Tamascelli, Dario; Benedetti, Claudia; Olivares, Stefano; Paris, Matteo G. A.

    2016-10-01

    We address the characterization of qubit chains and assess the performances of local measurements compared to those provided by Feynman probes, i.e., nonlocal measurements realized by coupling a single-qubit register to the chain. We show that local measurements are suitable to estimate small values of the coupling and that a Bayesian strategy may be successfully exploited to achieve optimal precision. For larger values of the coupling Bayesian local strategies do not lead to a consistent estimate. In this regime, Feynman probes may be exploited to build a consistent Bayesian estimator that saturates the Cramér-Rao bound, thus providing an effective characterization of the chain. Finally, we show that ultimate bounds to precision, i.e., saturation of the quantum Cramér-Rao bound, may be achieved by a two-step scheme employing Feynman probes followed by local measurements.

  1. 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.

  2. 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.

  3. Dynamical Response of Continuum Regime Langmuir Probe

    NASA Astrophysics Data System (ADS)

    Rappaport, H. L.

    2009-11-01

    Probe dynamic response is sometimes used as a way to increase the amount of information obtained from Langmuir probes [1]. In this poster, the effects of frequency dependent probe capacitance and coupling of probe fields to damped Langmuir waves and damped ion acoustic waves are considered. In the continuum regime, with small Debye length to spherical probe radius ratio, the probe DC current vs. voltage characteristic displays a hard saturation at sufficiently large probe potential [2]. In this regime, the sheath thickness varies little with the applied voltage although the plasma response can still be measured. A goal of the present investigation is to show that the probe dynamical response is richer as a result of modulation of sheath thickness or shielding particularly in the larger Debye length to probe radius ratio regime. Inertia inhibits ion response at sufficiently high frequency and deviation from the DC characteristic is shown.[4pt] [1] D. N. Walker, R.F. Fernsler, D.D. Blackwell, and W.E. Amatucci, Phys. Plasmas 15, 123506 (2008).[0pt] [2] E. Baum and R.L. Chapkis, AIAA J. 8, 1073 (1970).

  4. 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.

  5. 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.

  6. Astrophysical Probes of Fundamental Physics

    NASA Astrophysics Data System (ADS)

    Martins, C. J. A. P.

    I review the theoretical motivation for varying fundamental couplings and discuss how these measurements can be used to constrain a number of fundamental physics scenarios that would otherwise be inacessible to experiment. As a case study I will focus on the relation between varying couplings and dark energy, and explain how varying coupling measurements can be used to probe the nature of dark energy, with important advantages over the standard methods. Assuming that the current observational evidence for varying α. and μ is correct, a several-sigma detection of dynamical dark energy is feasible within a few years, using currently operational ground-based facilities. With forthcoming instruments like CODEX, a high-accuracy reconstruction of the equation of state may be possible all the way up to redshift z ˜ 4.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. a General Transformation to Canonical Form for Potentials in Pairwise Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Walton, Jay R.; Rivera-Rivera, Luis A.; Lucchese, Robert R.; Bevan, John W.

    2015-06-01

    A generalized formulation of explicit transformations is introduced to investigate the concept of a canonical potential in both fundamental chemical and intermolecular bonding. Different classes of representative ground electronic state pairwise interatomic interactions are referenced to a single canonical potential illustrating application of explicit transformations. Specifically, accurately determined potentials of the diatomic molecules H_2, H_2^+, HF, LiH, argon dimer, and one-dimensional dissociative coordinates in Ar-HBr, OC-HF, and OC-Cl_2 are investigated throughout their bound potentials. The advantages of the current formulation for accurately evaluating equilibrium dissociation energies and a fundamentally different unified perspective on nature of intermolecular interactions will be emphasized. In particular, this canonical approach has relevance to previous assertions that there is no very fundamental distinction between van der Waals bonding and covalent bonding or for that matter hydrogen and halogen bonds.

  16. Pharmaceutical cocrystals, salts and multicomponent systems; intermolecular interactions and property based design.

    PubMed

    Berry, David J; Steed, Jonathan W

    2017-03-23

    As small molecule drugs become harder to develop and less cost effective for patient use, efficient strategies for their property improvement become increasingly important to global health initiatives. Improvements in the physical properties of Active Pharmaceutical Ingredients (APIs), without changes in the covalent chemistry, have long been possible through the application of binary component solids. This was first achieved through the use of pharmaceutical salts, within the last 10-15years with cocrystals and more recently coamorphous systems have also been consciously applied to this problem. In order to rationally discover the best multicomponent phase for drug development, intermolecular interactions need to be considered at all stages of the process. This review highlights the current thinking in this area and the state of the art in: pharmaceutical multicomponent phase design, the intermolecular interactions in these phases, the implications of these interactions on the material properties and the pharmacokinetics in a patient.

  17. Intermolecular potential and second virial coefficient of the water-nitrogen complex.

    PubMed

    Tulegenov, Akyl S; Wheatley, Richard J; Hodges, Matthew P; Harvey, Allan H

    2007-03-07

    The authors construct a rigid-body (five-dimensional) potential energy surface for the water-nitrogen complex using the systematic intermolecular potential extrapolation routine. The intermolecular potential is then extrapolated to the limit of a complete basis set. An analytic fit of this surface is obtained, and, using this, the global minimum energy is found. The minimum is located in an arrangement in which N2 is near the H atom of H2O, almost collinear with the OH bond. The best estimate of the binding energy is 441 cm-1 (1 cm-1 approximately 1.986 43x10(-23) J). The extrapolated potential is then used to calculate the second cross virial coefficient over a wide temperature range (100-3000 K). These calculated second virial coefficients are generally consistent with experimental data, but for the most part the former have smaller uncertainties.

