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Sample records for intermolecular transfer integral

  1. Intermolecular transfer integrals for organic molecular materials: can basis set convergence be achieved?

    NASA Astrophysics Data System (ADS)

    Huang, Jingsong; Kertesz, Miklos

    2004-05-01

    Intermolecular transfer integrals, and associated band-structures of organic molecular materials can be calculated through a dimer approach. Extensive numerical studies are performed on an ethylene π-dimer to investigate the basis sets dependence of transfer integrals. Convergence of calculated transfer integrals is achieved with respect to both Gaussian and plane-wave basis sets, provided the same level of theory is used. Effects of diffuse and polarization Gaussian functions on transfer integrals are identified. Comparison of experimental and theoretical values of transfer integrals of the TTF-TCNQ charge transfer salt is also presented.

  2. 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. PMID:16008473

  3. Frontier orbital symmetry control of intermolecular electron transfer

    SciTech Connect

    Stevens, B.

    1990-11-01

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

  4. Fluorescence photoactivation by intermolecular proton transfer.

    PubMed

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

    2012-10-11

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

  5. 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.

  6. 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.

  7. Frontier orbital symmetry control of intermolecular electron transfer. Final report, September 15, 1988--December 31, 1994

    SciTech Connect

    Stevens, B.

    1997-07-01

    This report discusses the following topics: the recovery of intermolecular transfer parameters from fluorescence quenching in liquids; photoinduced intramolecular electron transfer in flexible donor/space/acceptor systems containing an extended unsaturated spacer; electron transfer sensitized reaction; the recovery of solute and fractal dimensions from electron transfer quenching data; and frontier orbital symmetry control of back electron transfer.

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

    SciTech Connect

    Kato, Nobuhiko; Ida, Tomonori; Endo, Kazunaka

    2004-04-30

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

  9. Intermolecular nonradiative energy transfer in clusters with plasmonic nanoparticles

    NASA Astrophysics Data System (ADS)

    Kucherenko, M. G.; Stepanov, V. N.; Kruchinin, N. Yu.

    2015-01-01

    The influence of carbon (fullerenes, nanotubes) and metal (Ni, Co, Cu, Ag) nanoparticles on the nonradiative electronic excitation energy transfer between the molecules of organic dyes (acrylic orange as a donor and Nile blue as an acceptor) in alcohol solutions of polyvinylbutyral is studied. It is found that, at particular concentrations of the mixture components, plasmonic nanoparticles affect the nonradiative electronic excitation energy transfer, which is manifested in an increase in the intensity of sensitized fluorescence of acceptors with simultaneous quenching of the fluorescence of donors. A very simple model is proposed to illustrate the observed redistribution of luminescence intensity between the spectral bands of the general spectrum. Molecular-dynamic calculations of the structure of nanocomposites performed for the same purpose confirmed the formation of associated molecular plasmonic complexes fixed by macrochain links.

  10. Intermolecular forces in phase-change heat transfer: 1998 Kern award review

    SciTech Connect

    Wayner, P.C. Jr.

    1999-10-01

    The variation of long-range intermolecular forces near interfaces profoundly affects the performance of change-of-phase heat exchangers. Starting with the fundamental electromagnetic force between molecules (dielectric properties), the effects of shape (Kelvin effect), temperature (Clapeyron effect) and concentration on the heat-transfer characteristics of thin films and larger systems are reviewed and connected. A judicious selection of literature gives a consistent set of models of particular use in heat transfer. Examples of experimental verification of these interfacial models in this rapidly developing field are also presented.

  11. Nonresonant and resonant mode-specific intermolecular vibrational energy transfers in electrolyte aqueous solutions.

    PubMed

    Bian, Hongtao; Chen, Hailong; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2011-10-27

    The donor/acceptor energy mismatch and vibrational coupling strength dependences of interionic vibrational energy transfer kinetics in electrolyte aqueous solutions were investigated with ultrafast multiple-dimensional vibrational spectroscopy. An analytical equation derived from the Fermi's Golden rule that correlates molecular structural parameters and vibrational energy transfer kinetics was found to be able to describe the intermolecular mode specific vibrational energy transfer. Under the assumption of the dipole-dipole approximation, the distance between anions in the aqueous solutions was obtained from the vibrational energy transfer measurements, confirmed with measurements on the corresponding crystalline samples. The result demonstrates that the mode-specific vibrational energy transfer method holds promise as an angstrom molecular ruler. PMID:21916443

  12. TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4'-dimethylaminoflavonol in ethanol solvent.

    PubMed

    Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

    2015-02-25

    Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4'-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule. PMID:25282020

  13. Rates of intra- and intermolecular electron transfers in hydrogenase deduced from steady-state activity measurements.

    PubMed

    Dementin, Sébastien; Burlat, Bénédicte; Fourmond, Vincent; Leroux, Fanny; Liebgott, Pierre-Pol; Abou Hamdan, Abbas; Léger, Christophe; Rousset, Marc; Guigliarelli, Bruno; Bertrand, Patrick

    2011-07-01

    Electrons are transferred over long distances along chains of FeS clusters in hydrogenases, mitochondrial complexes, and many other respiratory enzymes. It is usually presumed that electron transfer is fast in these systems, despite the fact that there has been no direct measurement of rates of FeS-to-FeS electron transfer in any respiratory enzyme. In this context, we propose and apply to NiFe hydrogenase an original strategy that consists of quantitatively interpreting the variations of steady-state activity that result from changing the nature of the FeS clusters which connect the active site to the redox partner, and/or the nature of the redox partner. Rates of intra- and intermolecular electron transfer are deduced from such large data sets. The mutation-induced variations of electron transfer rates cannot be explained by changes in intercenter distances and reduction potentials. This establishes that FeS-to-FeS rate constants are extremely sensitive to the nature and coordination of the centers. PMID:21615141

  14. Effect of intermolecular orientation upon proton transfer within a polarizable medium.

    PubMed Central

    Scheiner, S; Duan, X

    1991-01-01

    Ab initio calculations are used to investigate the proton transfer process in bacteriorhodopsin. HN = CH2 serves as a small prototype of the Schiff base while HCOO- models its carboxylate-containing counterion and HO- the hydroxyl group of water of tyrosine, leading to the HCOO-..H+..NHCH2 and HO-..H+..NHCH2 complexes. In isolation, both complexes prefer a neutral pair configuration wherein the central proton is associated with the anion. However, the Schiff base may be protonated in the former complex, producing the HCOO-..+HNHCH2 ion pair, when there is a high degree of dielectric coupling with an external polarizable medium. Within a range of intermediate level coupling, the equilibrium position of the proton (on either the carboxylate or Schiff base) can be switched by suitable changes in the intermolecular angle. pK shift resulting from a 60 degrees reorientation are calculated to be some 5-12 pK U within the coupling range where proton transfers are possible. The energy barrier to proton transfer reinforces the ability of changes in angle and dielectric coupling to induce a proton transfer. PMID:1660318

  15. Evidence of pressure induced intermolecular proton transfer via mutarotation: the case of supercooled d-fructose.

    PubMed

    Cecotka, Adam; Tripathy, Satya N; Paluch, Marian

    2015-07-15

    This paper describes a systematic investigation on the role of pressure in mutarotation kinetics of supercooled d-fructose using dielectric spectroscopy. The structural relaxation time acts as a suitable dynamical observable to monitor the mutarotation process that enables the construction of the kinetic curves. The reaction kinetic shapes have been analyzed using the Avrami model. At low temperature, sigmoidal kinetic curves are noted, which correspond to the high concentration of furanosidic forms. The magnitude of activation energy of the process significantly decreases with increasing pressure and is comparable to the solvated systems at 100 MPa. A potential connection between cooperative motion and the origin of intermolecular proton transfer via mutarotation at elevated pressure is also discussed. These experimental observations have fundamental significance on theoretical explanation of the mechanism involving mutarotation in sugars. PMID:26144525

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

    PubMed

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

    2016-03-14

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

  17. 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.

  18. 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.

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

    PubMed

    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(1)) is the measure of the fastest ET rate (tau(1)=tau(ET) (fast)=(k(ET) (fast))(-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(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(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(A)) is found to be approximately 0.4 for aromatic amines and approximately 0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the tau(1) values are seen to increase very sharply. The large difference in the critical x(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 (2000)] can give suitable V(el) and thus

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  1. Energy Decomposition Analysis with a Stable Charge-Transfer Term for Interpreting Intermolecular Interactions.

    PubMed

    Lao, Ka Un; Herbert, John M

    2016-06-14

    Many schemes for decomposing quantum-chemical calculations of intermolecular interaction energies into physically meaningful components can be found in the literature, but the definition of the charge-transfer (CT) contribution has proven particularly vexing to define in a satisfactory way and typically depends strongly on the choice of basis set. This is problematic, especially in cases of dative bonding and for open-shell complexes involving cation radicals, for which one might expect significant CT. Here, we analyze CT interactions predicted by several popular energy decomposition analyses and ultimately recommend the definition afforded by constrained density functional theory (cDFT), as it is scarcely dependent on basis set and provides results that are in accord with chemical intuition in simple cases, and in quantitative agreement with experimental estimates of the CT energy, where available. For open-shell complexes, the cDFT approach affords CT energies that are in line with trends expected based on ionization potentials and electron affinities whereas some other definitions afford unreasonably large CT energies in large-gap systems, which are sometimes artificially offset by underestimation of van der Waals interactions by density functional theory. Our recommended energy decomposition analysis is a composite approach, in which cDFT is used to define the CT component of the interaction energy and symmetry-adapted perturbation theory (SAPT) defines the electrostatic, polarization, Pauli repulsion, and van der Waals contributions. SAPT/cDFT provides a stable and physically motivated energy decomposition that, when combined with a new implementation of open-shell SAPT, can be applied to supramolecular complexes involving molecules, ions, and/or radicals. PMID:27049750

  2. Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

    2011-08-01

    A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

  3. Determination of stepsize parameters for intermolecular vibrational energy transfer. Final report, May 1, 1987--December 31, 1991

    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.

  4. MOLECULAR PACKING AND NPT-MOLECULAR DYNAMICS INVESTIGATION OF THE TRANSFERABILITY OF THE RDX INTERMOLECULAR POTENTIAL TO 2,4,6,8,1O,12- HEXANITROHEXAAZAISOWURTZITANE (HNIW)

    EPA Science Inventory

    We have explored the degree to which an intermolecular potential for the explosive hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) is transferable for predictions of crystal structures (within the approximation of rigid molecules) of a similar chemical system,in this case, polymo...

  5. Protein phosphorylation and intermolecular electron transfer: a joint experimental and computational study of a hormone biosynthesis pathway.

    PubMed

    Zöllner, Andy; Pasquinelli, Melissa A; Bernhardt, Rita; Beratan, David N

    2007-04-11

    Protein phosphorylation is a common regulator of enzyme activity. Chemical modification of a protein surface, including phosphorylation, could alter the function of biological electron-transfer reactions. However, the sensitivity of intermolecular electron-transfer kinetics to post-translational protein modifications has not been widely investigated. We have therefore combined experimental and computational studies to assess the potential role of phosphorylation in electron-transfer reactions. We investigated the steroid hydroxylating system from bovine adrenal glands, which consists of adrenodoxin (Adx), adrenodoxin reductase (AdR), and a cytochrome P450, CYP11A1. We focused on the phosphorylation of Adx at Thr-71, since this residue is located in the acidic interaction domain of Adx, and a recent study has demonstrated that this residue is phosphorylated by casein kinase 2 (CK2) in vitro.1 Optical biosensor experiments indicate that the presence of this phosphorylation slightly increases the binding affinity of oxidized Adx with CYP11A1ox but not AdRox. This tendency was confirmed by KA values extracted from Adx concentration-dependent stopped-flow experiments that characterize the interaction between AdRred and Adxox or between Adxred and CYP11A1ox. In addition, acceleration of the electron-transfer kinetics measured with stopped-flow is seen only for the phosphorylated Adx-CYP11A1 reaction. Biphasic reaction kinetics are observed only when Adx is phosphorylated at Thr-71, and the Brownian dynamics (BD) simulations suggest that this phosphorylation may enhance the formation of a secondary Adx-CYP11A1 binding complex that provides an additional electron-transfer pathway with enhanced coupling. PMID:17358057

  6. Intermolecular electron transfer rate in diffusion limited region: Picosecond fluorescence studies

    NASA Astrophysics Data System (ADS)

    Venkataraman, B.; Periasamy, N.; Modi, S.; Dutt, G. Bhaskar; Doraiswamy, S.

    1992-12-01

    The temporal profiles of the quenched fluorescence decay of the free base meso-tetraphenyl porphyrin (H 2TPP) and its Zn derivative (ZnTPP) with quenchers such as quinones and m-dinitrobenzene have been analysed by methods developed for short time regimes which are known to be diffusion influenced [N. Periasamy et al., J. Chem. Phys.88, 1638 (1988); 89, 4799 (1988); Chem. Phys. Lett.160, 457 (1989); N. Periasamy, Biophys. J.. 54, 961 (1988); R. Das and N. Periasamy, Chem. Phys. 136, 361 (1989); G.C. Joshi et al., J. Phys. Chem.94, 2908 (1990)]. These quenchers are known to participate in an electron transfer reaction leading to a charge separation. The intrinsic rate constant ( ka) derived from the analysis is examined as a function of the change in free energy in the electron transfer reaction. Such a comparison indicates that ka can be related to the electron transfer rate, ket. The electron transfer rates measured in acetonitrile (solvent reorganization energy, λ s = 1.35) and toluene (λ s = 0.1) do not indicate the existence of an inverted region as predicted by Marcus. The trend agrees with the findings of Rehm and Weller [ Isr. J. Chem.8, 259 (1970)], except that the rate constants are at least one order of magnitude larger than the diffusion limited values.

  7. Mode-specific intermolecular vibrational energy transfer. I. Phenyl selenocyanate and deuterated chloroform mixture

    NASA Astrophysics Data System (ADS)

    Bian, Hongtao; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2010-05-01

    Vibrational energy transfer from the first excited state (2252 cm-1) of the C-D stretch of deuterated chloroform (DCCl3) to the 0-1 transition (2155 cm-1) of the CN stretch of phenyl selenocyanate (C6H5SeCN) in their 1:1 liquid mixture was observed with a pump/probe two-color two dimensional infrared spectroscopic technique. The mode-specific energy transfer can occur mainly because of the long vibrational lifetime of the CN stretch first excited state (˜300 ps) and the relatively strong hydrogen-bond between the C-D and CN (calculated H-bond formation energy in gas phase ˜-5.4 kcal/mol). The mode-specific energy transfer is relatively low efficient (only ˜2%), which is mainly because of the relatively short vibrational lifetime (˜9 ps) of the C-D stretch first excited state and the big donor/acceptor energy mismatch (97 cm-1) and the slow transfer kinetics (1/kCD→CN=330 ps).

  8. Inner reorganization limiting electron transfer controlled hydrogen bonding: intra- vs. intermolecular effects.

    PubMed

    Martínez-González, Eduardo; Frontana, Carlos

    2014-05-01

    In this work, experimental evidence of the influence of the electron transfer kinetics during electron transfer controlled hydrogen bonding between anion radicals of metronidazole and ornidazole, derivatives of 5-nitro-imidazole, and 1,3-diethylurea as the hydrogen bond donor, is presented. Analysis of the variations of voltammetric EpIcvs. log KB[DH], where KB is the binding constant, allowed us to determine the values of the binding constant and also the electron transfer rate k, confirmed by experiments obtained at different scan rates. Electronic structure calculations at the BHandHLYP/6-311++G(2d,2p) level for metronidazole, including the solvent effect by the Cramer/Truhlar model, suggested that the minimum energy conformer is stabilized by intramolecular hydrogen bonding. In this structure, the inner reorganization energy, λi,j, contributes significantly (0.5 eV) to the total reorganization energy of electron transfer, thus leading to a diminishment of the experimental k. PMID:24653999

  9. Combining intra- and intermolecular charge-transfer: a new strategy towards molecular ferromagnets and multiferroics

    PubMed Central

    Di Maiolo, Francesco; Sissa, Cristina; Painelli, Anna

    2016-01-01

    Organic ferroelectric materials are currently a hot research topic, with mixed stack charge transfer crystals playing a prominent role with their large, electronic-in-origin polarization and the possibility to tune the transition temperature down to the quantum limit and/or to drive the ferroelectric transition via an optical stimulus. By contrast, and in spite of an impressive research effort, organic ferromagnets are rare and characterized by very low transition temperatures. Coexisting magnetic and electric orders in multiferroics offer the possibility to control magnetic (electric) properties by an applied electric (magnetic) field with impressive technological potential. Only few examples of multiferroics are known today, based on inorganics materials. Here we demonstrate that, by decorating mixed stack charge transfer crystals with organic radicals, a new family of robust molecular ferromagnets can be designed, stable up to ambient temperature, and with a clear tendency towards multiferroic behaviour. PMID:26790963

  10. Combining intra- and intermolecular charge-transfer: a new strategy towards molecular ferromagnets and multiferroics

    NASA Astrophysics Data System (ADS)

    di Maiolo, Francesco; Sissa, Cristina; Painelli, Anna

    2016-01-01

    Organic ferroelectric materials are currently a hot research topic, with mixed stack charge transfer crystals playing a prominent role with their large, electronic-in-origin polarization and the possibility to tune the transition temperature down to the quantum limit and/or to drive the ferroelectric transition via an optical stimulus. By contrast, and in spite of an impressive research effort, organic ferromagnets are rare and characterized by very low transition temperatures. Coexisting magnetic and electric orders in multiferroics offer the possibility to control magnetic (electric) properties by an applied electric (magnetic) field with impressive technological potential. Only few examples of multiferroics are known today, based on inorganics materials. Here we demonstrate that, by decorating mixed stack charge transfer crystals with organic radicals, a new family of robust molecular ferromagnets can be designed, stable up to ambient temperature, and with a clear tendency towards multiferroic behaviour.

  11. Combining intra- and intermolecular charge-transfer: a new strategy towards molecular ferromagnets and multiferroics.

    PubMed

    Di Maiolo, Francesco; Sissa, Cristina; Painelli, Anna

    2016-01-01

    Organic ferroelectric materials are currently a hot research topic, with mixed stack charge transfer crystals playing a prominent role with their large, electronic-in-origin polarization and the possibility to tune the transition temperature down to the quantum limit and/or to drive the ferroelectric transition via an optical stimulus. By contrast, and in spite of an impressive research effort, organic ferromagnets are rare and characterized by very low transition temperatures. Coexisting magnetic and electric orders in multiferroics offer the possibility to control magnetic (electric) properties by an applied electric (magnetic) field with impressive technological potential. Only few examples of multiferroics are known today, based on inorganics materials. Here we demonstrate that, by decorating mixed stack charge transfer crystals with organic radicals, a new family of robust molecular ferromagnets can be designed, stable up to ambient temperature, and with a clear tendency towards multiferroic behaviour. PMID:26790963

  12. Communication: Modeling of concentration dependent water diffusivity in ionic solutions: Role of intermolecular charge transfer

    SciTech Connect

    Yao, Yi; Berkowitz, Max L. E-mail: ykanai@unc.edu; Kanai, Yosuke E-mail: ykanai@unc.edu

    2015-12-28

    The translational diffusivity of water in solutions of alkali halide salts depends on the identity of ions, exhibiting dramatically different behavior even in solutions of similar salts of NaCl and KCl. The water diffusion coefficient decreases as the salt concentration increases in NaCl. Yet, in KCl solution, it slightly increases and remains above bulk value as salt concentration increases. Previous classical molecular dynamics simulations have failed to describe this important behavior even when polarizable models were used. Here, we show that inclusion of dynamical charge transfer among water molecules produces results in a quantitative agreement with experiments. Our results indicate that the concentration-dependent diffusivity reflects the importance of many-body effects among the water molecules in aqueous ionic solutions. Comparison with quantum mechanical calculations shows that a heterogeneous and extended distribution of charges on water molecules around the ions due to ion-water and also water-water charge transfer plays a very important role in controlling water diffusivity. Explicit inclusion of the charge transfer allows us to model accurately the difference in the concentration-dependent water diffusivity between Na{sup +} and K{sup +} ions in simulations, and it is likely to impact modeling of a wide range of systems for medical and technological applications.

  13. Communication: Modeling of concentration dependent water diffusivity in ionic solutions: Role of intermolecular charge transfer

    NASA Astrophysics Data System (ADS)

    Yao, Yi; Berkowitz, Max L.; Kanai, Yosuke

    2015-12-01

    The translational diffusivity of water in solutions of alkali halide salts depends on the identity of ions, exhibiting dramatically different behavior even in solutions of similar salts of NaCl and KCl. The water diffusion coefficient decreases as the salt concentration increases in NaCl. Yet, in KCl solution, it slightly increases and remains above bulk value as salt concentration increases. Previous classical molecular dynamics simulations have failed to describe this important behavior even when polarizable models were used. Here, we show that inclusion of dynamical charge transfer among water molecules produces results in a quantitative agreement with experiments. Our results indicate that the concentration-dependent diffusivity reflects the importance of many-body effects among the water molecules in aqueous ionic solutions. Comparison with quantum mechanical calculations shows that a heterogeneous and extended distribution of charges on water molecules around the ions due to ion-water and also water-water charge transfer plays a very important role in controlling water diffusivity. Explicit inclusion of the charge transfer allows us to model accurately the difference in the concentration-dependent water diffusivity between Na+ and K+ ions in simulations, and it is likely to impact modeling of a wide range of systems for medical and technological applications.

  14. Dynamical aspects of intermolecular proton transfer in liquid water and low-density amorphous ices.

    PubMed

    Tahat, Amani; Martí, Jordi

    2014-05-01

    The microscopic dynamics of an excess proton in water and in low-density amorphous ices has been studied by means of a series of molecular dynamics simulations. Interaction of water with the proton species was modelled using a multistate empirical valence bond Hamiltonian model. The analysis of the effects of low temperatures on proton diffusion and transfer rates has been considered for a temperature range between 100 and 298 K at the constant density of 1 g cm(-3). We observed a marked slowdown of proton transfer rates at low temperatures, but some episodes are still seen at 100 K. In a similar fashion, mobility of the lone proton gets significantly reduced when temperature decreases below 273 K. The proton transfer in low-density amorphous ice is an activated process with energy barriers between 1-10 kJ/mol depending of the temperature range considered and eventually showing Arrhenius-like behavior. Spectroscopic data indicated the survival of both Zundel and Eigen structures along the whole temperature range, revealed by significant spectral frequency shifts. PMID:25353762

  15. Intramolecular photo-switching and intermolecular energy transfer as primary photoevents in photoreceptive processes: The case of Euglena gracilis

    SciTech Connect

    Mercatelli, Raffaella; Quercioli, Franco; Barsanti, Laura; Evangelista, Valter; Coltelli, Primo; Passarelli, Vincenzo; Frassanito, Anna Maria; Gualtieri, Paolo

    2009-07-24

    In this paper we report the results of measurements performed by FLIM on the photoreceptor of Euglenagracilis. This organelle consists of optically bistable proteins, characterized by two thermally stable isomeric forms: A{sub 498,} non fluorescent and B{sub 462}, fluorescent. Our data indicate that the primary photoevent of Euglena photoreception upon photon absorption consists of two contemporaneous different phenomena: an intramolecular photo-switch (i.e., A{sub 498} becomes B{sub 462}), and a intermolecular and unidirectional Forster-type energy transfer. During the FRET process, the fluorescent B{sub 462} form acts as donor for the non-fluorescent A{sub 498} form of the protein nearby, which acts as acceptor. We hypothesize that in nature these phenomena follow each other with a domino progression along the orderly organized and closely packed proteins in the photoreceptor layer(s), modulating the isomeric composition of the photoreceptive protein pool. This mechanism guarantees that few photons are sufficient to produce a signal detectable by the cell.

  16. Intermolecular Energy Transfer Dynamics at a Hot-Spot Interface in RDX Crystals.

    PubMed

    Joshi, Kaushik; Losada, Martin; Chaudhuri, Santanu

    2016-02-01

    The phonon mediated vibrational up-pumping mechanisms assume an intact lattice and climbing of a vibrational ladder using strongly correlated multiphonon dynamics under equilibrium or near-equilibrium conditions. Important dynamic processes far from-equilibrium in regions of large temperature gradient after the onset of decomposition reactions in energetic solids are relatively unknown. In this work, we present a classical molecular dynamics (MD) simulation-based study of such processes using a nonreactive and a reactive potential to study a fully reacted and unreacted zone in RDX (1,3,5-trinitro-1,3,5-triazocyclohexane) crystal under nonequilibrium conditions. The energy transfer rate is evaluated as a function of temperature difference between the reacted and unreacted regions, and for different widths and cross-sectional area of unreacted RDX layers. Vibrational up-pumping processes probed using velocity autocorrelation functions indicate that the mechanisms at high-temperature interfaces are quite different from the standard phonon-based models proposed in current literature. In particular, the up-pumping of high-frequency vibrations are seen in the presence of small molecule collisions at the hot-spot interface with strong contributions from bending modes. It also explains some major difference in the order of decomposition of C-N and N-N bonds as seen in recent literature on initiation chemistry. PMID:26741283

  17. Intermolecular interactions and proton transfer in the hydrogen halide-superoxide anion complexes.

    PubMed

    Lee, Sebastian J R; Mullinax, J Wayne; Schaefer, Henry F

    2016-02-17

    The superoxide radical anion O2(-) is involved in many important chemical processes spanning different scientific disciplines (e.g., environmental and biological sciences). Characterizing its interaction with various substrates to help elucidate its rich chemistry may have far reaching implications. Herein, we investigate the interaction between O2(-) (X[combining tilde] (2)Πg) and the hydrogen halides (X[combining tilde] (1)Σ) with coupled-cluster theory. In contrast to the short (1.324 Å) hydrogen bond formed between the HF and O2(-) monomers, a barrierless proton transfer occurs for the heavier hydrogen halides with the resulting complexes characterized as long (>1.89 Å) hydrogen bonds between halide anions and the HO2 radical. The dissociation energy with harmonic zero-point vibrational energy (ZPVE) for FHO2(-) (X[combining tilde] (2)A'') → HF (X[combining tilde] (1)Σ) + O2(-) (X[combining tilde] (2)Πg) is 31.2 kcal mol(-1). The other dissociation energies with ZPVE for X(-)HO2 (X[combining tilde] (2)A'') → X(-) (X[combining tilde] (1)Σ) + HO2 (X[combining tilde] (2)A'') are 25.7 kcal mol(-1) for X = Cl, 21.9 kcal mol(-1) for X = Br, and 17.9 kcal mol(-1) for X = I. Additionally, the heavier hydrogen halides can form weak halogen bonds H-XO2(-) (X[combining tilde] (2)A'') with interaction energies including ZPVE of -2.3 kcal mol(-1) for HCl, -8.3 kcal mol(-1) for HBr, and -16.7 kcal mol(-1) for HI. PMID:26852733

  18. Effect of laser intensity on the determination of intermolecular electron transfer rate constants—Observation of Marcus inverted region in photoinduced back electron transfer reactions

    NASA Astrophysics Data System (ADS)

    Weng, Yu-Xiang; Chan, Kwok-Chu; Tzeng, Biing-Chiau; Che, Chi-Ming

    1998-10-01

    The light intensity and concentration dependence of the photoproduct yield are investigated in a monophotonic process. The relationship of the photoproduct yield with the laser intensity and the complex concentration for a monophotonic process is derived under laser flash photolysis. The relationship is confirmed experimentally in a monophotonic process, i.e., triplet-triplet transition for a Cu(I) complex Cu6(DMNSN')6 (DMNSN'=4,6-dimethylpyrimidine-2-thiolate). At low light intensity, the relationship can be approximated by a linear inverse square root dependence on the light intensity. Based on this equation, a method is proposed to determine the intrinsic back electron transfer rate constant kETb in photoinduced intermolecular electron transfer reactions, precluding the effect from the diffusional encounter pairs. The Marcus "inverted region" is observed by using the method in photoinduced back electron transfer reactions of [Au2(dppm)2](ClO4)2 (dppm=bis(diphenylphosphino)methane) with a series of substituted pyridinium acceptors.

  19. Kinetics of intra- and intermolecular excited-state proton transfer of ω -(2-hydroxynaphthyl-1)-decanoic acid in homogeneous and micellar solutions

    NASA Astrophysics Data System (ADS)

    Solntsev, Kyril M.; Popov, Alexander V.; Solovyeva, Vera A.; Abou Al-Ainain, Sami; Il'ichev, Yuri V.; Hernandez, Rigoberto; Kuzmin, Michael G.

    2016-03-01

    The bifunctional photoacid ω-(2-hydroxynaphthyl-1)-decanoic acid (1S2N) takes part both in intramolecular excited-state proton transfer (ESPT) to the anion of a fatty acid and in intermolecular ESPT in the presence of a water solvent. Excited-state intra- and intermolecular proton transfer of 1S2N was investigated in homogeneous ethanol/water solution and in micellar solutions of various surfactants. The interfacial potential of micelles was changed by using cationic (CTAB), non-ionic (Brij-35) and anionic (SDS) surfactants. With the decrease of the interfacial potential, the protolytic photodissociation of naphthol and the diffusion-controlled intramolecular ESPT to carboxylic anion were suppressed.

  20. Substituent-induced intermolecular interaction in organic crystals revealed by precise band-dispersion measurements.

    PubMed

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-23

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5 meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents. PMID:24010459

  1. Substituent-Induced Intermolecular Interaction in Organic Crystals Revealed by Precise Band-Dispersion Measurements

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-01

    We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F16ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents.

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

    SciTech Connect

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

    2015-10-21

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

  3. Photophysical properties and photo-induced intermolecular electron transfer of a novel aryl benzyl ester dendritic axially substituted silicon (IV) phthalocyanine

    NASA Astrophysics Data System (ADS)

    Chen, Xiuqin; Ma, Dongdong; Wang, Xiongwei; Chen, Jianling; Ruan, Youhong; Qi, Yiling; Ye, Qiuhao; Peng, Yiru

    2014-11-01

    The photophysical properties of a novel dendritic phthalocyanine di-{3,5-di-(4-methoxycarbonyl group benzyloxy) benzyloxy) benzyloxy} axially substituted silicon (IV) phthalocyanine (DSiPc) were studied by UV/Vis, steady state and time-resolved spectroscopic methods. The effect of dendritic structure on the photophysical properties and photoinduced intermolecular electron transfer were investigated. The maximum absorption, fluorescence intensity, lifetime and fluorescence quantum yield of DSiPc were greatly sensitized by the dendritic structure on the axially position of silicon (IV) phthalocyanine. The photoinduced intermolecular electron transfer between this novel macromolecule and benzoquinone (BQ) was studied. The results showed that the fluorescence emission of this dendritic phthalocyanine could be quenched by BQ with KSV value of DSiPc is 52.84 dm3 mol-1. The cyclic voltammogram and square wave voltammogram of DSiPc in DMF further evidenced the electron was transfer from DSiPc to BQ from thermodynamics. Therefore, this novel dendritic phthalocyanine was an effective new electron donor and transmission complex could be used as a potential artificial photosynthesis system.

  4. Training Transfer: An Integrative Literature Review

    ERIC Educational Resources Information Center

    Burke, Lisa A.; Hutchins, Holly M.

    2007-01-01

    Given the proliferation of training transfer studies in various disciplines, we provide an integrative and analytical review of factors impacting transfer of training. Relevant empirical research for transfer across the management, human resource development (HRD), training, adult learning, performance improvement, and psychology literatures is…

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  6. Broadband visible light-harvesting naphthalenediimide (NDI) triad: study of the intra-/intermolecular energy/electron transfer and the triplet excited state.

    PubMed

    Wu, Shuang; Zhong, Fangfang; Zhao, Jianzhang; Guo, Song; Yang, Wenbo; Fyles, Tom

    2015-05-21

    A triad based on naphthalenediimides (NDI) was prepared to study the intersystem crossing (ISC), the fluorescence-resonance-energy-transfer (FRET), as well as the photoinduced electron transfer (PET) processes. In the triad, the 2-bromo-6-alkylaminoNDI moiety was used as singlet energy donor and the spin converter, whereas 2,6-dialkylaminoNDI was used as the singlet/triplet energy acceptor. This unique structural protocol and thus alignment of the energy levels ensures the competing ISC and FRET in the triad. The photophysical properties of the triad and the reference compounds were studied with steady-state UV-vis absorption spectra, fluorescence spectra, nanosecond transient absorption spectra, cyclic voltammetry, and DFT/TDDFT calculations. FRET was confirmed with steady-state UV-vis absorption and fluorescence spectroscopy. Intramolecular electron transfer was observed in polar solvents, demonstrated by the quenching of both the fluorescence and triplet state of the energy acceptor. Nanosecond transient absorption spectroscopy shows that the T1 state of the triad is exclusively localized on the 2,6-dialkylaminoNDI moiety in the triad upon selective photoexcitation into the energy donor, which indicates the intramolecular triplet state energy transfer. The intermolecular triplet state energy transfer between the two reference compounds was investigated with nanosecond transient absorption spectroscopy. The photophysical properties were rationalized by TDDFT calculations. PMID:25919420

  7. Theory and assignment of intermolecular charge transfer states in squaraines and their impact on efficiency in bulk heterojunction solar cells (Presentation Recording)

    NASA Astrophysics Data System (ADS)

    Collison, Christopher J.; Zheng, Chenyu; Hestand, Nicholas; Cona, Brandon; Penmetcha, Anirudh; Spencer, Susan; Cody, Jeremy; Spano, Frank

    2015-10-01

    Squaraines are targeted for organic photovoltaic devices because of their high extinction coefficients over a broad wavelength range from visible to near infra-red (NIR). Moreover, their side groups can be changed with profound effects upon their ability to crystallize, leading to improvements in charge mobility and exciton diffusion. The broadening in squaraine absorption is often qualitatively attributed to H- and J-aggregates based on the exciton model, proposed by Kasha. However, such assignment is misleading considering that spectral shifts can arise from sources other than excitonic coupling. Our group has shown that packing structure influences the rate of charge transfer; thus a complete and accurate reassessment of the excited states must be completed before the true charge transfer mechanism can be confirmed. In this work, we will show how squaraine H-aggregates can pack in complete vertical stacks or slipped vertical stacks depending upon sidegroups and processing conditions. Hence, we uncover the contribution of an intermolecular charge transfer (IMCT) state through essential states modeling validated by spectroscopic and X-Ray diffraction data. We further show external quantum efficiency data that describe the influence of the IMCT state on the efficiency of our devices. This comprehensive understanding of squaraine aggregates drives the development of more efficient organic photovoltaic devices, leading towards a prescription for derivatives that can be tailored for optimized exciton diffusion, charge transfer, higher mobilities and reduced recombination in small molecule OPV devices.

  8. 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.

  9. Effect of surface-plasmon polaritons on spontaneous emission and intermolecular energy-transfer rates in multilayered geometries

    SciTech Connect

    Marocico, C. A.; Knoester, J.

    2011-11-15

    We use a Green's tensor method to investigate the spontaneous emission rate of a molecule and the energy-transfer rate between molecules placed in two types of layered geometries: a slab geometry and a planar waveguide. We focus especially on the role played by surface-plasmon polaritons in modifying the spontaneous emission and energy-transfer rates as compared to free space. In the presence of more than one interface, the surface-plasmon polariton modes split into several branches, and each branch can contribute significantly to modifying the electromagnetic properties of atoms and molecules. Enhancements of several orders of magnitude both in the spontaneous emission rate of a molecule and the energy-transfer rate between molecules are obtained and, by tuning the parameters of the geometry, one has the ability to control the range and magnitude of these enhancements. For the energy-transfer rate interference effects between contributions of different plasmon-polariton branches are observed as oscillations in the distance dependence of this rate.

  10. Calculations of transfer integrals for tetracyanoquinodimethane salts

    NASA Astrophysics Data System (ADS)

    van Smaalen, Sander; Kommandeur, Jan

    1985-06-01

    Calculations of the transfer integral for the one-dimensional electron band of 7,7,8,8-tetracyanoquinodimethane (TCNQ) salts are presented. A critical discussion of the method is given, from which it follows that accurate estimates of these quantities are hard to obtain. However, relative values are expected to be more reliable. For the series of N-substituted morpholinium TCNQ salts a qualitative agreement between dc electrical conductivity and calculated transfer integral was found. For 1,2,6-trimethylpyridinium TCNQ, a counter-intuitive result is obtained, the ``crystallophic'' dimer and the ``electronic'' dimer being different.

  11. MHD Technology Transfer, Integration and Review Committee

    SciTech Connect

    Not Available

    1992-01-01

    This fifth semi-annual status report of the MHD Technology Transfer, Integration, and Review Committee (TTIRC) summarizes activities of the TTIRC during the period April 1990 through September 1990. It includes summaries and minutes of committee meetings, progress summaries of ongoing Proof-of-Concept (POC) contracts, discussions pertaining to technical integration issues in the POC program, and planned activities for the next six months.

  12. Intermolecular perturbation theory

    NASA Astrophysics Data System (ADS)

    Hayes, I. C.; Hurst, G. J. B.; Stone, A. J.

    The new intermolecular perturbation theory described in the preceding papers is applied to some van der Waals molecules. HeBe is used as a test case, and the perturbation method converges well at interatomic distances down to about 4 a0, giving results in excellent agreement with supermolecule calculations. ArHF and ArHCl have been studied using large basis sets, and the results agree well with experimental data. The ArHX configuration is favoured over the ArXH configuration mainly because of larger polarization and charge-transfer contributions. In NeH2 the equilibrium geometry is determined by a delicate balance between opposing effects; with a double-zeta-polarization basis the correct configuration is predicted.

  13. Vehicle/engine integration. [orbit transfer vehicles

    NASA Technical Reports Server (NTRS)

    Cooper, L. P.; Vinopal, T. J.; Florence, D. E.; Michel, R. W.; Brown, J. R.; Bergeron, R. P.; Weldon, V. A.

    1984-01-01

    VEHICLE/ENGINE Integration Issues are explored for orbit transfer vehicles (OTV's). The impact of space basing and aeroassist on VEHICLE/ENGINE integration is discussed. The AOTV structure and thermal protection subsystem weights were scaled as the vehicle length and surface was changed. It is concluded that for increased allowable payload lengths in a ground-based system, lower length-to-diameter (L/D) is as important as higher mixture ration (MR) in the range of mid L/D ATOV's. Scenario validity, geometry constraints, throttle levels, reliability, and servicing are discussed in the context of engine design and engine/vehicle integration.

  14. DFT study of isocyanate chemisorption on Cu(100): Correlation between substrate-adsorbate charge transfer and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Belelli, Patricia G.; Garda, Graciela R.; Ferullo, Ricardo M.

    2011-07-01

    The adsorption of isocyanate (- NCO) species on Cu(100) was studied using the density functional theory (DFT) and the periodic slab model. The calculations indicate that at low and intermediate coverages NCO adsorbs preferentially on bridge and hollow sites. Work function and dipole moment changes show a significant negative charge transfer from Cu to NCO. The resulting charged NCO species interact repulsively among themselves being these dipole-dipole interactions particularly intensive when they are adsorbed in adjacent sites. Consequently, isocyanates tend to be separated from each other generating the vacant sites required for the dissociation to N and CO. This condition for NCO dissociation has been suggested in the past from experimental observations. A comparison was also performed with the NCO adsorption on Pd(100). In particular, the calculated minimal energy barrier for NCO dissociation was found to be higher on Cu(100) than on Pd(100) in accord with the well known higher NCO stability on Cu(100).

  15. Mechanochromism of piroxicam accompanied by intermolecular proton transfer probed by spectroscopic methods and solid-phase changes.

    PubMed

    Sheth, Agam R; Lubach, Joseph W; Munson, Eric J; Muller, Francis X; Grant, David J W

    2005-05-11

    Structural and solid-state changes of piroxicam in its crystalline form under mechanical stress were investigated using cryogenic grinding, powder X-ray diffractometry, diffuse-reflectance solid-state ultraviolet-visible spectroscopy, variable-temperature solid-state (13)C nuclear magnetic resonance spectroscopy, and solid-state diffuse-reflectance infrared Fourier transform spectroscopy. Crystalline piroxicam anhydrate exists as colorless single crystals irrespective of the polymorphic form and contains neutral piroxicam molecules. Under mechanical stress, these crystals become yellow amorphous piroxicam, which has a strong propensity to recrystallize to a colorless crystalline phase. The yellow color of amorphous piroxicam is attributed to charged piroxicam molecules. Variable-temperature solid-state (13)C NMR spectroscopy indicates that most of the amorphous piroxicam consists of neutral piroxicam molecules; the charged species comprise only about 8% of the amorphous phase. This ability to quantify the fractions of charged and neutral molecules of piroxicam in the amorphous phase highlights the unique capability of solid-state NMR to quantify mixtures in the absence of standards. Other compounds of piroxicam, which are yellow, are known to contain zwitterionic piroxicam molecules. The present work describes a system in which proton transfer accompanies both solid-state disorder and a change in color induced by mechanical stress, a phenomenon which may be termed mechanochromism of piroxicam. PMID:15869285

  16. Valence anions in complexes of adenine and 9-methyladenine with formic acid: stabilization by intermolecular proton transfer.