  18. Investigation of intermolecular interactions in perylene films on Au(111) by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Ding, Li; Schulz, Philip; Farahzadi, Azadeh; Shportko, Kostiantyn V.; Wuttig, Matthias

    2012-02-01

    Intermolecular interactions in crystalline perylene films on Au(111) have been investigated by Fourier transform infrared spectroscopy. Dimer modes of vibrations are observed in the crystalline film, in contrast to the monomer modes found for isolated perylene molecules. These dimers are formed via hydrogen bonding in the sandwich herringbone structure of the crystalline α-phase. Davydov splitting of both the monomer and the dimer modes is observed due to resonance dynamic intermolecular interaction. The splitting of monomer modes into three distinct vibrations and the occurrence of the dimer modes confirm that the film crystallizes in the α phase, which is in line with the x-ray diffraction results. The frequency shift and band broadening at elevated temperature have been attributed to the cubic and quartic anharmonic interactions.

  19. 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.

  20. 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.

  1. Nucleophilic Additions to Coordinated 1,10-Phenanthroline: Intramolecular, Intermolecular, Reversible, and Irreversible.

    PubMed

    Arévalo, Rebeca; Menéndez, M Isabel; López, Ramón; Merino, Isabel; Riera, Lucía; Pérez, Julio

    2016-12-12

    KN(SiMe3 )2 reacts with [Re(CO)3 (phen)(PMe3 )]OTf via reversible addition to the phen ligand and irreversible deprotonation of the PMe3 ligand followed by intramolecular attack to phen by the deprotonated phosphane, whereas MeLi irreversibly adds to phen. The addition of MeLi has been shown to be intermolecular, unlike previously known nucleophilic additions to pyridines.

  2. 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.

  3. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.

  4. Intermolecular dynamical charge fluctuations in water: a signature of the H-bond network.

    PubMed

    Sharma, Manu; Resta, Raffaele; Car, Roberto

    2005-10-28

    We report a simulation of deuterated water using a Car-Parrinello approach based on maximally localized Wannier functions. This provides local information on the dynamics of the hydrogen-bond network and on the origin of the low-frequency infrared activity. The oscillator strength of the translational modes, peaked around approximately 200 cm-1, is anisotropic and originates from intermolecular--not intramolecular--charge fluctuations. These fluctuations are a signature of a tetrahedral hydrogen-bonding environment.

  5. A Catalytic, Brønsted Base Strategy for Intermolecular Allylic C—H Amination

    PubMed Central

    Reed, Sean A.; Mazzotti, Anthony R.; White, M. Christina

    2009-01-01

    A Brønsted base activation mode for oxidative, Pd(II)/sulfoxide catalyzed, intermolecular C—H allylic amination is reported. N,N-diisopropylethylamine was found to promote amination of unactivated terminal olefins, forming the corresponding linear allylic amine products with high levels of stereo-, regio-, and chemoselectivity. The predictable and high selectivity of this C—H oxidation method enables late-stage incorporation of nitrogen into advanced synthetic intermediates and natural products. PMID:19645492

  6. Supramolecular methods for controlling intermolecular [2+2] photocycloaddition reactions of unsaturated compounds in solutions

    NASA Astrophysics Data System (ADS)

    Ushakov, E. N.; Gromov, S. P.

    2015-08-01

    This review deals with the methods of supramolecular chemistry used for controlling the efficiency and stereoselectivity of intermolecular [2+2] photocycloaddition of olefins and other unsaturated compounds in homogeneous solutions. The best-studied methods are self-assembly through cation-macrocycle interactions, complexation with molecular templates through hydrogen bonding, and confinement of the reactants in supramolecular containers. The possibilities of using anionic templates and combined supramolecular approaches are discussed. The bibliography includes 107 references.

  7. 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

  8. Air speed and attitude probe

    NASA Technical Reports Server (NTRS)

    Baker, G. J.; Economu, M. A. (Inventor)

    1980-01-01

    An air speed and attitude probe characterized by a pivot shaft normally projected from a data boom and supported thereby for rotation about an axis of rotation coincident with the longitudinal axis of the shaft is described. The probe is a tubular body supported for angular displacement about the axis of rotation and has a fin mounted on the body for maintaining one end of the body in facing relation with relative wind and has a pair of transducers mounted in the body for providing intelligence indicative of total pressure and static pressure for use in determining air speed. A stack of potentiometers coupled with the shaft to provide intelligence indicative of aircraft attitude, and circuitry connecting the transducers and potentiometers to suitable telemetry circuits are described.

  9. The CO-Ne van der Waals complex: ab initio intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces, and second virial coefficients.

    PubMed

    Baranowska, Angelika; Fernández, Berta; Rizzo, Antonio; Jansík, Branislav

    2009-11-14

    The intermolecular potential energy, interaction induced electric dipole moment and polarizability surfaces of the CO-Ne van der Waals complex are calculated using coupled cluster methods and the d-aug-cc-pVTZ basis set extended with a set of 3s3p2d1f1g midbond functions placed in the middle of the van der Waals bond. After fitting the interaction properties to appropriate analytical functions the surfaces are further used in semiclassical calculations of the pressure, the dielectric and the refractivity second virial coefficients of the system. The interaction potential energy surface has a single minimum (-49.9952 cm(-1)), which corresponds to R = 3.383 A and theta = 79.4 degrees. The computed dielectric second virial coefficient B(epsilon) approximately -0.27 cm(6) mol(-2) around the room temperature.

  10. 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.

  11. Inter-molecular crosslinking activity is engendered by the dimeric form of transglutaminase 2.

    PubMed

    Kim, Nayeon; Lee, Won-Kyu; Lee, Seon-Hyeong; Jin, Kyeong Sik; Kim, Kyung-Hee; Lee, Younho; Song, Minsoo; Kim, Soo-Youl

    2017-03-01

    Transglutaminase 2 (TGase 2) catalyzes a crosslink between protein bound-glutamine and -lysine. We proposed the mechanism of TGase 2 activation depends on conformation change from unfolded monomer to unfolded dimer. We found that TGase 2 has temperature-sensitive conformation change system at 30 °C. Small-angle X-ray scattering analysis showed that the enzyme was maintained as an unfolded monomer at temperatures below 30 °C, but changed to an unfolded dimer at over 30 °C. Mass analysis revealed that the C-terminus of TGase 2 was the critical region for dimerization. Furthermore, this conformational switch creates new biochemical reactivity that catalyzed inter-molecular crosslink at above 30 °C as an unfolded dimer of TGase 2 while catalyzed intra-molecular crosslink at below 30 °C as an unfolded monomer of TGase 2. The mechanism of TGase 2 activation depends on temperature-sensitive conformation change from unfolded monomer to unfolded dimer at over 30 °C. Furthermore, inter-molecular crosslinking activity is generated by the dimeric form of TGase 2. TGase 2 switches its conformation from a monomer to a dimer following a change in temperature, which engendered unique catalytic function of enzyme as inter-molecular crosslinking activity with calcium.