    PubMed

    Mazurkiewicz, Kamil; Harańczyk, Maciej; Gutowski, Maciej; Rak, Janusz; Radisic, Dunja; Eustis, Soren N; Wang, Di; Bowen, Kit H

    2007-02-01

    Photoelectron spectra of adenine-formic acid (AFA(-)) and 9-methyladenine-formic acid (MAFA(-)) anionic complexes have been recorded with 2.540 eV photons. These spectra reveal broad features with maxima at 1.5-1.4 eV that indicate formation of stable valence anions in the gas phase. The neutral and anionic complexes of adenine/9-methyladenine and formic acid were also studied computationally at the B3LYP, second-order Møller-Plesset, and coupled-cluster levels of theory with the 6-31++G** and aug-cc-pVDZ basis sets. The neutral complexes form cyclic hydrogen bonds, and the most stable dimers are bound by 17.7 and 16.0 kcal/mol for AFA and MAFA, respectively. The theoretical results indicate that the excess electron in both AFA(-) and MAFA(-) occupies a pi* orbital localized on adenine/9-methyladenine, and the adiabatic stability of the most stable anions amounts to 0.67 and 0.54 eV for AFA(-) and MAFA(-), respectively. The attachment of the excess electron to the complexes induces a barrier-free proton transfer (BFPT) from the carboxylic group of formic acid to a N atom of adenine or 9-methyladenine. As a result, the most stable structures of the anionic complexes can be characterized as neutral radicals of hydrogenated adenine (9-methyladenine) solvated by a deprotonated formic acid. The BFPT to the N atoms of adenine may be biologically relevant because some of these sites are not involved in the Watson-Crick pairing scheme and are easily accessible in the cellular environment. We suggest that valence anions of purines might be as important as those of pyrimidines in the process of DNA damage by low-energy electrons. PMID:17263404

  17. Integrated modeling, data transfers, and physical models

    NASA Astrophysics Data System (ADS)

    Brookshire, D. S.; Chermak, J. M.

    2003-04-01

    Difficulties in developing precise economic policy models for water reallocation and re-regulation in various regional and transboundary settings has been exacerbated not only by climate issues but also by institutional changes reflected in the promulgation of environmental laws, changing regional populations, and an increased focus on water quality standards. As complexity of the water issues have increased, model development at a micro-policy level is necessary to capture difficult institutional nuances and represent the differing national, regional and stakeholders' viewpoints. More often than not, adequate "local" or specific micro-data are not available in all settings for modeling and policy decisions. Economic policy analysis increasingly deals with this problem through data transfers (transferring results from one study area to another) and significant progress has been made in understanding the issue of the dimensionality of data transfers. This paper explores the conceptual and empirical dimensions of data transfers in the context of integrated modeling when the transfers are not only from the behavioral, but also from the hard sciences. We begin by exploring the domain of transfer issues associated with policy analyses that directly consider uncertainty in both the behavioral and physical science settings. We then, through a stylized, hybrid, economic-engineering model of water supply and demand in the Middle Rio Grand Valley of New Mexico (USA) analyze the impacts of; (1) the relative uncertainty of data transfers methods, (2) the uncertainty of climate data and, (3) the uncertainly of population growth. These efforts are motivated by the need to address the relative importance of more accurate data both from the physical sciences as well as from demography and economics for policy analyses. We evaluate the impacts by empirically addressing (within the Middle Rio Grand model): (1) How much does the surrounding uncertainty of the benefit transfer

  18. Integrating emissions transfers into policy-making

    NASA Astrophysics Data System (ADS)

    Springmann, Marco

    2014-03-01

    Net emissions transfers via international trade from developing to developed countries have increased fourfold in the past two decades--from 0.4 GtCO2 in 1990 to 1.6 GtCO2 in 2008. Consumption of goods and services in developed countries is one of the main driving forces of those emissions transfers. Therefore several proposals have been made to assign the responsibility for those emissions to the beneficiary, that is, to the consumer. Although consumption-based analyses have become popular, few proposals have been made for integrating emissions transfers into actual policy making. This study advances and critically evaluates three potential policy options that could be integrated in the climate-policy framework of developed countries. An energy-economic model with global coverage is used for the analysis. I find that connecting emissions transfers to international offset responsibilities is the most promising option from an environmental and economic perspective and may provide another rationale for international climate finance. The two alternative policy options of adjusting domestic emissions targets in developed countries and of implementing carbon-related tariffs and export subsidies are found to be environmentally ineffective in the latter case and economically detrimental, especially for developing countries, in both cases.

  19. MHD technology transfer, integration, and review committee

    NASA Astrophysics Data System (ADS)

    1990-05-01

    As part of Task 8 of the magnetohydrodynamic (MHD) Integrated Topping Cycle (ITC) project, TRW was given the responsibility to organize, charter and co-chair, with the Department of Energy (DOE), an MHD Technology Transfer, Integration and Review Committee (TTIRC). The TTIRC consists of an Executive Committee (EC) which acts as the governing body, and a General Committee (GC), also referred to as the main or full committee, consisting of representatives from the various POC contractors, participating universities and national laboratories, utilities, equipment suppliers, and other potential MHD users or investors. The purpose of the TTIRC is to: (1) review all Proof-of-Concept (POC) projects and schedules in the national MHD program; to assess their compatibility with each other and the first commercial MHD retrofit plant; (2) establish and implement technology transfer formats for users of this technology; (3) identify interfaces, issues, and funding structures directly impacting the success of the commercial retrofit; (4) investigate and identify the manner in which, and by whom, the above should be resolved; and (5) investigate and assess other participation (foreign and domestic) in the U.S. MHD Program. There are seven sections: introduction; Executive Committee and General Committee activity; Committee activities related to technology transfer; ongoing POC integration activities being performed under the auspices of the Executive Committee; recommendations passed on to the DOE by the Executive Committee; Planned activities for the next six months.

  20. Intermolecular energy-band dispersion in PTCDA multilayers

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kera, Satoshi; Okudaira, Koji K.; Yoshimura, Daisuke; Seki, Kazuhiko; Ueno, Nobuo

    2003-07-01

    The electronic structure of a well-oriented perylene-3,4,9,10-tetracarboxylic acid-dianhydride multilayer prepared on MoS2 single crystal surface were studied by angle-resolved ultraviolet photoemission spectroscopy using synchrotron radiation. From the photon energy dependence of normal emission spectra, we observed an intermolecular energy-band dispersion of about 0.2 eV for the highest occupied molecular orbital (HOMO) band of single π character. The observed energy-band dispersion showed a cosine curve, which originates from the intermolecular π-π interaction. Analyses using the tight-binding model gave that the transfer integral of about 0.05 eV for the π-π interaction, the effective mass of HOMO hole m*h=5.28m0, and the hole mobility μh>3.8 cm2/V s. This is the first observation of the intermolecular energy-band dispersion of a conventional single-component organic semiconductor only with the weak intermolecular van der Waals interaction.

  1. MHD Technology Transfer, Integration and Review Committee

    SciTech Connect

    Not Available

    1989-10-01

    As part of the MHD Integrated Topping Cycle (ITC) project, TRW was given the responsibility to organize, charter and co-chair, with the Department of Energy (DOE), an MHD Technology Transfer, Integration and Review Committee (TTIRC). The Charter of the TTIRC, which was approved by the DOE in June 1988 and distributed to the committee members, is included as part of this Summary. As stated in the Charter, the purpose of this committee is to: (1) review all Proof-of-Concept (POC) projects and schedules in the national MHD program; to assess their compatibility with each other and the first commercial MHD retrofit plant; (2) establish and implement technology transfer formats for users of this technology; (3) identify interfaces, issues, and funding structures directly impacting the success of the commercial retrofit; (4) investigate and identify the manner in which, and by whom, the above should be resolved; and (5) investigate and assess other participation (foreign and domestic) in the US MHD Program. The DOE fiscal year 1989 MHD Program Plan Schedule is included at the end of this Summary. The MHD Technology Transfer, Integration and Review Committee's activities to date have focused primarily on the technology transfer'' aspects of its charter. It has provided a forum for the dissemination of technical and programmatic information among workers in the field of MHD and to the potential end users, the utilities, by holding semi-annual meetings. The committee publishes this semi-annual report, which presents in Sections 2 through 11 capsule summaries of technical progress for all DOE Proof-of-Concept MHD contracts and major test facilities.

  2. Probing intermolecular couplings in liquid water with two-dimensional infrared photon echo spectroscopy

    NASA Astrophysics Data System (ADS)

    Paarmann, A.; Hayashi, T.; Mukamel, S.; Miller, R. J. D.

    2008-05-01

    Two-dimensional infrared photon echo and pump probe studies of the OH stretch vibration provide a sensitive probe of the correlations and couplings in the hydrogen bond network of liquid water. The nonlinear response is simulated using numerical integration of the Schrödinger equation with a Hamiltonian constructed to explicitly treat intermolecular coupling and nonadiabatic effects in the highly disordered singly and doubly excited vibrational exciton manifolds. The simulated two-dimensional spectra are in close agreement with our recent experimental results. The high sensitivity of the OH stretch vibration to the bath dynamics is found to arise from intramolecular mixing between states in the two-dimensional anharmonic OH stretch potential. Surprisingly small intermolecular couplings reproduce the experimentally observed intermolecular energy transfer times.

  3. Motivation to Transfer Training: An Integrative Literature Review

    ERIC Educational Resources Information Center

    Gegenfurtner, Andreas; Veermans, Koen; Festner, Dagmar; Gruber, Hans

    2009-01-01

    Motivation to transfer is essential for the transfer of training. Without motivation, newly acquired knowledge and skills will not be applied at work. The purpose of this integrative literature review is to summarize, critique, and synthesize past transfer motivation research and to offer directions for future investigations. First, seven…

  4. Orbital transfer vehicle engine integration study

    NASA Technical Reports Server (NTRS)

    Ketchum, W. J.

    1984-01-01

    NASA-LeRC is sponsoring industry studies to establish the technology base for an advanced engine for orbital transfer vehicles for mid-1990s IOC. Engine contractors are being assisted by vehicle contractors to define the requirements, interface conditions, and operational design criteria for new LO2-LH2 propulsion systems applicable to future orbit transfer vehicles and to assess the impacts on space basing, man rating, and low-G transfer missions on propulsion system design requirements. The results of a study is presented. The primary study emphasis was to determine what the OTV engine thrust level should be, how many engines are required on the OTV, and how the OTV engine should be designed. This was accomplished by evaluating planned OTV missions and concepts to determine the requirements for the OTV propulsion system, conducting tradeoffs and comparisons to optimize OTV capability, and evaluating reliability and maintenance to determine the recommended OTV engine design for future development.

  5. The Role of Facebook in Fostering Transfer Student Integration

    ERIC Educational Resources Information Center

    Nehls, Kimberly

    2014-01-01

    Persistence of transfer students is greatly influenced by academic and social integration at receiving institutions. The purpose of this study was to examine how transfer students and student affairs professionals used Facebook during the initial transition to campus. Findings from 15 different institutional Facebook groups revealed that transfer…

  6. Orbital transfer vehicle engine integration study

    NASA Technical Reports Server (NTRS)

    Ketchum, W. J.

    1985-01-01

    Industry studies were undertaken to establish the technology base for an advanced engine for Orbital Transfer Vehicles for mid-1990s IOC. This paper presents the results of a study conducted by General Dynamics Convair Division, under contract to Aerojet TechSystems Company for NASA-LeRC, to define requirements, interface conditions, and operational design criteria for new LO2/LH2 propulsion systems applicable to future Orbit Transfer Vehicles, and to assess the impacts of space basing, man rating, and low-g transfer on propulsion system design requirements. The primary study emphasis was to determine what the OTV engine thrust level should be, how many engines are required on the OTV, and how the OTV engine should be designed. This was accomplished by evaluating planned OTV missions and concepts to determine the requirements for the OTV propulsion system, conducting tradeoffs and comparisons to optimize OTV capability, and evaluating reliability and maintenance to determine the recommended OTV engine design for future development.

  7. Mikrokristallbildung und intermolekulare Triplett-Triplett-Energieiibertragung in festen transparenten Glasern bei 77 K. Das System N-Methylcarbazol/Naphthalin / Microcrystal Formation and Intermolecular Triplet-Triplet Energy Transfer in Rigid Transparent Glasses at 77 K. The System N-Methyl-earbazole / Naphthalene

    NASA Astrophysics Data System (ADS)

    Zander, M.

    1984-05-01

    The efficient intermolecular triplet-triplet energy transfer between N-methylcarbazole (donor) and naphthalene (acceptor) observed at 10-2 ᴍ concentration of donor and acceptor in a rigid transparent methylcyclohexane/n-pentane glass at 77 K is shown to occur in microcrystals of the donor containing small amounts of the acceptor

  8. Intermolecular electron transfer states of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium iodide obtained by constrained density functional theory.

    PubMed

    Otsuka, Takao; Sumita, Masato; Izawa, Hironori; Morihashi, Kenji

    2016-07-21

    Electron transfer (ET) states of 1-methyl-3-(N-(1,8-naphthalimidyl)ethyl)imidazolium iodide are responsible for its photophysics. Investigation of an ET state based on constrained density functional theory (CDFT) revealed that nonradiative decay from the ET excited state is mediated by the interaction of the iodine atom with the 1,8-naphthalimide or the imidazolium group. PMID:27222312

  9. Theoretical study of the transfer integral and density of states in spiro-linked triphenylamine derivatives.

    PubMed

    Kirkpatrick, James; Nelson, Jenny

    2005-08-22

    We present a method for calculating the parameters that control hopping transport in disordered molecular solids, i.e., the transfer integrals and the distribution of transport site energies. Average values of these parameters are obtained by performing quantum-chemical calculations on a large ensemble of bimolecular complexes in random relative orientations. The method is applied to triphenylamine (TPA) and three differently substituted spiro-linked phenylamine compounds, 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (spiro-MeOTAD), 2,2'7,7'-tetrakis-(N,N-diphenylhenylamino)-9,9'-spirobifluorene (spiro-TAD), and 2,2',7,7'-tetrakis-(N,N-di-m-methylphenylamino)-9,9'-spirobifluorene (spiro-m-TTB). In the case of TPA, the dependence of the root-mean-square hole transfer integral J on intermolecular separation r for the ensemble of relative orientations is compared with that obtained by performing the same calculations for a fixed, approximately cofacial, orientation of the two TPA molecules. The calculation for the disordered geometry predicts a larger localization radius r0, where J approximately exp(-r/r0), than the calculation for the fixed orientation and is in better agreement with experiment. In the case of the spiro-linked compounds, results from our method are compared with parameters extracted from time-of-flight mobility measurements analyzed with the Gaussian disorder model (GDM). We find that the highest occupied molecular-orbital (HOMO) energies of the bimolecular complexes are distributed on an asymmetric peak, whose width varies in qualitative agreement with the value of the energetic disorder sigma obtained from experimental data using the GDM. The mean-square hole transfer integral varies in accordance with the experimentally determined value of the mobility prefactor micro0. The differences between the differently substituted compounds are interpreted in terms of differences in the spatial extent of the wave function. Spiro

  10. Desensitization of metastable intermolecular composites

    DOEpatents

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

    2011-04-26

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

  11. A simple transfer function for nonlinear dendritic integration

    PubMed Central

    Singh, Matthew F.; Zald, David H.

    2015-01-01

    Relatively recent advances in patch clamp recordings and iontophoresis have enabled unprecedented study of neuronal post-synaptic integration (“dendritic integration”). Findings support a separate layer of integration in the dendritic branches before potentials reach the cell's soma. While integration between branches obeys previous linear assumptions, proximal inputs within a branch produce threshold nonlinearity, which some authors have likened to the sigmoid function. Here we show the implausibility of a sigmoidal relation and present a more realistic transfer function in both an elegant artificial form and a biophysically derived form that further considers input locations along the dendritic arbor. As the distance between input locations determines their ability to produce nonlinear interactions, models incorporating dendritic topology are essential to understanding the computational power afforded by these early stages of integration. We use the biophysical transfer function to emulate empirical data using biophysical parameters and describe the conditions under which the artificial and biophysically derived forms are equivalent. PMID:26321940

  12. Integrating proton coupled electron transfer (PCET) and excited states

    SciTech Connect

    Gagliardi, Christopher J.; Westlake, Brittany C.; Kent, Caleb A.; Paul, Jared J.; Papanikolas, John M.; Meyer, Thomas J.

    2010-11-01

    In many of the chemical steps in photosynthesis and artificial photosynthesis, proton coupled electron transfer (PCET) plays an essential role. An important issue is how excited state reactivity can be integrated with PCET to carry out solar fuel reactions such as water splitting into hydrogen and oxygen or water reduction of CO2 to methanol or hydrocarbons. The principles behind PCET and concerted electron–proton transfer (EPT) pathways are reasonably well understood. In Photosystem II antenna light absorption is followed by sensitization of chlorophyll P680 and electron transfer quenching to give P680+. The oxidized chlorophyll activates the oxygen evolving complex (OEC), a CaMn4 cluster, through an intervening tyrosine–histidine pair, YZ. EPT plays a major role in a series of four activation steps that ultimately result in loss of 4e-/4H+ from the OEC with oxygen evolution. The key elements in photosynthesis and artificial photosynthesis – light absorption, excited state energy and electron transfer, electron transfer activation of multiple-electron, multiple-proton catalysis – can also be assembled in dye sensitized photoelectrochemical synthesis cells (DS-PEC). In this approach, molecular or nanoscale assemblies are incorporated at separate electrodes for coupled, light driven oxidation and reduction. Separate excited state electron transfer followed by proton transfer can be combined in single semi-concerted steps (photo-EPT) by photolysis of organic charge transfer excited states with H-bonded bases or in metal-to-ligand charge transfer (MLCT) excited states in pre-associated assemblies with H-bonded electron transfer donors or acceptors. In these assemblies, photochemically induced electron and proton transfer occur in a single, semi-concerted event to give high-energy, redox active intermediates.

  13. Early Integration and Other Outcomes for Community College Transfer Students

    ERIC Educational Resources Information Center

    D'Amico, Mark M.; Dika, Sandra L.; Elling, Theodore W.; Algozzine, Bob; Ginn, Donna J.

    2014-01-01

    The purpose of this study was to explore academic and social integration and other outcomes for community college transfer students. The study used Tinto's ("Leaving college: Rethinking the causes and cures of student attrition," 1993) "Longitudinal Model of Institutional Departure" and Deil-Amen's ("J Higher…

  14. Double-shell tank waste transfer facilities integrity assessment plan

    SciTech Connect

    Hundal, T.S.

    1998-09-30

    This document presents the integrity assessment plan for the existing double-shell tank waste transfer facilities system in the 200 East and 200 West Areas of Hanford Site. This plan identifies and proposes the integrity assessment elements and techniques to be performed for each facility. The integrity assessments of existing tank systems that stores or treats dangerous waste is required to be performed to be in compliance with the Washington State Department of Ecology Dangerous Waste Regulations, Washington Administrative Code WAC-173-303-640 requirements.

  15. Prediction of local and integrated heat transfer in nozzles using an integral turbulent boundary layer method

    NASA Technical Reports Server (NTRS)

    Boldman, D. R.; Schmidt, J. F.; Ehlers, R. C.

    1972-01-01

    An empirical modification of an existing integral energy turbulent boundary layer method is proposed in order to improve the estimates of local heat transfer in converging-diverging nozzles and consequently, provide better assessments of the total or integrated heat transfer. The method involves the use of a modified momentum-heat analogy which includes an acceleration term comprising the nozzle geometry and free stream velocity. The original and modified theories are applied to heat transfer data from previous studies which used heated air in 30 deg - 15 deg, 45 deg - 15 deg, and 60 deg - 15 deg water-cooled nozzles.

  16. New Type of Dual Solid-State Thermochromism: Modulation of Intramolecular Charge Transfer by Intermolecular π-π Interactions, Kinetic Trapping of the Aci-Nitro Group, and Reversible Molecular Locking

    NASA Astrophysics Data System (ADS)

    Naumov, Panče; Lee, Sang Cheol; Ishizawa, Nobuo; Jeong, Young Gyu; Chung, Ihn Hee; Fukuzumi, Shunichi

    2009-09-01

    intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular π-π interactions and thermal intramolecular proton transfer to aromatic nitro group.

  17. New type of dual solid-state thermochromism: modulation of intramolecular charge transfer by intermolecular pi-pi interactions, kinetic trapping of the aci-nitro group, and reversible molecular locking.

    PubMed

    Naumov, Pance; Lee, Sang Cheol; Ishizawa, Nobuo; Jeong, Young Gyu; Chung, Ihn Hee; Fukuzumi, Shunichi

    2009-10-22

    by intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular pi-pi interactions and thermal intramolecular proton transfer to aromatic nitro group. PMID:19780605

  18. Intermolecular electrostatic energies using density fitting

    PubMed Central

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

    2009-01-01

    A method is presented to calculate the electron-electron and nuclear-electron intermolecular Coulomb interaction energy between two molecules by separately fitting the unperturbed molecular electron density of each monomer. This method is based on the variational Coulomb fitting method which relies on the expansion of the ab initio molecular electron density in site-centered auxiliary basis sets. By expanding the electron density of each monomer in this way the integral expressions for the intermolecular electrostatic calculations are simplified, lowering the operation count as well as the memory usage. Furthermore, this method allows the calculation of intermolecular Coulomb interactions with any level of theory from which a one-electron density matrix can be obtained. Our implementation is initially tested by calculating molecular properties with the density fitting method using three different auxiliary basis sets and comparing them to results obtained from ab initio calculations. These properties include dipoles for a series of molecules, as well as the molecular electrostatic potential and electric field for water. Subsequently, the intermolecular electrostatic energy is tested by calculating ten stationary points on the water dimer potential-energy surface. Results are presented for electron densities obtained at four different levels of theory using two different basis sets, fitted with three auxiliary basis sets. Additionally, a one-dimensional electrostatic energy surface scan is performed for four different systems (H2O dimer, Mg2+–H2O, Cu+–H2O, and n-methyl-formamide dimer). Our results show a very good agreement with ab initio calculations for all properties as well as interaction energies. PMID:16095348

  19. Maximizing Singlet Fission by Intermolecular Packing.

    PubMed

    Wang, Linjun; Olivier, Yoann; Prezhdo, Oleg V; Beljonne, David

    2014-10-01

    A novel nonadiabatic molecular dynamics scheme is applied to study the singlet fission (SF) process in pentacene dimers as a function of longitudinal and lateral displacements of the molecular backbones. Detailed two-dimensional mappings of both instantaneous and long-term triplet yields are obtained, characterizing the advantageous and unfavorable stacking arrangements, which can be achieved by chemical substitutions to the bare pentacene molecule. We show that the SF rate can be increased by more than an order of magnitude through tuning the intermolecular packing, most notably when going from cofacial to the slipped stacked arrangements encountered in some pentacene derivatives. The simulations indicate that the SF process is driven by thermal electron-phonon fluctuations at ambient and high temperatures, expected in solar cell applications. Although charge-transfer states are key to construct continuous channels for SF, a large charge-transfer character of the photoexcited state is found to be not essential for efficient SF. The reported time domain study mimics directly numerous laser experiments and provides novel guidelines for designing efficient photovoltaic systems exploiting the SF process with optimum intermolecular packing. PMID:26278443

  20. Intermolecular Silacarbonyl Ylide Cycloadditions: A Direct Pathway to Oxasilacyclopentenes

    PubMed Central

    Bourque, Laura E.; Woerpel, K. A.

    2009-01-01

    Silacarbonyl ylides, generated by metal-catalyzed silylene transfer to carbonyls, participate in formal intermolecular 1,3-dipolar cycloaddition reactions with carbonyl compounds and alkynes to form dioxasilacyclopentane acetals and oxasilacyclopentenes in an efficient, one-step process. PMID:18922005

  1. Integration of Heat Transfer, Stress, and Particle Trajectory Simulation

    SciTech Connect

    Thuc Bui; Michael Read; Lawrence ives

    2012-05-17

    Calabazas Creek Research, Inc. developed and currently markets Beam Optics Analyzer (BOA) in the United States and abroad. BOA is a 3D, charged particle optics code that solves the electric and magnetic fields with and without the presence of particles. It includes automatic and adaptive meshing to resolve spatial scales ranging from a few millimeters to meters. It is fully integrated with CAD packages, such as SolidWorks, allowing seamless geometry updates. The code includes iterative procedures for optimization, including a fully functional, graphical user interface. Recently, time dependent, particle in cell capability was added, pushing particles synchronically under quasistatic electromagnetic fields to obtain particle bunching under RF conditions. A heat transfer solver was added during this Phase I program. Completed tasks include: (1) Added a 3D finite element heat transfer solver with adaptivity; (2) Determined the accuracy of the linear heat transfer field solver to provide the basis for development of higher order solvers in Phase II; (3) Provided more accurate and smoother power density fields; and (4) Defined the geometry using the same CAD model, while maintaining different meshes, and interfacing the power density field between the particle simulator and heat transfer solvers. These objectives were achieved using modern programming techniques and algorithms. All programming was in C++ and parallelization in OpenMP, utilizing state-of-the-art multi-core technology. Both x86 and x64 versions are supported. The GUI design and implementation used Microsoft Foundation Class.

  2. Integrated Charge Transfer in Organic Ferroelectrics for Flexible Multisensing Materials.

    PubMed

    Xu, Beibei; Ren, Shenqiang

    2016-09-01

    The ultimate or end point of functional materials development is the realization of strong coupling between all energy regimes (optical, electronic, magnetic, and elastic), enabling the same material to be utilized for multifunctionalities. However, the integration of multifunctionalities in soft materials with the existence of various coupling is still in its early stage. Here, the coupling between ferroelectricity and charge transfer by combining bis(ethylenedithio)tetrathiafulvalene-C60 charge-transfer crystals with ferroelectric polyvinylidene fluoride polymer matrix is reported, which enables external stimuli-controlled polarization, optoelectronic and magnetic field sensing properties. Such flexible composite films also display a superior strain-dependent capacitance and resistance change with a giant piezoresistance coefficient of 7.89 × 10(-6) Pa(-1) . This mutual coupled material with the realization of enhanced couplings across these energy domains opens up the potential for multisensing applications. PMID:27378088

  3. State-transfer simulation in integrated waveguide circuits

    NASA Astrophysics Data System (ADS)

    Latmiral, L.; Di Franco, C.; Mennea, P. L.; Kim, M. S.

    2015-08-01

    Spin-chain models have been widely studied in terms of quantum information processes, for instance for the faithful transmission of quantum states. Here, we investigate the limitations of mapping this process to an equivalent one through a bosonic chain. In particular, we keep in mind experimental implementations, which the progress in integrated waveguide circuits could make possible in the very near future. We consider the feasibility of exploiting the higher dimensionality of the Hilbert space of the chain elements for the transmission of a larger amount of information, and the effects of unwanted excitations during the process. Finally, we exploit the information-flux method to provide bounds to the transfer fidelity.

  4. Integrated controls and health monitoring for chemical transfer propulsion

    NASA Technical Reports Server (NTRS)

    Millis, Marc G.; Binder, Michael P.

    1990-01-01

    NASA is reviewing various propulsion technologies for exploring space. The requirements are examined for one enabling propulsion technology: Integrated Controls and Health Monitoring (ICHM) for Chemical Transfer Propulsion (CTP). Functional requirements for a CTP-ICHM system are proposed from tentative mission scenarios, vehicle configurations, CTP specifications, and technical feasibility. These CTP-ICHM requirements go beyond traditional reliable operation and emergency shutoff control to include: (1) enhanced mission flexibility; (2) continuously variable throttling; (3) tank-head start control; (4) automated prestart and post-shutoff engine check; (5) monitoring of space exposure degradation; and (6) product evolution flexibility. Technology development plans are also discussed.

  5. Transition-density-fragment interaction combined with transfer integral approach for excitation-energy transfer via charge-transfer states

    NASA Astrophysics Data System (ADS)

    Fujimoto, Kazuhiro J.

    2012-07-01

    A transition-density-fragment interaction (TDFI) combined with a transfer integral (TI) method is proposed. The TDFI method was previously developed for describing electronic Coulomb interaction, which was applied to excitation-energy transfer (EET) [K. J. Fujimoto and S. Hayashi, J. Am. Chem. Soc. 131, 14152 (2009)] and exciton-coupled circular dichroism spectra [K. J. Fujimoto, J. Chem. Phys. 133, 124101 (2010)]. In the present study, the TDFI method is extended to the exchange interaction, and hence it is combined with the TI method for applying to the EET via charge-transfer (CT) states. In this scheme, the overlap correction is also taken into account. To check the TDFI-TI accuracy, several test calculations are performed to an ethylene dimer. As a result, the TDFI-TI method gives a much improved description of the electronic coupling, compared with the previous TDFI method. Based on the successful description of the electronic coupling, the decomposition analysis is also performed with the TDFI-TI method. The present analysis clearly shows a large contribution from the Coulomb interaction in most of the cases, and a significant influence of the CT states at the small separation. In addition, the exchange interaction is found to be small in this system. The present approach is useful for analyzing and understanding the mechanism of EET.

  6. Design study of an integrated aerobraking orbital transfer vehicle

    NASA Technical Reports Server (NTRS)

    Scott, C. D.; Roberts, B. B.; Nagy, K.; Taylor, P.; Gamble, J. D.; Ceremeli, C. J.; Knoll, K. R.; Li, C. P.; Reid, R. C.

    1985-01-01

    An aerobraking orbital transfer vehicle (AOTV) concept, which has an aerobrake structure that is integrated with the propulsion stage, is discussed. The concept vehicle is to be assembled in space and is space-based. The advantages of aeroassist over an all propulsive vehicle are discussed and it is shown that the vehicle considered is very competitive with inflatable and deployable concepts from mass and performance aspects. The aerobrake geometry is an ellipsoidally blunted, raked-off, elliptical wide-angle cone with a toroidal skirt. Propellant tanks, engines, and subsystems are integrated into a closed, isogrid aerobrake structure which provides rigidity. The vehicle has two side-firing, gimbaled RL-10 type engines and carries 38,000 kg of useable propellant. The trajectory during aerobraking is determined from an adaptive guidance logic, and the heating is determined from engineering correlations as well as 3-D Navier-Stokes solutions. The AOTV is capable of placing 13,500 kg payload into geosynchronous Earth orbit (GEO) or carrying a LEO-GEO-LEO round-trip payload of 7100 kg. A two-stage version considered for lunar missions results in a lunar surface delivery capability of 18,000 kg or a round-trip capability of 6800 kg with 3860 kg delivery-only capability.

  7. Academic Transfer Shock and Social Integration: A Comparison of Outcomes for Traditional and Nontraditional Students Transferring from 2-Year to 4-Year Institutions

    ERIC Educational Resources Information Center

    Strahn-Koller, Brooke Lindsey

    2012-01-01

    The purpose of this study was to explore whether traditional and nontraditional students who transferred from 2-year to 4-year institutions experienced differences in transfer shock, academic integration, and social integration. A substantial body of knowledge comparing transfer students to native students on transfer shock exists, while only a…

  8. 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.

  9. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

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

    2010-09-07

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

  10. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    SciTech Connect

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  11. Kinetic theory for flows of nonhomogeneous rodlike liquid crystalline polymers with a nonlocal intermolecular potential.

    PubMed

    Wang, Qi; E, Weinan; Liu, Chun; Zhang, Pingwen

    2002-05-01

    The Doi kinetic theory for flows of homogeneous, rodlike liquid crystalline polymers (LCPs) is extended to model flows of nonhomogeneous, rodlike LCPs through a nonlocal (long-range) intermolecular potential. The theory features (i) a nonlocal, anisotropic, effective intermolecular potential in an integral form that is consistent with the chemical potential, (ii) short-range elasticity as well as long-range isotropic and anisotropic elasticity, (iii) a closed-form stress expression accounting for the nonlocal molecular interaction, and (iv) an extra elastic body force exclusively associated with the integral form of the intermolecular potential. With the effective intermolecular potential, the theory is proven to be well posed in that it warrants a positive entropy production and thereby the second law of thermodynamics. Approximate theories are obtained by gradient expansions of the number density function in the free energy density. PMID:12059561

  12. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

    High resolution spectroscopy of the low frequency van der Waals vibrations (also referred to as Vibration -Rotation-Tunneling (VRT) spectroscopy) in weakly bound complexes provides the means to probe intermolecular forces with unprecedented detail and precision. We present an overview of the experimental information on intermolecular forces and intermolecular dynamics which has been obtained by far infrared VRT spectroscopy of 18 complexes. We then turn to a detailed examination of the Ar-H_2O complex, a simple prototype for the study of intermolecular forces. The measurement and analysis of 9 VRT bands is described. These data are first used to obtain a qualitative description of the intermolecular potential energy surface (IPS). A new simple and efficient method for calculating the eigenvalues of the multidimensional intermolecular dynamics on the IPS has been developed. This algorithm (an adaptation of the Collocation Method) was then used in a direct fit to obtain an accurate and detailed description of the intermolecular forces acting within the Ar-H_2O complex.

  13. 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

  14. Advising Underprepared Transfer Students: Integrating English Assessment and Academic Advising.

    ERIC Educational Resources Information Center

    Cooper, Elizabeth J.; Franke, Johannah S.

    1992-01-01

    The City University of New York's Lehman College requires entering transfer students to demonstrate writing proficiency for appropriate placement. Academic advising is used to help students understand the need for this assessment. The relatively complex system has been found to save students' time, promote academic achievement, and improve…

  15. Teaching for Transfer through Integrated Online and Traditional Art Instruction

    ERIC Educational Resources Information Center

    Erickson, Mary

    2005-01-01

    This is an exploratory, design-based study of the development and implementation of an online art unit designed to teach for transfer. Secondary art teachers implemented a traditional and then a revised Web version of the unit. Four kinds of knowledge (content, procedural, strategic, and dispositional) provide the structure for reporting: a)…

  16. Lateral Transfer Students: The Role of Housing in Social Integration and Transition

    ERIC Educational Resources Information Center

    Utter, Mary; DeAngelo, Linda

    2015-01-01

    Social integration for lateral transfer students (four-to-four-year) is promoted by a living environment that encourages learning about campus, connecting to resources, and developing peer groups. Interviews with 27 lateral transfer students revealed that those who had previously lived on campus had expectations that residence halls would provide…

  17. Transfer of plasmid RP4 to Myxococcus xanthus and evidence for its integration into the chromosome.

    PubMed Central

    Breton, A M; Jaoua, S; Guespin-Michel, J

    1985-01-01

    The broad-host-range plasmid RP4 and its derivative R68.45 were transferred to Myxococcus xanthus DK101 and DZ1; RP4 was maintained integrated in the chromosome. Loss of plasmid markers occurred during the growth of the transconjugants, which could be prevented by selective pressure with oxytetracycline. The integrated plasmid was transferred back to Escherichia coli often as RP4-prime plasmids carrying various segments of the M. xanthus chromosome. It also mediated chromosomal transfer between M. xanthus strains. Images PMID:3918015

  18. Investigating Practices in Teacher Education That Promote and Inhibit Technology Integration Transfer in Early Career Teachers

    ERIC Educational Resources Information Center

    Brenner, Aimee M.; Brill, Jennifer M.

    2016-01-01

    The purpose of this study was to identify instructional technology integration strategies and practices in preservice teacher education that contribute to the transfer of technology integration knowledge and skills to the instructional practices of early career teachers. This study used a two-phase, sequential explanatory strategy. Data were…

  19. Controlled electrical doping of organic semiconductors: a combined intra- and intermolecular perspective from first principles.

    PubMed

    Joo, Bora; Kim, Eung-Gun

    2016-07-21

    The process of introducing extra charge carriers into organic semiconductors, or simply molecular doping, takes place via intermolecular charge transfer from the donor to the acceptor molecule. Using density functional theory calculations on diverse donor-acceptor pairs, we show that there are two modes of charge transfer; in one, charge transfer is controlled by the sign and in the other, by the magnitude of the donor HOMO-acceptor LUMO level offset. Despite doping being an intermolecular process, the identification of the transfer modes requires a full account of intramolecular geometric changes during charge transfer. We further show that the degree of charge transfer can be represented entirely by the reorganization energy, a common measure of geometric changes, of either the donor or the acceptor. PMID:27314750

  20. Computer integrated manufacturing and technology transfer for improving aerospace productivity

    NASA Astrophysics Data System (ADS)

    Farrington, P. A.; Sica, J.

    1992-03-01

    This paper reviews a cooperative effort, between the Alabama Industial Development Training Institute and the University of Alabama in Huntsville, to implement a prototype computer integrated manufacturing system. The primary use of this system will be to educate Alabama companies on the organizational and technological issues involved in the implementation of advanced manufacturing systems.

  1. A New Integrated Approach for the Transfer of Knowledge

    ERIC Educational Resources Information Center

    Lazanas, P.

    2006-01-01

    One of the purposes of knowledge generation at the higher education level is the creation of expertise. However, the mental structures that an expert uses to process information are not generally considered. Instead, information alone is presented to the learner and it is hoped that he or she will somehow integrate this information into knowledge…

  2. Activated-Carbon Sorbent With Integral Heat-Transfer Device

    NASA Technical Reports Server (NTRS)

    Jones, Jack A.; Yavrouian, Andre

    1996-01-01

    Prototype adsorption device used, for example, in adsorption heat pump, to store natural gas to power automobile, or to separate components of fluid mixtures. Device includes activated carbon held together by binder and molded into finned heat-transfer device providing rapid heating or cooling to enable rapid adsorption or desorption of fluids. Concepts of design and fabrication of device equally valid for such other highly thermally conductive devices as copper-finned tubes, and for such other high-surface-area sorbents as zeolites or silicates.

  3. Fractional integration and radiative transfer in a multifractal atmosphere

    SciTech Connect

    Naud, C.; Schertzer, D.; Lovejoy, S.

    1996-04-01

    Recently, Cess et al. (1995) and Ramathan et al. (1995) cited observations which exhibit an anomalous absorption of cloudy skies in comparison with the value predicted by usual models and which thus introduce large uncertainties for climatic change assessments. These observation raise questions concerning the way general circulation models have been tuned for decades, relying on classical methods, of both radiative transfer and dynamical modeling. The observations also tend to demonstrate that homogeneous models are simply not relevant in relating the highly variable properties of clouds and radiation fields. However smoothed, the intensity of cloud`s multi-scattered radiation fields reflect this extreme variability.

  4. Intermolecular Hydropyridylation of Unactivated Alkenes.

    PubMed

    Ma, Xiaoshen; Herzon, Seth B

    2016-07-20

    A general method for the hydropyridylation of unactivated alkenes is described. The transformation connects metal-mediated hydrogen atom transfer to alkenes and Minisci addition reactions. The reaction proceeds under mild conditions with high site-selectivities and allows for the construction of tertiary and quaternary centers from simple alkene starting materials. PMID:27384921

  5. Time delay and integration detectors using charge transfer devices

    NASA Technical Reports Server (NTRS)

    Mccann, D. H.; White, M. H.; Turly, A. P.

    1981-01-01

    An imaging system comprises a multi-channel matrix array of CCD devices wherein a number of sensor cells (pixels) in each channel are subdivided and operated in discrete intercoupled groups of subarrays with a readout CCD shift register terminating each end of the channels. Clock voltages, applied to the subarrays, selectively cause charge signal flow in each subarray in either direction independent of the other subarrays. By selective application of four phase clock voltages, either one, two or all three of the sections subarray sections cause charge signal flow in one direction, while the remainder cause charge signal flow in the opposite direction. This creates a form of selective electronic exposure control which provides an effective variable time delay and integration of three, six or nine sensor cells or integration stages. The device is constructed on a semiconductor sustrate with a buried channel and is adapted for front surface imaging through transparent doped tin oxide gates.

  6. 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.

  7. Conjugative transposons: an unusual and diverse set of integrated gene transfer elements.

    PubMed Central

    Salyers, A A; Shoemaker, N B; Stevens, A M; Li, L Y

    1995-01-01

    Conjugative transposons are integrated DNA elements that excise themselves to form a covalently closed circular intermediate. This circular intermediate can either reintegrate in the same cell (intracellular transposition) or transfer by conjugation to a recipient and integrate into the recipient's genome (intercellular transposition). Conjugative transposons were first found in gram-positive cocci but are now known to be present in a variety of gram-positive and gram-negative bacteria also. Conjugative transposons have a surprisingly broad host range, and they probably contribute as much as plasmids to the spread of antibiotic resistance genes in some genera of disease-causing bacteria. Resistance genes need not be carried on the conjugative transposon to be transferred. Many conjugative transposons can mobilize coresident plasmids, and the Bacteroides conjugative transposons can even excise and mobilize unlinked integrated elements. The Bacteroides conjugative transposons are also unusual in that their transfer activities are regulated by tetracycline via a complex regulatory network. PMID:8531886

  8. Integration of laser die transfer and magnetic self-assembly for ultra-thin chip placement

    NASA Astrophysics Data System (ADS)

    Eda Kuran, Emine; Berg, Yuval; Tichem, Marcel; Kotler, Zvi

    2015-04-01

    In this paper, we demonstrate the integration of a novel self-assembly method with laser die transfer for ultra-thin chip (UTC) placement. The laser die transfer technique provides high speed chip presentation into the assembly positions on the substrate, where the magnetic self-assembly traps and aligns the chips. Combination of these two technologies allows handling of UTCs without a direct mechanical contact throughout the assembly flow and provides high precision chip placement.