  12. 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.

  13. 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.

  14. 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

  15. Intermolecular disintegration and intramolecular strand transfer activities of wild-type and mutant HIV-1 integrase.

    PubMed Central

    Mazumder, A; Engelman, A; Craigie, R; Fesen, M; Pommier, Y

    1994-01-01

    We report the activities of HIV integrase protein on a novel DNA substrate, consisting of a pair of gapped duplex molecules. Integrase catalyzed an intermolecular disintegration reaction that requires positioning of a pair of the gapped duplexes in a configuration that resembles the intgration intermediate. However, the major reaction resulted from an intramolecular reaction involving a single gapped duplex, giving rise to a hairpin. Surprisingly, a deletion mutant of integrase that lacks both the amino and carboxyl terminal regions still catalyzed the intermolecular disintegration reaction, but supported only a very low level of the intramolecular reaction. The central core region of integrase is therefore sufficient to both bind the gapped duplex DNA and juxtapose a pair of such molecules through protein-protein interactions. We suggest that the branched DNA structures of the previously reported disintegration substrate, and the intermolecular disintegration substrate described here, assist in stabilizing protein-protein interactions that otherwise require the amino and carboxy terminal regions of integrase. Images PMID:8152908

  16. The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

    PubMed

    Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

    2010-09-02

    The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

  17. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining.

    PubMed

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L; Tomkinson, Alan E; Tainer, John A; Ellenberger, Tom

    2015-08-18

    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.

  18. Hot-wire probe

    NASA Technical Reports Server (NTRS)

    Mikulla, V.

    1976-01-01

    High-temperature platinum probe measures turbulence and Reynolds shear stresses in high-temperature compressible flows. Probe does not vibrate at high velocities and does not react like strain gage on warmup.

  19. 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.

  20. Altering intra- to inter-molecular hydrogen bonding by dimethylsulfoxide: A TDDFT study of charge transfer for coumarin 343

    NASA Astrophysics Data System (ADS)

    Liu, Xiaochun; Yin, Hang; Li, Hui; Shi, Ying

    2017-04-01

    DFT and TDDFT methods were carried out to investigate the influences of intramolecular and intermolecular hydrogen bonding on excited state charge transfer for coumarin 343 (C343). Intramolecular hydrogen bonding is formed between carboxylic acid group and carbonyl group in C343 monomer. However, in dimethylsulfoxide (DMSO) solution, DMSO 'opens up' the intramolecular hydrogen bonding and forms solute-solvent intermolecular hydrogen bonded C343-DMSO complex. Analysis of frontier molecular orbitals reveals that intramolecular charge transfer (ICT) occurs in the first excited state both for C343 monomer and complex. The results of optimized geometric structures indicate that the intramolecular hydrogen bonding interaction is strengthened while the intermolecular hydrogen bonding is weakened in excited state, which is confirmed again by monitoring the shifts of characteristic peaks of infrared spectra. We demonstrated that DMSO solvent can not only break the intramolecular hydrogen bonding to form intermolecular hydrogen bonding with C343 but also alter the mechanism of excited state hydrogen bonding strengthening.

  1. Accurate description of intermolecular interactions involving ions using symmetry-adapted perturbation theory.

    PubMed

    Lao, Ka Un; Schäffer, Rainer; Jansen, Georg; Herbert, John M

    2015-06-09

    Three new data sets for intermolecular interactions, AHB21 for anion-neutral dimers, CHB6 for cation-neutral dimers, and IL16 for ion pairs, are assembled here, with complete-basis CCSD(T) results for each. These benchmarks are then used to evaluate the accuracy of the single-exchange approximation that is used for exchange energies in symmetry-adapted perturbation theory (SAPT), and the accuracy of SAPT based on wave function and density-functional descriptions of the monomers is evaluated. High-level SAPT calculations afford poor results for these data sets, and this includes the recently proposed "gold", "silver", and "bronze standards" of SAPT, namely, SAPT2+(3)-δMP2/aug-cc-pVTZ, SAPT2+/aug-cc-pVDZ, and sSAPT0/jun-cc-pVDZ, respectively [ Parker , T. M. , et al. , J. Chem. Phys. 2014 , 140 , 094106 ]. Especially poor results are obtained for symmetric shared-proton systems of the form X(-)···H(+)···X(-), for X = F, Cl, or OH. For the anionic data set, the SAPT2+(CCD)-δMP2/aug-cc-pVTZ method exhibits the best performance, with a mean absolute error (MAE) of 0.3 kcal/mol and a maximum error of 0.7 kcal/mol. For the cationic data set, the highest-level SAPT method, SAPT2+3-δMP2/aug-cc-pVQZ, outperforms the rest of the SAPT methods, with a MAE of 0.2 kcal/mol and a maximum error of 0.4 kcal/mol. For the ion-pair data set, the SAPT2+3-δMP2/aug-cc-pVTZ performs the best among all SAPT methods with a MAE of 0.3 kcal/mol and a maximum error of 0.9 kcal/mol. Overall, SAPT2+3-δMP2/aug-cc-pVTZ affords a small and balanced MAE (<0.5 kcal/mol) for all three data sets, with an overall MAE of 0.4 kcal/mol. Despite the breakdown of perturbation theory for ionic systems at short-range, SAPT can still be saved given two corrections: a "δHF" correction, which requires a supermolecular Hartree-Fock calculation to incorporate polarization effects beyond second order, and a "δMP2" correction, which requires a supermolecular MP2 calculation to account for higher

  2. 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.

  3. 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.

  4. A Magnetoresistance Measuring Probe.

    DTIC Science & Technology

    The in line four point probe, commonly used for measuring the sheet resistance in a conductor, cannot measure the anisotropic ferromagnetic magnetoresistance. However, the addition of two contact points that are not collinear with the current contacts give the probe the ability to non-destructively measure the anistropic magnetoresistance. Keywords: Magnetoresistance; Anisotropic; Thin-Film; Permalloy; Four Point Probe; Anisotropic Resistance.

  5. Production of Protonated Methanol Ions Via Intermolecular Reactions within Van der Waals Clusters of Dime Dimethyl Ether. Revision

    DTIC Science & Technology

    1990-02-02

    preparation (17) This result also suggests that the protonated methanol ion is not produced via a reaction between the DME cluster and a water impurity. In...include Security Classification) Production ol Protonated Methanol Ions via "Intermolecular" Reactions within van der Waals Clusters of Dimethyl Ether...2/90 Production of Protonated Methanol Ions via "Intermolecular" Reactions within van der Waals Clusters of Dimethyl Ether M. Todd Coolbaugh, William

  6. Glass Probe Stimulation of Hair Cell Stereocilia.

    PubMed

    Peng, Anthony W; Ricci, Anthony J

    2016-01-01

    Hair cells are designed to sense mechanical stimuli of sound using their apical stereocilia hair bundles. Mechanical deflection of this hair bundle is converted into an electrical signal through gating of mechano-electric transduction channels. Stiff probe stimulation of hair bundles is an invaluable tool for studying the transduction channel and its associated processes because of the speed and ability to precisely control hair bundle position. Proper construction of these devices is critical to their ultimate performance as is appropriate placement of the probe onto the hair bundle. Here we describe the construction and use of a glass probe coupled to a piezo-electric actuator for stimulating hair bundles, including the basic technique for positioning of the stimulating probe onto the hair bundle. These piezo-electric stimulators can be adapted to other mechanically sensitive systems.

  7. 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.

  8. 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.

  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. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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; ...

    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

  17. 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.

  18. 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

  19. Multiple intermolecular bend vibrational excitation of a hydrogen bond: An extended infrared study of OCOHF

    NASA Astrophysics Data System (ADS)

    Nesbitt, David J.; Lovejoy, Christopher M.

    1990-12-01

    We report the use of near infrared tunable difference frequency laser absorption methods to investigate low-frequency bending of the intermolecular hydrogen bond in OCOHF complexes. By deliberate thermal warming of the slit jet expansion to 16 K, we observe bending ``hot band'' transitions built on the fundamental vHF=1←0 HF stretch from the lowest five internally excited bending states (i.e., vlbend=00←00, 11←11, 20←20, 22←22, and 31←31) which correspond to low-frequency, skeletal bending of the intermolecular hydrogen bond. In addition, much weaker parallel (Δl=0) combination band transitions (vlbend=20←00 and 31←11 ) are observed at ≲5% of the 00←00 intensity. Furthermore, measurements of the extremely weak 11←00 perpendicular (Δl=1) band are obtained at ≲1% of the 00←00 intensity. The fundamental, hot band, and combination band data permit quantitative measurement of the absolute vibrational energies of all vibrational levels for the l=0 and 1 manifolds in both HF excited (vHF=1) and ground-state (vHF=0) complexes. The bending frequencies are surprisingly low (˜10 cm-1 ) and exhibit positive anharmonicity (i.e., the energy level spacings increase with vlbend ). The results suggest nearly unrestricted bending of the hydrogen bond in a very flat, highly anharmonic angular potential. In contrast with many other weakly bound complexes, the lowest bending frequency decreases dramatically upon HF excitation, which signals a vHF vibrationally induced shift from a linear to a nonlinear equilibrium geometry for the vHF=1 excited OCOHF potential surface. Excess Lorentzian line widths are observed in all OCOHF transitions, attributable to vibrational predissociation lifetimes that vary smoothly from 1.2 ns (vlbend=00) to 650 ps (vlbend=31) as a function of intermolecular bending excitation.

  20. N-heterocyclic carbene catalyzed asymmetric intermolecular Stetter reaction: origin of enantioselectivity and role of counterions.

    PubMed

    Kuniyil, Rositha; Sunoj, Raghavan B

    2013-10-04

    The mechanism and the role of KOtBu in an enantioselective NHC-catalyzed Stetter reaction between p-chlorobenzaldehyde and N-acylamido acrylate is established using DFT(M06-2X) methods. The Gibbs free energies are found to be significantly lower for transition states with explicit bound KOtBu as compared to the conventional pathways without the counterions. An intermolecular proton transfer from HOtBu to the prochiral carbon is identified as the stereocontrolling step. The computed enantioselectivities are in excellent agreement with the experimental results.

  1. Correlated and cooperative motions in segmental relaxation: Influence of constitutive unit weight and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Rijal, Bidur; Soto Puente, Jorge Arturo; Atawa, Bienvenu; Delbreilh, Laurent; Fatyeyeva, Kateryna; Saiter, Allisson; Dargent, Eric

    2016-12-01

    This work clarifies the notion of correlated and cooperative motions appearing during the α-relaxation process through the role of the molecular weight of the constitutive units and of the interchain dipolar interactions. By studying amorphous copolymers of poly(ethylene-co-vinyl acetate) with different vinyl acetate contents, we show that the correlated motions are not sensitive to the interchain dipolar interactions, in contrast to the cooperative motions, which increase with a strengthening of the intermolecular interactions for this sample family. Concerning the influence of the molecular weight m0, the notion of "correlated motions" seems to be equivalent to the notion of "cooperative motions" only for low m0 systems.