  9. Demonstration of strong near-field radiative heat transfer between integrated nanostructures.

    PubMed

    St-Gelais, Raphael; Guha, Biswajeet; Zhu, Linxiao; Fan, Shanhui; Lipson, Michal

    2014-12-10

    Near-field heat transfer recently attracted growing interest but was demonstrated experimentally only in macroscopic systems. However, several projected applications would be relevant mostly in integrated nanostructures. Here we demonstrate a platform for near-field heat transfer on-chip and show that it can be the dominant thermal transport mechanism between integrated nanostructures, overcoming background substrate conduction and the far-field limit (by factors 8 and 7, respectively). Our approach could enable the development of active thermal control devices such as thermal rectifiers and transistors. PMID:25420115

  10. Development of Innovative Integrated Simulator on Shipboard Crane Considering Ship Sway and Transfer Control

    NASA Astrophysics Data System (ADS)

    Ito, Ryuji; Terashima, Kazuhiko; Noda, Yoshiyuki; Iwasa, Takahiro

    In this paper, in order to systemize the state analysis of a shipboard crane, the integrated computer simulator tool of rotary crane with ship behavior in consideration of ship sway is newly built. The integrated simulator of shipboard crane considering ship sway was realized by corporating an external force interface routine of a component with Fluid analysis software. The transfer control system is conducted by HSA (Hybrid Shape Approach) using STT (Straight Transfer Transformation) method. The proposal method was confirmed to be effective in order to reduce both sway of a ship and a load by the simulation analysis.

  11. Shedding light on the photostability of two intermolecular charge-transfer complexes between highly fluorescent bis-1,8-naphthalimide dyes and some π-acceptors: A spectroscopic study in solution and solid states

    NASA Astrophysics Data System (ADS)

    Refat, Moamen S.; Ismail, Lamia A.; Adam, Abdel Majid A.

    2015-01-01

    Given the great importance of the various uses of 1,8-naphthalimides in the trends of biology, medicine and industry, the current study focused on extending the scope of these dyes by introducing some of their charge-transfer (CT) complexes. For this purpose, two highly fluorescent bis-1,8-naphthalimide dyes and their complexes with some π-acceptors have been synthesized and characterized spectroscopically. The π-acceptors include picric acid (PA), chloranilic acid (CLA), tetracyanoquinodimethane (TCNQ) and dichlorodicyanobenzoquinone (DDQ). The molecular structure, spectroscopic and fluorescence properties as well as the binding modes were deduced from IR, UV-vis and 1H NMR spectral studies. The binding ratio of complexation was determined to be 1:1 according to the elemental analyses and photometric titrations. It has been found that the order of acceptance ability for the different acceptors is TCNQ > DDQ > CLA > PA. The photostability of 1,8-naphthalimide dye as a donor and its charge-transfer complex doped in polymethyl methacrylate/PMMA were exposed to UV-Vis radiation and the change in the absorption spectra was achieved at different times during irradiation period.

  12. Shedding light on the photostability of two intermolecular charge-transfer complexes between highly fluorescent bis-1,8-naphthalimide dyes and some π-acceptors: a spectroscopic study in solution and solid states.

    PubMed

    Refat, Moamen S; Ismail, Lamia A; Adam, Abdel Majid A

    2015-01-01

    Given the great importance of the various uses of 1,8-naphthalimides in the trends of biology, medicine and industry, the current study focused on extending the scope of these dyes by introducing some of their charge-transfer (CT) complexes. For this purpose, two highly fluorescent bis-1,8-naphthalimide dyes and their complexes with some π-acceptors have been synthesized and characterized spectroscopically. The π-acceptors include picric acid (PA), chloranilic acid (CLA), tetracyanoquinodimethane (TCNQ) and dichlorodicyanobenzoquinone (DDQ). The molecular structure, spectroscopic and fluorescence properties as well as the binding modes were deduced from IR, UV-vis and (1)H NMR spectral studies. The binding ratio of complexation was determined to be 1:1 according to the elemental analyses and photometric titrations. It has been found that the order of acceptance ability for the different acceptors is TCNQ>DDQ>CLA>PA. The photostability of 1,8-naphthalimide dye as a donor and its charge-transfer complex doped in polymethyl methacrylate/PMMA were exposed to UV-Vis radiation and the change in the absorption spectra was achieved at different times during irradiation period. PMID:25022501

  13. Estimation of intermolecular interactions in polymer networks

    SciTech Connect

    Subrananian, P.R.; Galiatsatos, V.

    1993-12-31

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

  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. 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

  16. Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane.

    PubMed

    Walters, Peter L; Makri, Nancy

    2015-12-17

    We employ the quantum-classical path integral methodology to simulate the outer sphere charge-transfer process of the ferrocene-ferrocenium pair in liquid hexane with unprecedented accuracy. Comparison of the simulation results to those obtained by mapping the solvent on an effective harmonic bath demonstrates the accuracy of linear response theory in this system. PMID:26673195

  17. Integrating Key Skills in Higher Education: Employability, Transferable Skills and Learning for Life.

    ERIC Educational Resources Information Center

    Fallows, Stephen, Ed.; Steven, Christine, Ed.

    This book addresses issues related to the skills agenda in higher education, focusing on key skills, employability skills, transferable skills, and core skills. The chapters provide a practical guide to the ways skills can be effectively integrated into courses and institutions. The chapters are: (1) "The Skills Agenda" (Stephen Fallows and…

  18. Measurements of the Influence of Integral Length Scale on Stagnation Region Heat Transfer

    NASA Technical Reports Server (NTRS)

    Vanfossen, G. James; Ching, Chang Y.

    1994-01-01

    The purpose was twofold: first, to determine if a length scale existed that would cause the greatest augmentation in stagnation region heat transfer for a given turbulence intensity and second, to develop a prediction tool for stagnation heat transfer in the presence of free stream turbulence. Toward this end, a model with a circular leading edge was fabricated with heat transfer gages in the stagnation region. The model was qualified in a low turbulence wind tunnel by comparing measurements with Frossling's solution for stagnation region heat transfer in a laminar free stream. Five turbulence generating grids were fabricated; four were square mesh, biplane grids made from square bars. Each had identical mesh to bar width ratio but different bar widths. The fifth grid was an array of fine parallel wires that were perpendicular to the axis of the cylindrical leading edge. Turbulence intensity and integral length scale were measured as a function of distance from the grids. Stagnation region heat transfer was measured at various distances downstream of each grid. Data were taken at cylinder Reynolds numbers ranging from 42,000 to 193,000. Turbulence intensities were in the range 1.1 to 15.9 percent while the ratio of integral length scale to cylinder diameter ranged from 0.05 to 0.30. Stagnation region heat transfer augmentation increased with decreasing length scale. An optimum scale was not found. A correlation was developed that fit heat transfer data for the square bar grids to within +4 percent. The data from the array of wires were not predicted by the correlation; augmentation was higher for this case indicating that the degree of isotropy in the turbulent flow field has a large effect on stagnation heat transfer. The data of other researchers are also compared with the correlation.

  19. Clean graphene interfaces by selective dry transfer for large area silicon integration.

    PubMed

    Na, S R; Rahimi, S; Tao, L; Chou, H; Ameri, S K; Akinwande, D; Liechti, K M

    2016-03-31

    Here we present a very fast, selective mechanical approach for transferring graphene with low levels of copper contamination from seed wafers on which it was grown to target wafers for very large scale integration (VLSI) electronics. We found that graphene/copper or copper/silicon oxide delamination paths could be selected by slow and faster separation rates, respectively. Thus graphene can be transferred to a target wafer, either exposed or protected by the seed copper layer, which can later be removed by etching. Delamination paths were identified by SEM and Raman spectroscopy. The sheet resistance of the graphene produced by the two approaches was slightly higher than graphene transferred by a PMMA wet-transfer process, indicating reduced impurity doping, and the variation in the sheet resistance values was much lower. Copper contamination levels, quantitatively established by TOF-SIMS, were several orders of magnitude lower than the values for PMMA assisted transfer. In addition, we demonstrated that top-gated transistor devices from our mechanical, delamination transferred graphene exhibited superior transistor behavior to PMMA-assisted wet transfer graphene. The adhesion energy, strength and range of the interactions were quantitatively determined by nonlinear fracture analyses, and suggest that the roughness of the interface between graphene and copper plays an important role with implications for improvements in manufacturing processes. PMID:26902897

  20. Computational modelling of placental amino acid transfer as an integrated system.

    PubMed

    Panitchob, N; Widdows, K L; Crocker, I P; Johnstone, E D; Please, C P; Sibley, C P; Glazier, J D; Lewis, R M; Sengers, B G

    2016-07-01

    Placental amino acid transfer is essential for fetal development and its impairment is associated with poor fetal growth. Amino acid transfer is mediated by a broad array of specific plasma membrane transporters with overlapping substrate specificity. However, it is not fully understood how these different transporters work together to mediate net flux across the placenta. Therefore the aim of this study was to develop a new computational model to describe how human placental amino acid transfer functions as an integrated system. Amino acid transfer from mother to fetus requires transport across the two plasma membranes of the placental syncytiotrophoblast, each of which contains a distinct complement of transporter proteins. A compartmental modelling approach was combined with a carrier based modelling framework to represent the kinetics of the individual accumulative, exchange and facilitative classes of transporters on each plasma membrane. The model successfully captured the principal features of transplacental transfer. Modelling results clearly demonstrate how modulating transporter activity and conditions such as phenylketonuria, can increase the transfer of certain groups of amino acids, but that this comes at the cost of decreasing the transfer of others, which has implications for developing clinical treatment options in the placenta and other transporting epithelia. PMID:27045077

  1. Entropy-Based Analysis and Bioinformatics-Inspired Integration of Global Economic Information Transfer

    PubMed Central

    An, Sungbae; Kwon, Young-Kyun; Yoon, Sungroh

    2013-01-01

    The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs) between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis. PMID:23300959

  2. Entropy-based analysis and bioinformatics-inspired integration of global economic information transfer.

    PubMed

    Kim, Jinkyu; Kim, Gunn; An, Sungbae; Kwon, Young-Kyun; Yoon, Sungroh

    2013-01-01

    The assessment of information transfer in the global economic network helps to understand the current environment and the outlook of an economy. Most approaches on global networks extract information transfer based mainly on a single variable. This paper establishes an entirely new bioinformatics-inspired approach to integrating information transfer derived from multiple variables and develops an international economic network accordingly. In the proposed methodology, we first construct the transfer entropies (TEs) between various intra- and inter-country pairs of economic time series variables, test their significances, and then use a weighted sum approach to aggregate information captured in each TE. Through a simulation study, the new method is shown to deliver better information integration compared to existing integration methods in that it can be applied even when intra-country variables are correlated. Empirical investigation with the real world data reveals that Western countries are more influential in the global economic network and that Japan has become less influential following the Asian currency crisis. PMID:23300959

  3. Direct effects of ionizing radiation on integral membrane proteins. Noncovalent energy transfer requires specific interpeptide interactions

    SciTech Connect

    Jhun, E.; Jhun, B.H.; Jones, L.R.; Jung, C.Y. )

    1991-05-25

    The 12 transmembrane alpha helices (TMHs) of human erythrocyte glucose transporter were individually cut by pepsin digestion as membrane-bound 2.5-3.5-kDa peptide fragments. Radiation-induced chemical degradation of these fragments showed an average target size of 34 kDa. This is 10-12 x larger than the average size of an individual TMH, demonstrating that a significant energy transfer occurs among these TMHs in the absence of covalent linkage. Heating this TMH preparation at 100{degree}C for 15 min reduced the target size to 5 kDa or less, suggesting that the noncovalent energy transfer requires specific helix-helix interactions. Purified phospholamban, a small (6-kDa) integral membrane protein containing a single TMH, formed a pentameric assembly in sodium dodecyl sulfate. The chemical degradation target size of this phospholamban pentamer was 5-6 kDa, illustrating that not all integral membrane protein assemblies permit intersubunit energy transfer. These findings together with other published observations suggest strongly that significant noncovalent energy transfer can occur within the tertiary and quaternary structure of membrane proteins and that as yet undefined proper molecular interactions are required for such covalent energy transfer. Our results with pepsin-digested glucose transporter also illustrate the importance of the interhelical interaction as a predominating force in maintaining the tertiary structure of a transmembrane protein.

  4. Hydroeconomic optimization of integrated water management and transfers under stochastic surface water supply

    NASA Astrophysics Data System (ADS)

    Zhu, Tingju; Marques, Guilherme Fernandes; Lund, Jay R.

    2015-05-01

    Efficient reallocation and conjunctive operation of existing water supplies is gaining importance as demands grow, competitions among users intensify, and new supplies become more costly. This paper analyzes the roles and benefits of conjunctive use of surface water and groundwater and market-based water transfers in an integrated regional water system where agricultural and urban water users coordinate supply and demand management based on supply reliability and economic values of water. Agricultural users optimize land and water use for annual and perennial crops to maximize farm income, while urban users choose short-term and long-term water conservation actions to maintain reliability and minimize costs. The temporal order of these decisions is represented in a two-stage optimization that maximizes the net expected benefits of crop production, urban conservation and water management including conjunctive use and water transfers. Long-term decisions are in the first stage and short-term decisions are in a second stage based on probabilities of water availability events. Analytical and numerical analyses are made. Results show that conjunctive use and water transfers can substantially stabilize farmer's income and reduce system costs by reducing expensive urban water conservation or construction. Water transfers can equalize marginal values of water across users, while conjunctive use minimizes water marginal value differences in time. Model results are useful for exploring the integration of different water demands and supplies through water transfers, conjunctive use, and conservation, providing valuable insights for improving system management.

  5. Numerical Modeling of the Chilldown of Cryogenic Transfer Lines Using a Sinda/GFSSP Integrated Solver

    NASA Technical Reports Server (NTRS)

    LeClair, Andre

    2011-01-01

    An important first step in cryogenic propellant loading is the chilldown of transfer lines. During the chilldown of the transfer line, the flow is two-phase and unsteady, with solid to fluid heat transfer and therefore a coupled thermo-fluid analysis is necessary to model the system. This paper describes a numerical model of pipe chilldown that utilizes the Sinda/GFSSP Conjugate Integrator (SGCI). SGCI is a new analysis tool developed at NASA's Marshall Space Flight Center (MSFC). SGCI facilitates the solution of thermofluid problems in interconnected solid-fluid systems. The solid component of the system is modeled in MSC Patran and translated into an MSC Sinda thermal network model. The fluid component is modeled in GFSSP, the Generalized Fluid System Simulation Program. GFSSP is a general network flow solver developed at NASA/MSFC. GFSSP uses a finite-volume approach to model fluid systems that can include phase change, multiple species, fluid transients, and heat transfer to simple solid networks. SGCI combines the GFSSP Fortran code with the Sinda input file and compiles the integrated model. Sinda solves for the temperatures of the solid network, while GFSSP simultaneously solves the fluid network for pressure, temperature, and flow rate. The two networks are coupled by convection heat transfer from the solid wall to the cryogenic fluid. The model presented here is based on a series of experiments conducted in 1966 by the National Bureau of Standards (NBS). A vacuum-jacketed, 200 ft copper transfer line was chilled by liquid nitrogen and liquid hydrogen. The predictions of transient temperature profiles and chilldown time of the integrated Sinda/GFSSP model will be compared to the experimental measurements.

  6. Simulations of the THz spectrum of liquid water incorporating the effects of intermolecular charge fluxes through hydrogen bonds

    SciTech Connect

    Torii, Hajime

    2015-12-31

    The intensity of the band at ∼200 cm{sup −1} (∼6 THz) in the Terahertz spectrum of liquid water mainly arises from the modulations of the extent of intermolecular charge transfer through hydrogen bonds, called intermolecular charge fluxes, occurring upon molecular translations along the O…H hydrogen bonds. To obtain reasonable spectral profiles from simulations, it is necessary to effectively incorporate the effects of those intermolecular charge fluxes, but apparently it is not possible by simple classical molecular dynamics simulations with fixed atomic partial charges even if they are amended by molecular induced dipoles due to intermolecular electrostatic interactions. The present paper shows how we can do reasonably correct spectral simulations, without resorting to fully ab initio molecular dynamics.

  7. Efficient application of the spectrally integrated Voigt function to radiative transfer spectroscopy

    NASA Astrophysics Data System (ADS)

    Abrarov, Sanjar

    We present a new application of the spectrally integrated Voigt function (SIVF) to the radiative transfer spectroscopy that enables computation of the spectral radiance and radiance at reduced spectral resolution. Applying a technique based on the Fourier expansion of the exponential multiplier we obtain the series approximations providing high-accuracy and rapid SIVF computation. In contrast to traditional line-by-line (LBL) radiative transfer models, the proposed SIVF algorithm prevents underestimation in the absorption coefficients and, therefore, preserves the radiant energy. LBL sample computations utilizing SIVF algorithm show the advantages of the proposed methodology in terms of the accuracy and computational speed.

  8. Application of the spectrally integrated Voigt function to line-by-line radiative transfer modelling

    NASA Astrophysics Data System (ADS)

    Quine, B. M.; Abrarov, S. M.

    2013-09-01

    We show that a new approach based on the spectrally integrated Voigt function (SIVF) enables the computation of line-by-line (LBL) radiative transfer at reduced spectral resolution without loss of accuracy. The algorithm provides rapid and accurate computation of area under the Voigt function in a way that preserves spectral radiance and, consequently, radiant intensity. The error analysis we provide shows the high-accuracy of the proposed SIVF approximations. A comparison of the performance of the method with that of the traditional LBL approach is presented. Motivations for the use and advantage of the SIVF as a replacement for conventional line function computations in radiative transfer are discussed.

  9. The Use of Chromatin Insulators to Improve the Expression and Safety of Integrating Gene Transfer Vectors

    PubMed Central

    2011-01-01

    Abstract The therapeutic application of recombinant retroviruses and other integrating gene transfer vectors has been limited by problems of vector expression and vector-mediated genotoxicity. These problems arise in large part from the interactions between vector sequences and the genomic environment surrounding sites of integration. Strides have been made in overcoming both of these problems through the modification of deleterious vector sequences, the inclusion of better enhancers and promoters, and the use of alternative virus systems. However, these modifications often add other restrictions on vector design, which in turn can further limit therapeutic applications. As an alternative, several groups have been investigating a class of DNA regulatory elements known as chromatin insulators. These elements provide a means of blocking the interaction between an integrating vector and the target cell genome in a manner that is independent of the vector transgene, regulatory elements, or virus of origin. This review outlines the background, rationale, and evidence for using chromatin insulators to improve the expression and safety of gene transfer vectors. Also reviewed are topological factors that constrain the use of insulators in integrating gene transfer vectors, alternative sources of insulators, and the role of chromatin insulators as one of several components for optimal vector design. PMID:21247248

  10. Single-molecule magnets ``without'' intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Wernsdorfer, W.; Vergnani, L.; Rodriguez-Douton, M. J.; Cornia, A.; Neugebauer, P.; Barra, A. L.; Sorace, L.; Sessoli, R.

    2012-02-01

    Intermolecular magnetic interactions (dipole-dipole and exchange) affect strongly the magnetic relaxation of crystals of single-molecule magnets (SMMs), especially at low temperature, where quantum tunneling of the magnetization (QTM) dominates. This leads to complex many-body problems [l]. Measurements on magnetically diluted samples are desirable to clearly sort out the behaviour of magnetically-isolated SMMs and to reveal, by comparison, the effect of intermolecular interactions. Here, we diluted a Fe4 SMM into a diamagnetic crystal lattice, affording arrays of independent and iso-oriented magnetic units. We found that the resonant tunnel transitions are much sharper, the tunneling efficiency changes significantly, and two-body QTM transitions disappear. These changes have been rationalized on the basis of a dipolar shuffling mechanism and of transverse dipolar fields, whose effect has been analyzed using a multispin model. Our findings directly prove the impact of intermolecular magnetic couplings on the SMM behaviour and disclose the magnetic response of truly-isolated giant spins in a diamagnetic crystalline environment.[4pt] [1] W. Wernsdorfer, at al, PRL 82, 3903 (1999); PRL 89, 197201 (2002); Nature 416, 406 (2002); IS Tupitsyn, PCE Stamp, NV Prokof'ev, PRB 69, 132406 (2004).

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

    PubMed Central

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

    2014-01-01

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

  12. An isotopic mass effect on the intermolecular potential

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

    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 communication, 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. The analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  13. Interbasin water transfers and integrated water resources management: Where engineering, science and politics interlock

    NASA Astrophysics Data System (ADS)

    Gupta, J.; van der Zaag, P.

    As the pressure on water is increasing, the risk that the required amounts of water will not be available is also increasing in many semi-arid areas. Interbasin water transfers are designed to secure access by artificially conveying water to locations where people need it. These are typical supply oriented engineering measures to large societal challenges. The engineering works are frequently daunting, involving diversion works, tunnels and/or large pumping schemes and reservoirs, and the costs are correspondingly large. The scale of engineering works and funds required are indicative of the magnitude of the needs and interests to be served. Interbasin water transfers trigger pertinent questions from different interests groups and communities involved and affected. This paper assesses the phenomenon of interbasin water transfers from a multi-disciplinary perspective, and attempts to answer the question whether such transfers are compatible with the concept of integrated water resources management. The problems related to interbasin water transfers are first introduced by reviewing four selected interbasin transfers taking place in different parts of the world. Then the criteria for assessing such transfers as proposed by international commissions, policy communities and scientists are reviewed, from which a coherent set of evaluation criteria are distilled for interbasin transfer schemes. This set of criteria is subsequently applied to the River Linking project in India, in order to provide a preliminary assessment. This is followed by a discussion of the temporal, spatial and resource scale effects, and finally conclusions are drawn about the required institutional capacity to control water and to adapt to changing policy environments.

  14. Intermolecular shielding from molecular magnetic susceptibility. A new view of intermolecular ring current effects.

    PubMed

    Facelli, Julio C

    2006-03-01

    This paper presents calculations of the NICS (nuclear independent chemical shieldings) in a rectangular grid surrounding the molecules of benzene, naphthalene and coronene. Using the relationship between calculated NICS and the induced magnetic field, the calculated NICS are used to predict intermolecular effects due to molecular magnetic susceptibility or ring current effects. As expected from approximate ring current models, these intermolecular shielding effects are concentrated along the direction perpendicular to the molecular plane and they approach asymptotically to a dipolar functional dependence, i.e. (1-3 cos(2)theta)/r(3)). The deviations from the dipolar functional form require that the calculations of these intermolecular effects be done using a suitable interpolation scheme of the NICS calculated on the grid. The analysis of the NICS tensor components shows that these intermolecular shielding effects should be primarily expected on shielding components of the neighboring molecules nuclei, which are perpendicular to the molecular plane of the aromatic compound generating the induced field. The analysis of the calculated NICS along the series benzene, naphthalene and coronene shows that these intermolecular effects increase monotonically with the number of aromatic rings. PMID:16477673

  15. Optimization on microlattice materials for sound absorption by an integrated transfer matrix method.

    PubMed

    Cai, Xiaobing; Yang, Jun; Hu, Gengkai

    2015-04-01

    Materials with well-defined microlattice structures are superlight, stable, and thus bear great potential in sound absorption. An integrated transfer matrix method (TMM) is proposed to evaluate the sound absorbing efficiency of these lattice materials, in which a massive number of micropores are densely placed. A comparison between integrated TMM and conventional TMM reveals that the proposed approach offers better predictions on sound absorption of microlattice. This approach is then employed to optimize the microlattice material to determine the best pore and porosity that lead to maximum absorbing efficiency capability and minimum required thickness to attain a target sound absorption. PMID:25920886

  16. Clean graphene interfaces by selective dry transfer for large area silicon integration

    NASA Astrophysics Data System (ADS)

    Na, S. R.; Rahimi, S.; Tao, L.; Chou, H.; Ameri, S. K.; Akinwande, D.; Liechti, K. M.

    2016-03-01

    Here we present a very fast, selective mechanical approach for transferring graphene with low levels of copper contamination from seed wafers on which it was grown to target wafers for very large scale integration (VLSI) electronics. We found that graphene/copper or copper/silicon oxide delamination paths could be selected by slow and faster separation rates, respectively. Thus graphene can be transferred to a target wafer, either exposed or protected by the seed copper layer, which can later be removed by etching. Delamination paths were identified by SEM and Raman spectroscopy. The sheet resistance of the graphene produced by the two approaches was slightly higher than graphene transferred by a PMMA wet-transfer process, indicating reduced impurity doping, and the variation in the sheet resistance values was much lower. Copper contamination levels, quantitatively established by TOF-SIMS, were several orders of magnitude lower than the values for PMMA assisted transfer. In addition, we demonstrated that top-gated transistor devices from our mechanical, delamination transferred graphene exhibited superior transistor behavior to PMMA-assisted wet transfer graphene. The adhesion energy, strength and range of the interactions were quantitatively determined by nonlinear fracture analyses, and suggest that the roughness of the interface between graphene and copper plays an important role with implications for improvements in manufacturing processes.Here we present a very fast, selective mechanical approach for transferring graphene with low levels of copper contamination from seed wafers on which it was grown to target wafers for very large scale integration (VLSI) electronics. We found that graphene/copper or copper/silicon oxide delamination paths could be selected by slow and faster separation rates, respectively. Thus graphene can be transferred to a target wafer, either exposed or protected by the seed copper layer, which can later be removed by etching

  17. Development of highly accurate approximate scheme for computing the charge transfer integral.

    PubMed

    Pershin, Anton; Szalay, Péter G

    2015-08-21

    The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the "exact" scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the "exact" calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature. PMID:26298117

  18. Development of highly accurate approximate scheme for computing the charge transfer integral

    SciTech Connect

    Pershin, Anton; Szalay, Péter G.

    2015-08-21

    The charge transfer integral is a key parameter required by various theoretical models to describe charge transport properties, e.g., in organic semiconductors. The accuracy of this important property depends on several factors, which include the level of electronic structure theory and internal simplifications of the applied formalism. The goal of this paper is to identify the performance of various approximate approaches of the latter category, while using the high level equation-of-motion coupled cluster theory for the electronic structure. The calculations have been performed on the ethylene dimer as one of the simplest model systems. By studying different spatial perturbations, it was shown that while both energy split in dimer and fragment charge difference methods are equivalent with the exact formulation for symmetrical displacements, they are less efficient when describing transfer integral along the asymmetric alteration coordinate. Since the “exact” scheme was found computationally expensive, we examine the possibility to obtain the asymmetric fluctuation of the transfer integral by a Taylor expansion along the coordinate space. By exploring the efficiency of this novel approach, we show that the Taylor expansion scheme represents an attractive alternative to the “exact” calculations due to a substantial reduction of computational costs, when a considerably large region of the potential energy surface is of interest. Moreover, we show that the Taylor expansion scheme, irrespective of the dimer symmetry, is very accurate for the entire range of geometry fluctuations that cover the space the molecule accesses at room temperature.

  19. 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.

  20. Frontier orbital symmetry control of intermolecular electron transfer

    SciTech Connect

    Stevens, B.

    1991-09-01

    This report contains sections describing the selection of electron donor-acceptor systems, the synthesis and photophysical properties of linked electron-donor-acceptor systems, the estimation of photoinduced charge-separation rate constants from fluorescence quenching data, and radical ion-pair recombination by picosecond transient absorption spectroscopy. 9 refs., 1 fig., 7 tabs.

  1. MHD Technology Transfer, Integration and Review Committee. Second semiannual status report, July 1988--March 1989

    SciTech Connect

    Not Available

    1989-10-01

    As part of the MHD Integrated Topping Cycle (ITC) project, TRW was given the responsibility to organize, charter and co-chair, with the Department of Energy (DOE), an MHD Technology Transfer, Integration and Review Committee (TTIRC). The Charter of the TTIRC, which was approved by the DOE in June 1988 and distributed to the committee members, is included as part of this Summary. As stated in the Charter, the purpose of this committee is to: (1) review all Proof-of-Concept (POC) projects and schedules in the national MHD program; to assess their compatibility with each other and the first commercial MHD retrofit plant; (2) establish and implement technology transfer formats for users of this technology; (3) identify interfaces, issues, and funding structures directly impacting the success of the commercial retrofit; (4) investigate and identify the manner in which, and by whom, the above should be resolved; and (5) investigate and assess other participation (foreign and domestic) in the US MHD Program. The DOE fiscal year 1989 MHD Program Plan Schedule is included at the end of this Summary. The MHD Technology Transfer, Integration and Review Committee`s activities to date have focused primarily on the ``technology transfer`` aspects of its charter. It has provided a forum for the dissemination of technical and programmatic information among workers in the field of MHD and to the potential end users, the utilities, by holding semi-annual meetings. The committee publishes this semi-annual report, which presents in Sections 2 through 11 capsule summaries of technical progress for all DOE Proof-of-Concept MHD contracts and major test facilities.

  2. A STRUCTURAL INTEGRITY EVALUATION OF THE TANK FARM WASTE TRANSFER SYSTEM

    SciTech Connect

    Wiersma, B.

    2006-03-09

    Radioactive supernate, salt, and/or sludge wastes (i.e., high level wastes) are confined in 49 underground storage tanks at the Savannah River Site (SRS). The waste is transported between tanks within and between the F and H area tank farms and other facilities on site via underground and a limited number of aboveground transfer lines. The Department of Energy - Savannah River Operations Office (DOE-SR) performed a comprehensive assessment of the structural integrity program for the Tank Farm waste transfer system at the SRS. This document addresses the following issues raised during the DOE assessment: (1) Inspections of failed or replaced transfer lines indicated that the wall thickness of some core and jacket piping is less than nominal; (2) No corrosion allowance is utilized in the transfer line structural qualification calculations. No basis for neglecting corrosion was provided in the calculations; (3) Wall loss due to erosion is not addressed in the transfer line structural qualification calculations; and (4) No basis is provided for neglecting intergranular stress corrosion cracking in the transfer line structural qualification calculations. The common theme in most of these issues is the need to assess the potential for occurrence of material degradation of the transfer line piping. The approach used to resolve these issues involved: (1) Review the design and specifications utilized to construct and fabricate the piping system; (2) Review degradation mechanisms for stainless steel and carbon steel and determine their relevance to the transfer line piping; (3) Review the transfer piping inspection data; (4) Life estimation calculations for the transfer lines; and (5) A Fitness-For-Service evaluation for one of the transfer line jackets. The evaluation concluded that the transfer line system piping has performed well for over fifty years. Although there have been instances of failures of the stainless steel core pipe during off-normal service, no significant

  3. Cooperative Drought Adaptation: Integrating Infrastructure Development, Conservation, and Water Transfers into Adaptive Policy Pathways

    NASA Astrophysics Data System (ADS)

    Zeff, H. B.; Characklis, G. W.; Reed, P. M.; Herman, J. D.

    2015-12-01

    Water supply policies that integrate portfolios of short-term management decisions with long-term infrastructure development enable utilities to adapt to a range of future scenarios. An effective mix of short-term management actions can augment existing infrastructure, potentially forestalling new development. Likewise, coordinated expansion of infrastructure such as regional interconnections and shared treatment capacity can increase the effectiveness of some management actions like water transfers. Highly adaptable decision pathways that mix long-term infrastructure options and short-term management actions require decision triggers capable of incorporating the impact of these time-evolving decisions on growing water supply needs. Here, we adapt risk-based triggers to sequence a set of potential infrastructure options in combination with utility-specific conservation actions and inter-utility water transfers. Individual infrastructure pathways can be augmented with conservation or water transfers to reduce the cost of meeting utility objectives, but they can also include cooperatively developed, shared infrastructure that expands regional capacity to transfer water. This analysis explores the role of cooperation among four water utilities in the 'Research Triangle' region of North Carolina by formulating three distinct categories of adaptive policy pathways: independent action (utility-specific conservation and supply infrastructure only), weak cooperation (utility-specific conservation and infrastructure development with regional transfers), and strong cooperation (utility specific conservation and jointly developed of regional infrastructure that supports transfers). Results suggest that strong cooperation aids the utilities in meeting their individual objections at substantially lower costs and with fewer irreversible infrastructure options.

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

    SciTech Connect

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

    2010-01-01

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

  5. A STRUCTURAL INTEGRITY ASSESSMENT OF UNDERGROUND PIPING ASSOCIATED WITH THE TRANSFER OF RADIOACTIVE WASTE

    SciTech Connect

    Wiersma, B

    2006-04-25

    Radioactive wastes are confined in 49 underground storage tanks at the Savannah River Site. The waste is transported between tanks via underground transfer piping. An assessment of the structural integrity of the transfer piping was performed to ensure that the present condition of the piping was sound and to provide life expectancy estimates for the piping based on anticipated service. The assessment reviewed the original design of the piping, the potential and observed degradation mechanisms, the results from past inspections of the piping, and a Fitness-For-Service evaluation for a section of piping that experienced pitting in a locally thinned area. The assessment concluded that the piping was structurally sound. Assuming that service conditions remain the same, the piping will remain functional for its intended service life.

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

    PubMed

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

    2016-01-01

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

  7. 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

  8. Anisotropic light scattering in an inhomogeneous atmosphere. Invariance relations and integrals of radiative transfer equation

    SciTech Connect

    Yanovitskii, E.G.

    1981-01-01

    The general invariance principle (GIP) for arbitrary plane inhomogeneous atmospheres is formulated on the basis of ideas contained in (V. V. Ivanov, Sov. Astron. 19, 137 (1975)). All the known invariance relations follow as particular cases from the GIP. The problem of diffuse light reflection by a semi-infinite atmosphere and the Milne problem are analyzed in detail. The existence of a number of integrals, quadratic with respect to intensity, of the transfer equation is shown, the majority of which are invariant relative to optical depth.

  9. The phase-integral method for radiative transfer problems with highly-peaked phase functions

    NASA Technical Reports Server (NTRS)

    Fricke, C. L.

    1978-01-01

    Complete solutions to the radiative transfer equation, including both azimuth and depth dependence, are provided by the discrete-ordinate method of Chandrasekhar, but these solutions are often limited because of large computer requirements. This paper presents a 'phase-integral' method which greatly reduces the number of discrete ordinates needed in the solution for highly peaked phase functions. A composite quadrature method is shown to be effective in further reducing the number of discrete ordinates required for highly anisotropic phase functions. Examples are given to indicate convergence requirements and expected accuracy in the complete solution for Henyey-Greenstein and cloud-type phase functions.

  10. Computational attributes of the integral form of the equation of transfer

    NASA Technical Reports Server (NTRS)

    Frankel, J. I.

    1991-01-01

    Difficulties can arise in radiative and neutron transport calculations when a highly anisotropic scattering phase function is present. In the presence of anisotropy, currently used numerical solutions are based on the integro-differential form of the linearized Boltzmann transport equation. This paper, departs from classical thought and presents an alternative numerical approach based on application of the integral form of the transport equation. Use of the integral formalism facilitates the following steps: a reduction in dimensionality of the system prior to discretization, the use of symbolic manipulation to augment the computational procedure, and the direct determination of key physical quantities which are derivable through the various Legendre moments of the intensity. The approach is developed in the context of radiative heat transfer in a plane-parallel geometry, and results are presented and compared with existing benchmark solutions. Encouraging results are presented to illustrate the potential of the integral formalism for computation. The integral formalism appears to possess several computational attributes which are well-suited to radiative and neutron transport calculations.

  11. Heat Transfer Study of Heat-Integrated Distillation Column (HIDiC) Using Simulation Techniques

    NASA Astrophysics Data System (ADS)

    Pulido, Jeffrey León; Martínez, Edgar Leonardo; Wolf, Maria Regina; Filho, Rubens Maciel

    2011-08-01

    Separation processes is largely used in petroleum refining and alcohol industries. Distillation columns consume a huge amount of energy in industrial process. Therefore, the concept of Heat-Integrated Distillation Column (HIDiC) was studied using simulation techniques in order to overcome this drawback. In this configuration the column is composed for two concentric sections called rectifying and stripping. The heat transfer is conducted from the rectifying section (which works at higher pressure and temperature) to the stripping section (which works at lower pressure and temperature) using the heat present in the process and decreasing the energy charge required by the reboiler. The HIDiC column offers great potential to reduce energy consumption compared to conventional columns. However, the complexity of the internal configuration requires the development of rigorous works that enable a better understanding of the column operation. For this reason, techniques of simulation were used through of computational software. The current work presents a heat transfer study in a concentric stage of a HIDiC column. The results obtained by Aspen Plus and CFD simulation showed the internal heat transfer in a concentric tray as a promissory configuration in order to decrease energy consumption in distillation processes.

  12. Integration of Light Trapping Silver Nanostructures in Hydrogenated Microcrystalline Silicon Solar Cells by Transfer Printing.

    PubMed

    Mizuno, Hidenori; Sai, Hitoshi; Matsubara, Koji; Takato, Hidetaka; Kondo, Michio

    2015-01-01

    One of the potential applications of metal nanostructures is light trapping in solar cells, where unique optical properties of nanosized metals, commonly known as plasmonic effects, play an important role. Research in this field has, however, been impeded owing to the difficulty of fabricating devices containing the desired functional metal nanostructures. In order to provide a viable strategy to this issue, we herein show a transfer printing-based approach that allows the quick and low-cost integration of designed metal nanostructures with a variety of device architectures, including solar cells. Nanopillar poly(dimethylsiloxane) (PDMS) stamps were fabricated from a commercially available nanohole plastic film as a master mold. On this nanopatterned PDMS stamps, Ag films were deposited, which were then transfer-printed onto block copolymer (binding layer)-coated hydrogenated microcrystalline Si (µc-Si:H) surface to afford ordered Ag nanodisk structures. It was confirmed that the resulting Ag nanodisk-incorporated µc-Si:H solar cells show higher performances compared to a cell without the transfer-printed Ag nanodisks, thanks to plasmonic light trapping effect derived from the Ag nanodisks. Because of the simplicity and versatility, further device application would also be feasible thorough this approach. PMID:26575244

  13. Analysis of the depth of field in hexagonal array integral imaging systems based on modulation transfer function and Strehl ratio.

    PubMed

    Karimzadeh, Ayatollah

    2016-04-10

    Integral imaging is a technique for displaying three-dimensional images using microlens arrays. In this paper, a method for calculating root mean squared wavefront error and modulation transfer function (MTF) of a defocused integral imaging capture system with hexagonal aperture microlens arrays is introduced. Also, maximum allowable depth of field with Century MTF analyzing and Strehl criterion are obtained. PMID:27139873

  14. 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.

  15. a Conceptual Model of Integrating Sensor Network and Radiative Heat Transfer Equation for Ethylene Furnace

    NASA Astrophysics Data System (ADS)

    Abas, Z. Abal; Salleh, S.; Basari, A. S. Hassan; Ibrahim, Nuzulha Khilwani

    2010-11-01

    A conceptual model of integrating the sensor network and the radiative heat transfer equation is developed and presented in this paper. The idea is to present possible deployment of sensor networks in the Ethylene furnace so that valuable input in the form of boundary value can be generated in order to produce intensity distribution and heat flux distribution. Once the location of sensor deployment has been recommended, the mesh at the physical space between the furnace wall and the reactor tube is constructed. The paper concentrates only at 2D model with only 1 U-bend reactor tube in the ethylene furnace as an initial phase of constructing a complete simulation in real furnace design.

  16. Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions.

    PubMed

    Lee, Mi Kyung; Huo, Pengfei; Coker, David F

    2016-05-27

    This article reviews recent progress in the theoretical modeling of excitation energy transfer (EET) processes in natural light harvesting complexes. The iterative partial linearized density matrix path-integral propagation approach, which involves both forward and backward propagation of electronic degrees of freedom together with a linearized, short-time approximation for the nuclear degrees of freedom, provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes. Combined with a recently developed chromophore-protein interaction model that incorporates both accurate ab initio descriptions of intracomplex vibrations and chromophore-protein interactions treated with atomistic detail, these simulation tools are beginning to unravel the detailed EET pathways and relaxation dynamics in light harvesting complexes. PMID:27090842

  17. Semiclassical Path Integral Dynamics: Photosynthetic Energy Transfer with Realistic Environment Interactions

    NASA Astrophysics Data System (ADS)

    Lee, Mi Kyung; Huo, Pengfei; Coker, David F.

    2016-05-01

    This article reviews recent progress in the theoretical modeling of excitation energy transfer (EET) processes in natural light harvesting complexes. The iterative partial linearized density matrix path-integral propagation approach, which involves both forward and backward propagation of electronic degrees of freedom together with a linearized, short-time approximation for the nuclear degrees of freedom, provides an accurate and efficient way to model the nonadiabatic quantum dynamics at the heart of these EET processes. Combined with a recently developed chromophore-protein interaction model that incorporates both accurate ab initio descriptions of intracomplex vibrations and chromophore-protein interactions treated with atomistic detail, these simulation tools are beginning to unravel the detailed EET pathways and relaxation dynamics in light harvesting complexes.

  18. Lightweight ECC based RFID authentication integrated with an ID verifier transfer protocol.

    PubMed

    He, Debiao; Kumar, Neeraj; Chilamkurti, Naveen; Lee, Jong-Hyouk

    2014-10-01

    The radio frequency identification (RFID) technology has been widely adopted and being deployed as a dominant identification technology in a health care domain such as medical information authentication, patient tracking, blood transfusion medicine, etc. With more and more stringent security and privacy requirements to RFID based authentication schemes, elliptic curve cryptography (ECC) based RFID authentication schemes have been proposed to meet the requirements. However, many recently published ECC based RFID authentication schemes have serious security weaknesses. In this paper, we propose a new ECC based RFID authentication integrated with an ID verifier transfer protocol that overcomes the weaknesses of the existing schemes. A comprehensive security analysis has been conducted to show strong security properties that are provided from the proposed authentication scheme. Moreover, the performance of the proposed authentication scheme is analyzed in terms of computational cost, communicational cost, and storage requirement. PMID:25096968

  19. Orbit transfer rocket engine integrated control and health monitoring system technology readiness assessment

    NASA Technical Reports Server (NTRS)

    Bickford, R. L.; Collamore, F. N.; Gage, M. L.; Morgan, D. B.; Thomas, E. R.