  2. Dielectric spectroscopy investigation of ion-containing and intermolecular hydrogen-bonded polymer systems

    NASA Astrophysics Data System (ADS)

    Atorngitjawat, Pornpen

    Ion-containing and intermolecular hydrogen-bonded polymers are used widely in a variety of industrial and commercial applications, from food packaging to battery electrolytes to pharmaceuticals. Yet the dynamics of these polymers, which are both complex and important to the application, are poorly understood. This thesis provides the first systematic study of the dynamics of several ion-containing and intermolecular hydrogen-bonded polymers by broadband dielectric relaxation spectroscopy. The systems under consideration include sulfonated polystyrene (SPS) in acid (SPS-H) and neutralized forms, and mixtures of poly(2-vinylpyridine) (P2VPy) with lithium perchlorate (LiClO4) and low molecular weight phenolic molecules. Dynamic mechanical analysis, Fourier transform infrared spectroscopy, differential scanning calorimetry, small-angle X-ray scattering and wide-angle X-ray diffraction were employed in a complementary role. Multiple relaxations were generally observed at high temperatures. For SPS ionomers, the segmental process, Maxwell-Wagner-Sillars interfacial polarization, and electrode polarization were detected. Three relaxations were also found in spectra of SPS-H, attributed to the segmental process, hydrogen bond association/dissociation, and electrode polarization. Three dielectric relaxations above the segmental process were observed for P2VPy-LiClO4 mixtures: ion-mode relaxation, slow hindered segmental relaxation and electrode polarization. However, only electrode polarization was observed above the segmental relaxation for all P2VPy--small phenolic molecule mixtures, except P2VPy + 10 mol% 2,3,3,4,4,5-hexahydroxybenzophenone. This mixture exhibited an additional relaxation due to Maxwell-Wagner-Sillars interfacial polarization, arising from the existence of phase-separated complexes within the P2VPy matrix. Sub-Tg local relaxations were suppressed by ionic intermolecular interactions for SPS ionomers and P2VPy-LiClO4 mixtures. Intermolecular hydrogen

  3. 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.

  4. Profile of the intermolecular forces governing the interaction of drugs with mucin.

    PubMed

    Caron, Giulia; Visentin, Sonja; Pontremoli, Carlotta; Ermondi, Giuseppe

    2015-07-05

    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.

  5. 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.

  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. 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.

  8. Vibrational Circular Dichroism (VCD) Reveals Subtle Conformational Aspects and Intermolecular Interactions in the Carnitine Family.

    PubMed

    Mazzeo, Giuseppe; Abbate, Sergio; Longhi, Giovanna; Castiglioni, Ettore; Villani, Claudio

    2015-12-01

    Vibrational circular dichroism spectra (VCD) in the mid-IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N-trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines.

  9. Catalytic Selenium-Promoted Intermolecular Friedel-Crafts Alkylation with Simple Alkenes.

    PubMed

    Tang, E; Zhao, Yinjiao; Li, Wen; Wang, Weilin; Zhang, Meng; Dai, Xin

    2016-03-04

    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.

  10. Catalytic intermolecular amination of C-H bonds: method development and mechanistic insights.

    PubMed

    Fiori, Kristin Williams; Du Bois, J

    2007-01-24

    Reaction methodology for intermolecular C-H amination of benzylic and 3 degrees C-H bonds is described. This process uses the starting alkane as the limiting reagent, gives optically pure tetrasubstituted amines through stereospecific insertion into enantiomeric 3 degrees centers, displays high chemoselectivity for benzylic oxidation, and enables the facile preparation of isotopically enriched 15N-labeled compounds. Access to substituted amines, amino alcohols, and diamines is thereby made possible in a single transformation. Important information relevant to understanding the initial steps in the catalytic cycle, reaction chemoselectivity, the nature of the active oxidant, and pathways for catalyst inactivation has been gained through mechanistic analysis; these studies are also presented.

  11. Rational design of cyclopropane-based chiral PHOX ligands for intermolecular asymmetric Heck reaction

    PubMed Central

    Rubina, Marina; Sherrill, William M; Barkov, Alexey Yu

    2014-01-01

    Summary A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used to predict the optimal ligand structure and helped to design a very efficient and highly selective catalytic system. Employment of the optimized ligands in the asymmetric arylation of cyclic olefins allowed for achieving high enantioselectivities and significantly suppressing product isomerization. Factors affecting the selectivity and the rate of the isomerization were identified. It was shown that the nature of this isomerization is different from that demonstrated previously using chiral diphosphine ligands. PMID:25161709

  12. Solute Probes of Conformational Changes in Open Complex Formation by E. coli RNA Polymerase at the λPR Promoter: Evidence for Unmasking of the Active Site in the Isomerization Step and for Large-Scale Coupled Folding in the Subsequent Conversion to RPo†

    PubMed Central

    Kontur, Wayne S.; Saecker, Ruth M.; Davis, Caroline A.; Capp, Michael W.; Record, M. Thomas

    2008-01-01

    Transcription initiation is a multi-step process involving a series of requisite conformational changes in RNA polymerase (R) and promoter DNA (P) that create the open complex (RPo). Here we use the small solutes urea and glycine betaine (GB) to probe the extent and type of surface area changes in the formation of RPo between Eσ70 RNA polymerase and λPR promoter DNA. Effects of urea quantitatively reflect changes in amide surface and are particularly well suited to detect coupled protein folding events. GB provides a qualitative probe for the exposure or burial of anionic surface. Kinetics of formation and dissociation of RPo reveal strikingly large effects of the solutes on the final steps of RPo formation: urea dramatically increases the dissociation rate constant kd, whereas GB decreases the rate of dissociation. Formation of the first kinetically significant intermediate I1 is disfavored in urea, and moderately favored by GB. GB slows the rate-determining step that converts I1 to the second kinetically significant intermediate I2; urea has no effect on this step. The most direct interpretation of these data is that recognition of promoter DNA in I1 involves only limited conformational changes. Notably the data support the following hypotheses: 1) the negatively charged N-terminal domain of σ70 remains bound in the “jaws” of polymerase in I1; 2) the subsequent rate-determining isomerization step involves ejecting this domain from the jaws, thereby unmasking the active site; and 3) final conversion to RPo involves coupled folding of the mobile downstream clamp of polymerase. PMID:16475805

  13. 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.

  14. 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.

  15. Integrated microfluidic probe station.

    PubMed

    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.

  16. 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.

  17. Transient internal probe

    NASA Astrophysics Data System (ADS)

    Jarboe, Thomas R.; Mattick, Arthur T.

    1993-12-01

    The Transient Internal Probe (TIP) diagnostic is a novel method for probing the interior of hot magnetic fusion plasmas that are inaccessible with ordinary stationary probes. A small probe of magneto-optic (Verdet) material is fired through a plasma at speeds of several km/sec, illuminated by a laser beam. The beam's polarization is rotated in the probe by the local magnetic field and retroreflection back to a polarimetry detector allows determination of the B-field profile across the diameter of a plasma at a spatial resolution of better than 1-cm and an absolute B-field resolution of a few tens of Gauss. The principal components of a TIP diagnostic system were developed and tested. A two-stage light gas gun was constructed that accelerates 30-caliber projectiles to 3 km/sec, and methods were examined for stripping a lexan sabot from a probe prior to entry into a plasma. Probes of CdMnTe and FR-5 Verdet glass were fabricated, and a polarimetry system was constructed for resolving polarization to within 0.25 deg. The diagnostic was validated by measuring a static B-field with a moving (dropped) TIP probe, and finding agreement with Hall-probe measurements to within experimental accuracy (40 Gauss).

  18. Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions

    PubMed Central

    Archambault, Fabien; Soteras, Ignacio; Luque, F. Javier; Schulten, Klaus

    2010-01-01

    A complete derivation of polarizable intermolecular potentials based on high-level, gas-phase quantum-mechanical calculations is proposed. The importance of appreciable accuracy together with inherent simplicity represents a significant endeavor when enhancement of existing force fields for biological systems is sought. Toward this end, symmetry-adapted perturbation theory (SAPT) can provide an expansion of the total interaction energy into physically meaningful e.g. electrostatic, induction and van der Waals terms. Each contribution can be readily compared with its counterpart in classical force fields. Since the complexity of the different intermolecular terms cannot be fully embraced using a minimalist description, it is necessary to resort to polyvalent expressions capable of encapsulating overlooked contributions from the quantum-mechanical expansion. This choice results in consistent force field components that reflect the underlying physical principles of the phenomena. This simplified potential energy function is detailed and definitive guidelines are drawn. As a proof of concept, the methodology is illustrated through a series of test cases that include the interaction of water and benzene with halide and metal ions. In each case considered, the total energy is reproduced accurately over a range of biologically relevant distances. PMID:21113276

  19. Role of intermolecular interaction in crystal packing: A competition between halogen bond and electrostatic interaction

    NASA Astrophysics Data System (ADS)

    Chen, Peng-Yuan; Zhang, Lin; Zhu, Shun-Guan; Cheng, Guang-Bin

    2017-03-01

    To investigate the competition between halogen bond and electrostatic interaction and their influence on the crystal packing, four novel solvates of 1,3,5-trichloro-2,4,6-trinitrobenzene (TCTNB) and 1,3,5-tribromo-2,4,6-trinitrobenzene (TBTNB) were synthesized while the intermolecular forces and the contribution of each interaction were analyzed quantitatively. The electrostatic interaction is the main link between TCTNB, TBTNB and 1,4-dioxane respectively, while π-π interaction dominates in these two solvates of TCTNB/1,4-dimethylbenzene (PX) and TCTNB/mesitylene. The solvate interaction changes and varieties were illuminated by Hirshfeld surface analysis, and the group contributions were illustrated respectively. Molecular electrostatic potential surface (MEPs) with density functional theory (DFT) calculation was performed to compare the relative strength of electrostatic interaction and halogen bond. The result shows that MEPs can be used as a descriptor for determining the most possible intermolecular interaction under certain circumstances. The study presented here may provide the guidance for the design and synthesis of the complex with desired properties.

  20. 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%.

  1. Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges

    PubMed Central

    Min, Hye Jung; Yun, Hyosuk; Ji, Sehyeon; Rajasekaran, Ganesan; Kim, Jae Il; Kim, Jeong-Sun; Shin, Song Yub; Lee, Chul Won

    2017-01-01

    Defensin peptides are essential for innate immunity in humans and other living systems, as they provide protection against infectious pathogens and regulate the immune response. Here, we report the solution structure of rattusin (RTSN), an α-defensin-related peptide, which revealed a novel C2-symmetric disulfide-linked dimeric structure. RTSN was synthesized by solid-phase peptide synthesis (SPPS) and refolded by air oxidation in vitro. Dimerization of the refolded RTSN (r-RTSN) resulted from five intermolecular disulfide (SS) bond exchanges formed by ten cysteines within two protomer chains. The SS bond pairings of r-RTSN were determined by mass analysis of peptide fragments cleaved by trypsin digestion. In addition to mass analysis, nuclear magnetic resonance (NMR) experiments for a C15S mutant and r-RTSN confirmed that the intermolecular SS bond structure of r-RTSN showed an I-V’, II-IV’, III-III’, IV-II’, V-I’ arrangement. The overall structure of r-RTSN exhibited a cylindrical array, similar to that of β-sandwich folds, with a highly basic surface. Furthermore, fluorescence spectroscopy results suggest that r-RTSN exerts bactericidal activity by damaging membrane integrity. Collectively, these results provide a novel structural scaffold for designing highly potent peptide-based antibiotics suitable for use under various physiological conditions. PMID:28345637

  2. 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 .