    1992-01-01

    The objectives of this task were to: (1) estimate the technology readiness of an integrated control and health monitoring (ICHM) system for the Aerojet 7500 lbF Orbit Transfer Vehicle engine preliminary design assuming space based operations; and (2) estimate the remaining cost to advance this technology to a NASA defined 'readiness level 6' by 1996 wherein the technology has been demonstrated with a system validation model in a simulated environment. The work was accomplished through the conduct of four subtasks. In subtask 1 the minimally required functions for the control and monitoring system was specified. The elements required to perform these functions were specified in Subtask 2. In Subtask 3, the technology readiness level of each element was assessed. Finally, in Subtask 4, the development cost and schedule requirements were estimated for bringing each element to 'readiness level 6'.

  20. Communication: Predictive partial linearized path integral simulation of condensed phase electron transfer dynamics

    SciTech Connect

    Huo, Pengfei; Miller, Thomas F. III; Coker, David F.

    2013-10-21

    A partial linearized path integral approach is used to calculate the condensed phase electron transfer (ET) rate by directly evaluating the flux-flux/flux-side quantum time correlation functions. We demonstrate for a simple ET model that this approach can reliably capture the transition between non-adiabatic and adiabatic regimes as the electronic coupling is varied, while other commonly used semi-classical methods are less accurate over the broad range of electronic couplings considered. Further, we show that the approach reliably recovers the Marcus turnover as a function of thermodynamic driving force, giving highly accurate rates over four orders of magnitude from the normal to the inverted regimes. We also demonstrate that the approach yields accurate rate estimates over five orders of magnitude of inverse temperature. Finally, the approach outlined here accurately captures the electronic coherence in the flux-flux correlation function that is responsible for the decreased rate in the inverted regime.

  1. Fresnel integrals and irreversible energy transfer in an oscillatory system with time-dependent parameters.

    PubMed

    Kovaleva, Agnessa; Manevitch, Leonid I; Kosevich, Yuriy A

    2011-02-01

    We demonstrate that in significant limiting cases the problem of irreversible energy transfer in an oscillatory system with time-dependent parameters can be efficiently solved in terms of the Fresnel integrals. For definiteness, we consider a system of two weakly coupled linear oscillators in which the first oscillator with constant parameters is excited by an initial impulse, whereas the coupled oscillator with a slowly varying frequency is initially at rest but then acts as an energy trap. We show that the evolution equations of the slow passage through resonance are identical to the equations of the Landau-Zener tunneling problem, and therefore, the suggested asymptotic solution of the classical problem provides a simple analytic description of the quantum Landau-Zener tunneling with arbitrary initial conditions over a finite time interval. A correctness of approximations is confirmed by numerical simulations. PMID:21405919

  2. Study of Thermodynamic Vent and Screen Baffle Integration for Orbital Storage and Transfer of Liquid Hydrogen

    NASA Technical Reports Server (NTRS)

    Cady, E. C.

    1973-01-01

    A comprehensive analytical and experimental program was performed to determine the feasibility of integrating an internal thermodynamic vent system and a full wall-screen liner for the orbital storage and transfer of liquid hydrogen (LH2). Ten screens were selected from a comprehensive screen survey. The experimental study determined the screen bubble point, flow-through pressure loss, and pressure loss along rectangular channels lined with screen on one side, for the 10 screens using LH2 saturated at 34.5 N/cm2 (50 psia). The correlated experimental data were used in an analysis to determine the optimum system characteristics in terms of minimum weight for 6 tanks ranging from 141.6 m3 (5,000 ft3) to 1.416 m3 (50 ft3) for orbital storage times of 30 and 300 days.

  3. Protein Homeostasis Imposes a Barrier on Functional Integration of Horizontally Transferred Genes in Bacteria

    PubMed Central

    Bhattacharyya, Sanchari; Manhart, Michael; Choi, Jeong-Mo; Mu, Wanmeng; Zhou, Jingwen; Shakhnovich, Eugene I.

    2015-01-01

    Horizontal gene transfer (HGT) plays a central role in bacterial evolution, yet the molecular and cellular constraints on functional integration of the foreign genes are poorly understood. Here we performed inter-species replacement of the chromosomal folA gene, encoding an essential metabolic enzyme dihydrofolate reductase (DHFR), with orthologs from 35 other mesophilic bacteria. The orthologous inter-species replacements caused a marked drop (in the range 10–90%) in bacterial growth rate despite the fact that most orthologous DHFRs are as stable as E.coli DHFR at 37°C and are more catalytically active than E. coli DHFR. Although phylogenetic distance between E. coli and orthologous DHFRs as well as their individual molecular properties correlate poorly with growth rates, the product of the intracellular DHFR abundance and catalytic activity (k cat/KM), correlates strongly with growth rates, indicating that the drop in DHFR abundance constitutes the major fitness barrier to HGT. Serial propagation of the orthologous strains for ~600 generations dramatically improved growth rates by largely alleviating the fitness barriers. Whole genome sequencing and global proteome quantification revealed that the evolved strains with the largest fitness improvements have accumulated mutations that inactivated the ATP-dependent Lon protease, causing an increase in the intracellular DHFR abundance. In one case DHFR abundance increased further due to mutations accumulated in folA promoter, but only after the lon inactivating mutations were fixed in the population. Thus, by apparently distinguishing between self and non-self proteins, protein homeostasis imposes an immediate and global barrier to the functional integration of foreign genes by decreasing the intracellular abundance of their products. Once this barrier is alleviated, more fine-tuned evolution occurs to adjust the function/expression of the transferred proteins to the constraints imposed by the intracellular

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

    SciTech Connect

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

    2002-01-01

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

  5. Integration of an insertion-type transferred DNA vector from Agrobacterium tumefaciens into the Saccharomyces cerevisiae genome by gap repair.

    PubMed Central

    Risseeuw, E; Franke-van Dijk, M E; Hooykaas, P J

    1996-01-01

    Recently, it was shown that Agrobacterium tumefaciens can transfer transferred DNA (T-DNA) to Saccharomyces cerevisiae and that this T-DNA, when used as a replacement vector, is integrated via homologous recombination into the yeast genome. To test whether T-DNA can be a suitable substrate for integration via the gap repair mechanism as well, a model system developed for detection of homologous recombination events in plants was transferred to S. cerevisiae. Analysis of the yeast transformants revealed that an insertion type T-DNA vector can indeed be integrated via gap repair. Interestingly, the transformation frequency and the type of recombination events turned out to depend strongly on the orientation of the insert between the borders in such an insertion type T-DNA vector. PMID:8816506

  6. Integrative gene transfer in the truffle Tuber borchii by Agrobacterium tumefaciens-mediated transformation.

    PubMed

    Brenna, Andrea; Montanini, Barbara; Muggiano, Eleonora; Proietto, Marco; Filetici, Patrizia; Ottonello, Simone; Ballario, Paola

    2014-01-01

    Agrobacterium tumefaciens-mediated transformation is a powerful tool for reverse genetics and functional genomic analysis in a wide variety of plants and fungi. Tuber spp. are ecologically important and gastronomically prized fungi ("truffles") with a cryptic life cycle, a subterranean habitat and a symbiotic, but also facultative saprophytic lifestyle. The genome of a representative member of this group of fungi has recently been sequenced. However, because of their poor genetic tractability, including transformation, truffles have so far eluded in-depth functional genomic investigations. Here we report that A. tumefaciens can infect Tuber borchii mycelia, thereby conveying its transfer DNA with the production of stably integrated transformants. We constructed two new binary plasmids (pABr1 and pABr3) and tested them as improved transformation vectors using the green fluorescent protein as reporter gene and hygromycin phosphotransferase as selection marker. Transformants were stable for at least 12 months of in vitro culture propagation and, as revealed by TAIL- PCR analysis, integration sites appear to be heterogeneous, with a preference for repeat element-containing genome sites. PMID:24949275

  7. FAD oxidizes the ERO1-PDI electron transfer chain: The role of membrane integrity

    SciTech Connect

    Papp, Eszter; Nardai, Gabor; Mandl, Jozsef; Banhegyi, Gabor; Csermely, Peter . E-mail: csermely@puskin.sote.hu

    2005-12-16

    The molecular steps of the electron transfer in the endoplasmic reticulum from the secreted proteins during their oxidation are relatively unknown. We present here that flavine adenine dinucleotide (FAD) is a powerful oxidizer of the oxidoreductase system, Ero1 and PDI, besides the proteins of rat liver microsomes and HepG2 hepatoma cells. Inhibition of FAD transport hindered the action of FAD. Microsomal membrane integrity was mandatory for all FAD-related oxidation steps downstream of Ero1. The PDI inhibitor bacitracin could inhibit FAD-mediated oxidation of microsomal proteins and PDI, but did not hinder the FAD-driven oxidation of Ero1. Our data demonstrated that Ero1 can utilize FAD as an electron acceptor and that FAD-driven protein oxidation goes through the Ero1-PDI pathway and requires the integrity of the endoplasmic reticulum membrane. Our findings prompt further studies to elucidate the membrane-dependent steps of PDI oxidation and the role of FAD in redox folding.

  8. Integrative gene transfer in the truffle Tuber borchii by Agrobacterium tumefaciens-mediated transformation

    PubMed Central

    2014-01-01

    Agrobacterium tumefaciens-mediated transformation is a powerful tool for reverse genetics and functional genomic analysis in a wide variety of plants and fungi. Tuber spp. are ecologically important and gastronomically prized fungi (“truffles”) with a cryptic life cycle, a subterranean habitat and a symbiotic, but also facultative saprophytic lifestyle. The genome of a representative member of this group of fungi has recently been sequenced. However, because of their poor genetic tractability, including transformation, truffles have so far eluded in-depth functional genomic investigations. Here we report that A. tumefaciens can infect Tuber borchii mycelia, thereby conveying its transfer DNA with the production of stably integrated transformants. We constructed two new binary plasmids (pABr1 and pABr3) and tested them as improved transformation vectors using the green fluorescent protein as reporter gene and hygromycin phosphotransferase as selection marker. Transformants were stable for at least 12 months of in vitro culture propagation and, as revealed by TAIL- PCR analysis, integration sites appear to be heterogeneous, with a preference for repeat element-containing genome sites. PMID:24949275

  9. MAR-mediated integration of plasmid vectors for in vivo gene transfer and regulation

    PubMed Central

    2013-01-01

    Background The in vivo transfer of naked plasmid DNA into organs such as muscles is commonly used to assess the expression of prophylactic or therapeutic genes in animal disease models. Results In this study, we devised vectors allowing a tight regulation of transgene expression in mice from such non-viral vectors using a doxycycline-controlled network of activator and repressor proteins. Using these vectors, we demonstrate proper physiological response as consequence of the induced expression of two therapeutically relevant proteins, namely erythropoietin and utrophin. Kinetic studies showed that the induction of transgene expression was only transient, unless epigenetic regulatory elements termed Matrix Attachment Regions, or MAR, were inserted upstream of the regulated promoters. Using episomal plasmid rescue and quantitative PCR assays, we observed that similar amounts of plasmids remained in muscles after electrotransfer with or without MAR elements, but that a significant portion had integrated into the muscle fiber chromosomes. Interestingly, the MAR elements were found to promote plasmid genomic integration but to oppose silencing effects in vivo, thereby mediating long-term expression. Conclusions This study thus elucidates some of the determinants of transient or sustained expression from the use of non-viral regulated vectors in vivo. PMID:24295286

  10. Transfer of care and offload delay: continued resistance or integrative thinking?

    PubMed

    Schwartz, Brian

    2015-11-01

    The disciplines of paramedicine and emergency medicine have evolved synchronously over the past four decades, linked by emergency physicians with expertise in prehospital care. Ambulance offload delay (OD) is an inevitable consequence of emergency department overcrowding (EDOC) and compromises the care of the patient on the ambulance stretcher in the emergency department (ED), as well as paramedic emergency medical service response in the community. Efforts to define transfer of care from paramedics to ED staff with a view to reducing offload time have met with resistance from both sides with different agendas. These include the need to return paramedics to serve the community versus the lack of ED capacity to manage the patient. Innovative solutions to other system issues, such as rapid access to trauma teams, reducing door-to-needle time, and improving throughput in the ED to reduce EDOC, have been achieved by involving all stakeholders in an integrative thinking process. Only by addressing this issue in a similar integrative process will solutions to OD be realized. PMID:26012478

  11. Integration of solid-state nanopores in microfluidic networks via transfer printing of suspended membranes.

    PubMed

    Jain, Tarun; Guerrero, Ricardo Jose S; Aguilar, Carlos A; Karnik, Rohit

    2013-04-16

    Solid-state nanopores have emerged as versatile single-molecule sensors for applications including DNA sequencing, protein unfolding, micro-RNA detection, label-free detection of single nucleotide polymorphisms, and mapping of DNA-binding proteins involved in homologous recombination. While machining nanopores in dielectric membranes provides nanometer-scale precision, the rigid silicon support for the membrane contributes capacitive noise and limits integration with microfluidic networks for sample preprocessing. Herein, we demonstrate a technique to directly transfer solid-state nanopores machined in dielectric membranes from a silicon support into a microfluidic network. The resulting microfluidic-addressable nanopores can sense single DNA molecules at high bandwidths and with low noise, owing to significant reductions in membrane capacitance. This strategy will enable large-scale integration of solid-state nanopores with microfluidic upstream and downstream processing and permit new functions with nanopores such as complex manipulations for multidimensional analysis and parallel sensing in two and three-dimensional architectures. PMID:23347165

  12. Integration of Solid-State Nanopores in Microfluidic Networks via Transfer Printing of Suspended Membranes

    PubMed Central

    Jain, Tarun; Guerrero, Ricardo Jose S.; Aguilar, Carlos A.; Karnik, Rohit

    2013-01-01

    Solid-state nanopores have emerged as versatile single-molecule sensors for applications including DNA sequencing, protein unfolding, micro-RNA detection, label-free detection of single nucleotide polymorphisms, and mapping of DNA-binding proteins involved in homologous recombination. While machining nanopores in dielectric membranes provides nanometer-scale precision, the rigid silicon support for the membrane contributes capacitive noise and limits integration with microfluidic networks for sample pre-processing. Herein, we demonstrate a technique to directly transfer solid-state nanopores machined in dielectric membranes from a silicon support into a microfluidic network. The resulting microfluidic-addressable nanopores can sense single DNA molecules at high bandwidths and with low noise, owing to significant reductions in membrane capacitance. This strategy will enable large-scale integration of solid-state nanopores with microfluidic upstream and downstream processing and permit new functions with nanopores such as complex manipulations for multidimensional analysis and parallel sensing in two and three-dimensional architectures. PMID:23347165

  13. 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

  14. MHD Technology Transfer, Integration and Review Committee. Fifth semi-annual status report, April 1990--September 1990

    SciTech Connect

    Not Available

    1992-01-01

    This fifth semi-annual status report of the MHD Technology Transfer, Integration, and Review Committee (TTIRC) summarizes activities of the TTIRC during the period April 1990 through September 1990. It includes summaries and minutes of committee meetings, progress summaries of ongoing Proof-of-Concept (POC) contracts, discussions pertaining to technical integration issues in the POC program, and planned activities for the next six months.

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

    SciTech Connect

    Averbukh, V.; Cederbaum, L. S.

    2007-11-29

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

  16. Structural integrity of the corpus callosum predicts long-term transfer of fluid intelligence-related training gains in normal aging.

    PubMed

    Wolf, Dominik; Fischer, Florian Udo; Fesenbeckh, Johanna; Yakushev, Igor; Lelieveld, Irene Maria; Scheurich, Armin; Schermuly, Ingrid; Zschutschke, Lisa; Fellgiebel, Andreas

    2014-01-01

    Although cognitive training usually improves cognitive test performance, the capability to transfer these training gains into respective or functionally related cognitive domains varies significantly. Since most studies demonstrate rather limited transfer effects in older adults, aging might be an important factor in transfer capability differences. This study investigated the transfer capability of logical reasoning training gains to a measure of Fluid Intelligence (Gf) in relation to age, general intelligence, and brain structural integrity as measured by diffusion tensor imaging. In a group of 41 highly educated healthy elderly, 71% demonstrated successful transfer immediately after a 4-week training session (i.e. short-term transfer). In a subgroup of 22% of subjects transfer maintained over a 3-month follow-up period (i.e. long-term transfer). While short-term transfer was not related to structural integrity, long-term transfer was associated with increased structural integrity in corpus and genu of the corpus callosum. Since callosal structural integrity was also related to age (in the present and foregoing studies), previously observed associations between age and transfer might be moderated by the structural integrity. Surprisingly, age was not directly associated with transfer in this study which could be explained by the multi-dependency of the structural integrity (modulating factors beside age, e.g. genetics). In this highly educated sample, general intelligence was not related to transfer suggesting that high intelligence is not sufficient for transfer in normal aging. Further studies are needed to reveal the interaction of transfer, age, and structural integrity and delineate mechanisms of age-dependent transfer capabilities. PMID:22965837

  17. Density functional theory based calculations of the transfer integral in a redox-active single-molecule junction

    NASA Astrophysics Data System (ADS)

    Kastlunger, Georg; Stadler, Robert

    2014-03-01

    There are various quantum chemical approaches for an ab initio description of transfer integrals within the framework of Marcus theory in the context of electron transfer reactions. In our paper, we aim to calculate transfer integrals in redox-active single molecule junctions, where we focus on the coherent tunneling limit with the metal leads taking the position of donor and acceptor and the molecule acting as a transport mediating bridge. This setup allows us to derive a conductance, which can be directly compared with recent results from a nonequilibrium Green's function approach. Compared with purely molecular systems we face additional challenges due to the metallic nature of the leads, which rules out some of the common techniques, and due to their periodicity, which requires k-space integration. We present three different methods, all based on density functional theory, for calculating the transfer integral under these constraints, which we benchmark on molecular test systems from the relevant literature. We also discuss many-body effects and apply all three techniques to a junction with a Ruthenium complex in different oxidation states.

  18. An Integrative Model of Organizational Learning and Social Capital on Effective Knowledge Transfer and Perceived Organizational Performance

    ERIC Educational Resources Information Center

    Rhodes, Jo; Lok, Peter; Hung, Richard Yu-Yuan; Fang, Shih-Chieh

    2008-01-01

    Purpose: The purpose of this paper is to set out to examine the relationships of organizational learning, social capital and the effectiveness of knowledge transfer and perceived organisational performance. Integrating organizational learning capability with social capital networks to shape a holistic knowledge sharing and management enterprise…

  19. MHD Technology Transfer, Integration and Review Committee. Seventh semi-annual status report, April 1991--September 1991

    SciTech Connect

    Not Available

    1993-02-01

    This seventh semi-annual status report of the MHD Technology Transfer, Integration and Review Committee (TTIRC) summarizes activities of the TTIRC during the period April 1991 through September 1991. It includes a summary and minutes of the General Committee meeting, progress summaries of ongoing POC contracts, discussions pertaining to technical integration issues in the POC program, and planned activities for the next six months. The meeting included test plan with Western coal, seed regeneration economics, power management for the integrated topping cycle and status of the Clean Coal Technology Proposal activities. Appendices cover CDIF operations HRSR development, CFFF operations etc.

  20. Obtaining the Bidirectional Transfer Distribution Function ofIsotropically Scattering Materials Using an Integrating Sphere

    SciTech Connect

    Jonsson, Jacob C.; Branden, Henrik

    2006-10-19

    This paper demonstrates a method to determine thebidirectional transfer distribution function (BTDF) using an integratingsphere. Information about the sample's angle dependent scattering isobtained by making transmittance measurements with the sample atdifferent distances from the integrating sphere. Knowledge about theilluminated area of the sample and the geometry of the sphere port incombination with the measured data combines to an system of equationsthat includes the angle dependent transmittance. The resulting system ofequations is an ill-posed problem which rarely gives a physical solution.A solvable system is obtained by using Tikhonov regularization on theill-posed problem. The solution to this system can then be used to obtainthe BTDF. Four bulk-scattering samples were characterised using both twogoniophotometers and the described method to verify the validity of thenew method. The agreement shown is great for the more diffuse samples.The solution to the low-scattering samples contains unphysicaloscillations, butstill gives the correct shape of the solution. Theorigin of the oscillations and why they are more prominent inlow-scattering samples are discussed.

  1. Integrated control and health management. Orbit transfer rocket engine technology program

    NASA Technical Reports Server (NTRS)

    Holzmann, Wilfried A.; Hayden, Warren R.