  3. Glass-Forming Tendency of Molecular Liquids and the Strength of the Intermolecular Attractions

    PubMed Central

    Koperwas, Kajetan; Adrjanowicz, Karolina; Wojnarowska, Zaneta; Jedrzejowska, Agnieszka; Knapik, Justyna; Paluch, Marian

    2016-01-01

    When we cool down a liquid below the melting temperature, it can either crystallize or become supercooled, and then form a disordered solid called glass. Understanding what makes a liquid to crystallize readily in one case and form a stable glass in another is a fundamental problem in science and technology. Here we show that the crystallization/glass-forming tendencies of the molecular liquids might be correlated with the strength of the intermolecular attractions, as determined from the combined experimental and computer simulation studies. We use van der Waals bonded propylene carbonate and its less polar structural analog 3-methyl-cyclopentanone to show that the enhancement of the dipole-dipole forces brings about the better glass-forming ability of the sample when cooling from the melt. Our finding was rationalized by the mismatch between the optimal temperature range for the nucleation and crystal growth, as obtained for a modeled Lennard-Jones system with explicitly enhanced or weakened attractive part of the intermolecular 6–12 potential. PMID:27883011

  4. 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.

  5. Foot-and-mouth disease virus leader proteinase: structural insights into the mechanism of intermolecular cleavage.

    PubMed

    Steinberger, Jutta; Grishkovskaya, Irina; Cencic, Regina; Juliano, Luiz; Juliano, Maria A; Skern, Tim

    2014-11-01

    Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pro) (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4 G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells.

  6. Glass-Forming Tendency of Molecular Liquids and the Strength of the Intermolecular Attractions

    NASA Astrophysics Data System (ADS)

    Koperwas, Kajetan; Adrjanowicz, Karolina; Wojnarowska, Zaneta; Jedrzejowska, Agnieszka; Knapik, Justyna; Paluch, Marian

    2016-11-01

    When we cool down a liquid below the melting temperature, it can either crystallize or become supercooled, and then form a disordered solid called glass. Understanding what makes a liquid to crystallize readily in one case and form a stable glass in another is a fundamental problem in science and technology. Here we show that the crystallization/glass-forming tendencies of the molecular liquids might be correlated with the strength of the intermolecular attractions, as determined from the combined experimental and computer simulation studies. We use van der Waals bonded propylene carbonate and its less polar structural analog 3-methyl-cyclopentanone to show that the enhancement of the dipole-dipole forces brings about the better glass-forming ability of the sample when cooling from the melt. Our finding was rationalized by the mismatch between the optimal temperature range for the nucleation and crystal growth, as obtained for a modeled Lennard-Jones system with explicitly enhanced or weakened attractive part of the intermolecular 6–12 potential.

  7. Curcumin amorphous solid dispersions: the influence of intra and intermolecular bonding on physical stability.

    PubMed

    Wegiel, Lindsay A; Zhao, Yuhong; Mauer, Lisa J; Edgar, Kevin J; Taylor, Lynne S

    2014-12-01

    We have investigated the physical stability of amorphous curcumin dispersions and the role of curcumin-polymer intermolecular interactions in delaying crystallization. Curcumin is an interesting model compound as it forms both intra and intermolecular hydrogen bonds in the crystal. A structurally diverse set of amorphous dispersion polymers was investigated; poly(vinylpyrrolidone), Eudragit E100, carboxymethyl cellulose acetate butyrate, hydroxypropyl methyl cellulose (HPMC) and HPMC-acetate succinate. Mid-infrared spectroscopy was used to determine and quantify the extent of curcumin-polymer interactions. Physical stability under different environmental conditions was monitored by powder X-ray diffraction. Curcumin chemical stability was monitored by UV-Vis spectroscopy. Isolation of stable amorphous curcumin was difficult in the absence of polymers. Polymers proved to be effective curcumin crystallization inhibitors enabling the production of amorphous solid dispersions; however, the polymers showed very different abilities to inhibit crystallization during long-term storage. Curcumin intramolecular hydrogen bonding reduced the extent of its hydrogen bonding with polymers; hence most polymers were not highly effective crystallization inhibitors. Overall, polymers proved to be crystallization inhibitors, but inhibition was limited due to the intramolecular hydrogen bonding in curcumin, which leads to a decrease in the ability of the polymers to interact at a molecular level.

  8. 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.

  9. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide.

    PubMed

    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 N-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 N-H···S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  10. 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.

  11. Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.

    PubMed

    Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

    2014-06-05

    In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-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 NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  12. 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.

  13. Validation of intermolecular transfer integral and bandwidth calculations for organic molecular materials.

    PubMed

    Huang, Jingsong; Kertesz, Miklos

    2005-06-15

    We present an interpretation of the intermolecular transfer integral that is independent from the origin of the energy scale allowing convergence studies of this important parameter of organic molecular materials. We present extensive numerical studies by using an ethylene pi dimer to investigate the dependence of transfer integrals on the level of theory and intermolecular packing. Transfer integrals obtained from semiempirical calculations differ substantially from one another and from ab initio results. The ab initio results are consistent across all the levels used including Hartree-Fock, outer valence Green's function, and various forms of density functional theory (DFT). Validation of transfer integrals and bandwidths is performed by comparing the calculated values with the experimental values of tetrathiafulvalene-tetracyanoquinodimethane (TTF-TCNQ), bis[1,2,5]thiadiazolo-p-quinobis(1,3-dithiole), (BTQBT) K-TCNQ, and hexagonal graphite. DFT in one of its presently popular forms, such as Perdew-Wang functionals (PW91), in combination with sufficient basis sets provides reliable transfer integrals, and therefore can serve as a basis for energy band calculations for soft organic materials with van der Waals gaps.

  14. Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals.

    PubMed

    Khaliullin, Rustam Z; Cobar, Erika A; Lochan, Rohini C; Bell, Alexis T; Head-Gordon, Martin

    2007-09-13

    An energy decomposition analysis (EDA) method is proposed to isolate physically relevant components of the total intermolecular interaction energies such as the contribution from interacting frozen monomer densities, the energy lowering due to polarization of the densities, and the further energy lowering due to charge-transfer effects. This method is conceptually similar to existing EDA methods such as Morokuma analysis but includes several important new features. The first is a fully self-consistent treatment of the energy lowering due to polarization, which is evaluated by a self-consistent field calculation in which the molecular orbital coefficients are constrained to be block-diagonal (absolutely localized) in the interacting molecules to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation in the charge-transfer energy term using a perturbative approximation starting from the optimized block-diagonal reference. The newly proposed EDA method is used to understand the fundamental aspects of intermolecular interactions such as the degree of covalency in the hydrogen bonding in water and the contributions of forward and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method can be used to identify the factors controlling the interaction of the molecular hydrogen with open metal centers in potential hydrogen storage materials and the interaction of methane with rhenium complexes.

  15. Symmetry-adapted perturbation theory calculation of the He-HF intermolecular potential energy surface

    NASA Astrophysics Data System (ADS)

    Moszynski, Robert; Wormer, Paul E. S.; Jeziorski, Bogumil; van der Avoird, Ad

    1994-08-01

    Symmetry-adapted perturbation theory has been applied to compute the HeHF intermolecular potential energy surface for three internuclear distances in the HF subunit. The interaction energy is found to be dominated by the first-order exchange contribution and by the dispersion energy (including the intramonomer correlation effects). However, smaller corrections as the electrostatics, induction, and second-order exchange are found to be nonnegligible, and the final shape of the potential results from a delicate balance of attractive and repulsive contributions due to the four fundamental intermolecular interactions: electrostatics, exchange, induction, and dispersion. For a broad range of He-HF configurations the theoretical potential agrees very well with the empirical potential of Lovejoy and Nesbitt [C. M. Lovejoy and D. J. Nesbitt, J. Chem. Phys. 93, 5387 (1990)], which was adjusted to reproduce the near-infrared spectrum of the complex. Our potential has a global minimum of ɛm=-39.68 cm-1 for the linear He-HF geometry at Rm=6.16 bohr, and a secondary minimum of ɛm=-36.13 cm-1 for the linear He-FH geometry at Rm=5.59 bohr. These values are in very good agreement with the corresponding empirical results: ɛm=-39.20 cm-1 and Rm=6.17 bohr for the global minimum, and ɛm=-35.12 cm-1 and Rm=5.67 bohr for the secondary minimum.

  16. 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

  17. 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.

  18. Intermolecular Interactions and the Release Pattern of Electrospun Curcumin-Polyvinyl(pyrrolidone) Fiber.

    PubMed

    Rahma, Annisa; Munir, Muhammad Miftahul; Khairurrijal; Prasetyo, Anton; Suendo, Veinardi; Rachmawati, Heni

    2016-01-01

    An electrospun fiber of polyvinyl(pyrrolidone) (PVP)-Tween 20 (T20) with curcumin as the encapsulated drug has been developed. A study of intermolecular interactions was performed using Raman spectroscopy, Fourier transform infrared (FT-IR), differential scanning calorimetry (DSC), and X-ray diffraction (XRD). The Raman and FT-IR studies showed that curcumin preferrably interacted with T20 and altered PVP chain packing, as supported by XRD and physical stability data. The hydroxyl stretching band in PVP shifted to a lower wavenumber with higher intenstity in the presence of curcumin and PVP, indicating that hydrogen bond formation is more intense in a curcumin or curcumin-T20 containing fiber. The thermal pattern of the fiber did not indicate phase separation. The conversion of curcumin into an amorphous state was confirmed by XRD analysis. An in vitro release study in phosphate buffer pH 6.8 showed that intermolecular interactions between each material influenced the drug release rate. However, low porosity was found to limit the hydrogen bond-mediated release.

  19. Rh-Catalyzed Intermolecular Syn-Carboamination of Alkenes via a Transient Directing Group

    PubMed Central

    Piou, Tiffany; Rovis, Tomislav

    2015-01-01

    Alkenes are the most ubiquitous pro-chiral functional groups accessible to synthetic chemists. For this reason, difunctionalization reactions of alkenes are particularly important, as they can be used to access highly complex molecular architectures.1,2 Stereoselective oxidation reactions, including dihydroxylation, aminohydroxylation and halogenation reactions,3,4,5,6 are well-established methods for functionalizing alkenes. However, the intermolecular incorporation of both carbon- and nitrogen-based functionalities stereoselectively across an alkene has not been reported. In this manuscript, we describe the Rh(III)-catalyzed syn carboamination of alkenes initiated by a C–H activation event that uses enoxyphthalimides as the source of the carbon and the nitrogen functionalities. The reaction methodology allows for the stereospecific formation of one C–C and one C–N bond across an alkene in a fully intermolecular sense, which is unprecedented. The reaction design involves the in situ generation of a bidentate directing group and the use of a novel cyclopentadienyl ligand to control the reactivity of Rh(III). The results provide a new route to functionalized alkenes and are expected to lead to the more convergent and stereoselective assembly of amine-containing acyclic molecules. PMID:26503048

  20. Intermolecular interaction studies of winter flounder antifreeze protein reveal the existence of thermally accessible binding state.

    PubMed

    Nguyen, Dat H; Colvin, Michael E; Yeh, Yin; Feeney, Robert E; Fink, William H

    2004-10-05

    The physical nature underlying intermolecular interactions between two rod-like winter flounder antifreeze protein (AFP) molecules and their implication for the mechanism of antifreeze function are examined in this work using molecular dynamics simulations, augmented with free energy calculations employing a continuum solvation model. The energetics for different modes of interactions of two AFP molecules is examined in both vacuum and aqueous phases along with the water distribution in the region encapsulated by two antiparallel AFP backbones. The results show that in a vacuum two AFP molecules intrinsically attract each other in the antiparallel fashion, where their complementary charge side chains face each other directly. In the aqueous environment, this attraction is counteracted by both screening and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state and a dissociated state, result as a new aspect of intermolecular interaction in the paradigm for the mechanism of action of AFP. The relevance of these findings to the mechanism of function of freezing inhibition in the context of our work on Antarctic cod antifreeze glycoprotein (Nguyen et al., Biophysical Journal, 2002, Vol. 82, pp. 2892-2905) is discussed.