    1988-01-01

    To insure controllability of the baseline design for a 7500 pound thrust, 10:1 throttleable, dual expanded cycle, Hydrogen-Oxygen, orbit transfer rocket engine, an Integrated Controls and Health Monitoring concept was developed. This included: (1) Dynamic engine simulations using a TUTSIM derived computer code; (2) analysis of various control methods; (3) Failure Modes Analysis to identify critical sensors; (4) Survey of applicable sensors technology; and, (5) Study of Health Monitoring philosophies. The engine design was found to be controllable over the full throttling range by using 13 valves, including an oxygen turbine bypass valve to control mixture ratio, and a hydrogen turbine bypass valve, used in conjunction with the oxygen bypass to control thrust. Classic feedback control methods are proposed along with specific requirements for valves, sensors, and the controller. Expanding on the control system, a Health Monitoring system is proposed including suggested computing methods and the following recommended sensors: (1) Fiber optic and silicon bearing deflectometers; (2) Capacitive shaft displacement sensors; and (3) Hot spot thermocouple arrays. Further work is needed to refine and verify the dynamic simulations and control algorithms, to advance sensor capabilities, and to develop the Health Monitoring computational methods.

  2. Effect of intermolecular potential on compressible Couette flow in slip and transitional regimes

    NASA Astrophysics Data System (ADS)

    Weaver, Andrew B.; Venkattraman, A.; Alexeenko, Alina A.

    2014-10-01

    The effect of intermolecular potentials on compressible, planar flow in slip and transitional regimes is investigated using the direct simulation Monte Carlo method. Two intermolecular interaction models, the variable hard sphere (VHS) and the Lennard-Jones (LJ) models, are first compared for subsonic and supersonic Couette flows of argon at temperatures of 40, 273, and 1,000 K, and then for Couette flows in the transitional regime ranging from Knudsen numbers (Kn) of 0.0051 to 1. The binary scattering model for elastic scattering using the Lennard-Jones (LJ) intermolecular potential proposed recently [A. Venkattraman and A. Alexeenko, "Binary scattering model for Lennard-Jones potential: Transport coefficients and collision integrals for non-equilibrium gas flow simulations," Phys. Fluids 24, 027101 (2012)] is shown to accurately reproduce both the theoretical collision frequency in an equilibrium gas as well as the theoretical viscosity variation with temperature. The use of a repulsive-attractive instead of a purely repulsive potential is found to be most important in the continuum and slip regimes as well as in flows with large temperature variations. Differences in shear stress of up to 28% between the VHS and LJ models is observed at Kn=0.0051 and is attributed to differences in collision frequencies, ultimately affecting velocity gradients at the wall. For Kn=1 where the Knudsen layer expands the entire domain, the effect of the larger collision frequency in the LJ model relative to VHS diminishes, and a 7% difference in shear stress is observed.

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

    PubMed

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

    2016-03-31

    Many important energy-transfer and optical processes, in both biological and artificial systems, depend crucially on excitonic coupling that spans several chromophores. Such coupling can in principle be described in a straightforward manner by considering the coherent intermolecular dipole-dipole interactions involved. However, in practice, it is challenging to directly observe in real space the coherent dipole coupling and the related exciton delocalizations, owing to the diffraction limit in conventional optics. Here we demonstrate that the highly localized excitations that are produced by electrons tunnelling from the tip of a scanning tunnelling microscope, in conjunction with imaging of the resultant luminescence, can be used to map the spatial distribution of the excitonic coupling in well-defined arrangements of a few zinc-phthalocyanine molecules. The luminescence patterns obtained for excitons in a dimer, which are recorded for different energy states and found to resemble σ and π molecular orbitals, reveal the local optical response of the system and the dependence of the local optical response on the relative orientation and phase of the transition dipoles of the individual molecules in the dimer. We generate an in-line arrangement up to four zinc-phthalocyanine molecules, with a larger total transition dipole, and show that this results in enhanced 'single-molecule' superradiance from the oligomer upon site-selective excitation. These findings demonstrate that our experimental approach provides detailed spatial information about coherent dipole-dipole coupling in molecular systems, which should enable a greater understanding and rational engineering of light-harvesting structures and quantum light sources. PMID:27029277

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  5. Integration of Aquifer Storage Transfer and Recovery and HACCP for Ensuring Drinking Water Quality

    NASA Astrophysics Data System (ADS)

    Lee, S. I.; Ji, H. W.

    2015-12-01

    The integration of ASTR (Aquifer Storage Transfer and Recovery) and HACCP (Hazard Analysis and Critical Control Point) is being attempted to ensure drinking water quality in a delta area. ASTR is a water supply system in which surface water is injected into a well for storage and recovered from a different well. During the process natural water treatment is achieved in the aquifer. ASTR has advantages over surface reservoirs in that the water is protected from external contaminants and free from water loss by evaporation. HACCP, originated from the food industry, can efficiently manage hazards and reduce risks when it is introduced to the drinking water production. The study area is the located in the Nakdong River Delta, South Korea. Water quality of this region has been deteriorated due to the increased pollution loads from the upstream cities and industrial complexes. ASTR equipped with HACCP system is suggested as a means to heighten the public trust in drinking water. After the drinking water supply system using ASTR was decomposed into ten processes, principles of HACCP were applied. Hazardous event analysis was conducted for 114 hazardous events and nine major hazardous events were identified based on the likelihood and the severity assessment. Potential risk of chemical hazards, as a function of amounts, travel distance and toxicity, was evaluated and the result shows the relative threat a city poses to the drinking water supply facility. Next, critical control points were determined using decision tree analysis. Critical limits, maximum and/or minimum values to which biological, chemical or physical parameters must be controlled, were established. Other procedures such as monitoring, corrective actions and will be presented.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  7. Intermolecular artifacts in probe microscope images of C60 assemblies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. Qualitative change of character of dispersive interaction with intermolecular distance.

    PubMed

    Haslmayr, Johannes; Renger, Thomas

    2013-07-28

    The dispersive interaction between molecules results from Coulomb-correlated fluctuations of electrons and for large intermolecular distances it can be related to the molecular polarizabilities as in London's theory (F. London, Trans. Faraday Soc. 33, 8-26 (1937)). Here, we investigate the interaction between molecules with anisotropic polarizabilities at arbitrary distances using symmetry adapted perturbation theory, which allows us to analyze the different parts of the intermolecular potential separately. Whereas at large distances, in accordance with London's theory, there is no way to describe the dispersive interaction by a sum over pairwise isotropic atom-centered energy terms, at short distances such a description becomes possible. This surprising result has consequences for the development of molecular mechanics force fields, supports the dispersion energy terms applied in dispersion corrected density functional theory, and indicates that there is a qualitative change in electron correlation with distance. Apparently, at short distances intermolecular electron correlation is less influenced by intramolecular electron delocalization. PMID:23901956

  9. Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element.

    PubMed

    Delavat, François; Mitri, Sara; Pelet, Serge; van der Meer, Jan Roelof

    2016-06-14

    Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer. PMID:27247406

  10. Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element

    PubMed Central

    Delavat, François; Mitri, Sara; Pelet, Serge; van der Meer, Jan Roelof

    2016-01-01

    Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer. PMID:27247406

  11. Transfer-printing-based integration of single-mode waveguide-coupled III-V-on-silicon broadband light emitters.

    PubMed

    De Groote, Andreas; Cardile, Paolo; Subramanian, Ananth Z; Fecioru, Alin M; Bower, Christopher; Delbeke, Danae; Baets, Roel; Roelkens, Günther

    2016-06-27

    We present the first III-V opto-electronic components transfer printed on and coupled to a silicon photonic integrated circuit. Thin InP-based membranes are transferred to an SOI waveguide circuit, after which a single-spatial-mode broadband light source is fabricated. The process flow to create transfer print-ready coupons is discussed. Aqueous FeCl3 at 5°C was found to be the best release agent in combination with the photoresist anchoring structures that were used. A thin DVS-BCB layer provides a strong bond, accommodating the post-processing of the membranes. The resulting optically pumped LED has a 3 dB bandwidth of 130 nm, comparable to devices realized using a traditional die-to-wafer bonding method. PMID:27410539

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

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-01

    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. PMID:26261948

  13. "It Takes an Integrated, College-Wide Effort" and Other Lessons from Seven High Transfer Colleges

    ERIC Educational Resources Information Center

    Mery, Pamela; Schiorring, Eva

    2011-01-01

    The Successful Transfer Approach Research (STAR) Project investigated seven California Community Colleges with consistently high transfer rates. Teams of experienced researchers spent two days at each college, interviewing 16-18 administrators, faculty, researchers, and student support service professionals. Focus groups and interviews were also…

  14. 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

  15. Preoperational test report, cross-site transfer system integrated test (POTR-007)

    SciTech Connect

    Pacquet, E.A.

    1998-04-02

    This report documents the results obtained during the performance of Preoperational Test POTP-007, from December 12, 1997 to March 27, 1998. The main objectives were to demonstrate the operation of the following Cross-Site Transfer System components: Booster pumps P-3125A and P-3125B interlocks and controls, both local and remote; Booster pump P-3125A and P-3125B and associated variable speed drives VSD-1 and VSD-2 performance in both manual and automatic modes; and Water filling, circulation, venting and draining of the transfer headers (supernate and slurry line). As described in reference 1, the following components of the Cross-Site Transfer System that would normally be used during an actual waste transfer, are not used in this specific test: Water Flush System; Valving and instrumentation associated with the 241-SY-A valve pit jumpers; and Valving and instrumentation associated with the 244-A lift station.

  16. 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.

  17. 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…

  18. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  19. 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.

  20. 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.

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

    PubMed

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

    2015-06-22

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

  2. 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…

  3. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

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

  4. Spin radical enhanced magnetocapacitance effect in intermolecular excited states.

    PubMed

    Zang, Huidong; Wang, Jianguo; Li, Mingxing; He, Lei; Liu, Zitong; Zhang, Deqing; Hu, Bin

    2013-11-14

    This article reports the magnetocapacitance effect (MFC) based on both pristine polymer MEH-PPV and its composite system doped with spin radicals (6R-BDTSCSB). We observed that a photoexcitation leads to a significant positive MFC in the pristine MEH-PPV. Moreover, we found that a low doping of spin radicals in polymer MEH-PPV causes a significant change on the MFC signal: an amplitude increase and a line-shape narrowing under light illumination at room temperature. However, no MFC signal was observed under dark conditions in either the pristine MEH-PPV or the radical-doped MEH-PPV. Furthermore, the magnitude increase and line-shape narrowing caused by the doped spin radicals are very similar to the phenomena induced by increasing the photoexcitation intensity. Our studies suggest that the MFC is essentially originated from the intermolecular excited states, namely, intermolecular electron-hole pairs, generated by a photoexcitation in the MEH-PPV. More importantly, by comparing the effects of spin radicals and electrically polar molecules on the MFC magnitude and line shape, we concluded that the doped spin radicals can have the spin interaction with intermolecular excited states and consequently affect the internal spin-exchange interaction within intermolecular excited states in the development of MFC. Clearly, our experimental results indicate that dispersing spin radicals forms a convenient method to enhance the magnetocapacitance effect in organic semiconducting materials. PMID:24144347

  5. Electric Field Effects on the Intermolecular Interactions in Water Whiskers: Insight from Structures, Energetics, and Properties

    DOE PAGESBeta

    Bai, Yang; He, Hui-Min; Li, Ying; Zhou, Zhong-Jun; Wang, Jia-Jun; Wu, Di; Chen, Wei; Gu, Feng-Long; Sumpter, Bobby G.; Huang, Jingsong

    2015-02-19

    Modulation of intermolecular interactions in response to external electric fields could be fundamental to the formation of unusual forms of water, such as water whiskers. However, a detailed understanding of the nature of intermolecular interactions in such systems is lacking. In this study, we present novel theoretical results based on electron correlation calculations regarding the nature of H-bonds in water whiskers, which is revealed by studying their evolution under external electric fields with various field strengths. We find that the water whiskers consisting of 2-7 water molecules all have a chain-length dependent critical electric field. Under the critical electric field,more » the most compact chain structures are obtained, featuring very strong H-bonds, herein referred to as covalent H-bonds. In the case of a water dimer whisker, the bond length of the novel covalent H-bond shortens by 25%, the covalent bond order increases by 9 times, and accordingly the H-bond energy is strengthened by 5 times compared to the normal H-bond in a (H2O)2 cluster. Below the critical electric field, it is observed that with increasing field strength, H-bonding orbitals display gradual evolutions in the orbital energy, orbital ordering, and orbital nature (i.e., from typical -style orbital to unusual -style double H-bonding orbital). We also show that beyond the critical electric field, a single water whisker may disintegrate to form a loosely bound zwitterionic chain due to a relay-style proton transfer, whereas two water whiskers may undergo intermolecular cross-linking to form a quasi-two-dimensional water network. In conclusion, these results help shed new insight on the effects of electric fields on water whisker formation.« less

  6. 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.

  7. An Integrated Approach to Modeling Solar Electric Propulsion Vehicles During Long Duration, Near-Earth Orbit Transfers

    NASA Technical Reports Server (NTRS)

    Smith, David A.; Hojnicki, Jeffrey S.; Sjauw, Waldy K.

    2014-01-01

    Recent NASA interest in utilizing solar electronic propulsion (SEP) technology to transfer payloads, e.g. from low-Earth orbit (LEO) to higher energy geostationary-Earth orbit (GEO) or to Earth escape, has necessitated the development of high fidelity SEP vehicle models and simulations. These models and simulations need to be capable of capturing vehicle dynamics and sub-system interactions experienced during the transfer trajectories which are typically accomplished with continuous-burn (potentially interrupted by solar eclipse), long duration "spiral out" maneuvers taking several months or more to complete. This paper presents details of an integrated simulation approach achieved by combining a high fidelity vehicle simulation code with a detailed solar array model. The combined simulation tool gives researchers the functionality to study the integrated effects of various vehicle sub-systems (e.g. vehicle guidance, navigation and control (GN&C), electric propulsion system (EP)) with time varying power production. Results from a simulation model of a vehicle with a 50 kW class SEP system using the integrated tool are presented and compared to the results from another simulation model employing a 50 kW end-of-life (EOL) fixed power level assumption. These models simulate a vehicle under three degree of freedom dynamics (i.e. translational dynamics only) and include the effects of a targeting guidance algorithm (providing a "near optimal" transfer) during a LEO to near Earth escape (C (sub 3) = -2.0 km (sup 2) / sec (sup -2) spiral trajectory. The presented results include the impact of the fully integrated, time-varying solar array model (e.g. cumulative array degradation from traversing the Van Allen belts, impact of solar eclipses on the vehicle and the related temperature responses in the solar arrays due to operating in the Earth's thermal environment, high fidelity array power module, etc.); these are used to assess the impact on vehicle performance (i

  8. One-step transfer and integration of multifunctionality in CVD graphene by TiO₂/graphene oxide hybrid layer.

    PubMed

    Jeong, Hee Jin; Kim, Ho Young; Jeong, Hyun; Han, Joong Tark; Jeong, Seung Yol; Baeg, Kang-Jun; Jeong, Mun Seok; Lee, Geon-Woong

    2014-05-28

    We present a straightforward method for simultaneously enhancing the electrical conductivity, environmental stability, and photocatalytic properties of graphene films through one-step transfer of CVD graphene and integration by introducing TiO2/graphene oxide layer. A highly durable and flexible TiO2 layer is successfully used as a supporting layer for graphene transfer instead of the commonly used PMMA. Transferred graphene/TiO2 film is directly used for measuring the carrier transport and optoelectronic properties without an extra TiO2 removal and following deposition steps for multifunctional integration into devices because the thin TiO2 layer is optically transparent and electrically semiconducting. Moreover, the TiO2 layer induces charge screening by electrostatically interacting with the residual oxygen moieties on graphene, which are charge scattering centers, resulting in a reduced current hysteresis. Adsorption of water and other chemical molecules onto the graphene surface is also prevented by the passivating TiO2 layer, resulting in the long term environmental stability of the graphene under high temperature and humidity. In addition, the graphene/TiO2 film shows effectively enhanced photocatalytic properties because of the increase in the transport efficiency of the photogenerated electrons due to the decrease in the injection barrier formed at the interface between the F-doped tin oxide and TiO2 layers. PMID:24578338

  9. Arts Integration Professional Development: Teacher Perspective and Transfer to Instructional Practice

    ERIC Educational Resources Information Center

    Garrett, Jo Ann

    2010-01-01

    Limited data connect teacher training in arts integration (AI) to evidence that students benefit from arts integrated instruction. As teachers are challenged to facilitate instruction for a wide continuum of learning needs, and students are challenged to demonstrate learning through high-stakes testing, more data are needed on how teachers learn…

  10. Integrated Compartment Method appication to the transient heat transfer in gas-cooled reactor

    SciTech Connect

    Chen, N.C.J.; Yeh, G.T.

    1983-01-01

    Integrated Compartment Method (ICM), an effective numerical integration algorithm, was developed to solve the transient heat conduction coupled with convection. Application of the ICM to the mathematical model simulating a graphite test structure heated in an annular flow stream of hot helium has been successfully demonstrated. However, the model validation can not be performed until experimental data become available.

  11. Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. III. Exact stochastic path integral evaluation

    SciTech Connect

    Moix, Jeremy M.; Ma, Jian; Cao, Jianshu

    2015-03-07

    A numerically exact path integral treatment of the absorption and emission spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath spectral densities. With the numerically exact absorption and emission operators, one can also immediately compute energy transfer rates using the multi-chromophoric Förster resonant energy transfer formalism. Benchmark calculations on the emission spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion (see Paper II) is the only perturbative method capable of generating uniformly reliable energy transfer rates and emission spectra across a broad range of system parameters.

  12. Förster resonance energy transfer, absorption and emission spectra in multichromophoric systems. III. Exact stochastic path integral evaluation.

    PubMed

    Moix, Jeremy M; Ma, Jian; Cao, Jianshu

    2015-03-01

    A numerically exact path integral treatment of the absorption and emission spectra of open quantum systems is presented that requires only the straightforward solution of a stochastic differential equation. The approach converges rapidly enabling the calculation of spectra of large excitonic systems across the complete range of system parameters and for arbitrary bath spectral densities. With the numerically exact absorption and emission operators, one can also immediately compute energy transfer rates using the multi-chromophoric Förster resonant energy transfer formalism. Benchmark calculations on the emission spectra of two level systems are presented demonstrating the efficacy of the stochastic approach. This is followed by calculations of the energy transfer rates between two weakly coupled dimer systems as a function of temperature and system-bath coupling strength. It is shown that the recently developed hybrid cumulant expansion (see Paper II) is the only perturbative method capable of generating uniformly reliable energy transfer rates and emission spectra across a broad range of system parameters. PMID:25747062

  13. 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.

  14. High performance organic integrated device with ultraviolet photodetective and electroluminescent properties consisting of a charge-transfer-featured naphthalimide derivative

    NASA Astrophysics Data System (ADS)

    Wang, Hanyu; Zhou, Jie; Wang, Xu; Lu, Zhiyun; Yu, Junsheng

    2014-08-01

    A high performance organic integrated device (OID) with ultraviolet photodetective and electroluminescent (EL) properties was fabricated by using a charge-transfer-featured naphthalimide derivative of 6-{3,5-bis-[9-(4-t-butylphenyl)-9H-carbazol-3-yl]-phenoxy}-2-(4-t-butylphenyl)-benzo[de]isoquinoline-1,3-dione (CzPhONI) as the active layer. The results showed that the OID had a high detectivity of 1.5 × 1011 Jones at -3 V under the UV-350 nm illumination with an intensity of 0.6 mW/cm2, and yielded an exciplex EL light emission with a maximum brightness of 1437 cd/m2. Based on the energy band diagram, both the charge transfer feature of CzPhONI and matched energy level alignment were responsible for the dual ultraviolet photodetective and EL functions of OID.

  15. Differential, integral, and momentum-transfer cross sections for elastic electron scattering by neon - 5 to 100 eV

    NASA Technical Reports Server (NTRS)

    Register, D. F.; Trajmar, S.

    1984-01-01

    Relative elastic-scattering differential cross sections were measured in the 5-100-eV impact energy and 10-145 deg angular ranges. Normalization of these cross sections was achieved by utilizing accurate total electron-scattering cross sections. A phase-shift analysis of the angular distributions in terms of real phase shifts has been carried out. From the differential cross sections, momentum-transfer cross sections were obtained and the values of the critical energy and angle were established (associated with the lowest value of the differential cross section) as 62.5 + or - 2.5 eV and 101.7 deg + or - 1.5 deg, respectively. The present phase shifts, the critical parameters, and differential, integral, and momentum-transfer cross sections are compared to previous experimental and theoretical results. The error associated with the present data is about 10 percent.

  16. Promoting Transfer and an Integrated Understanding for Pre-Service Teachers of Technology Education

    ERIC Educational Resources Information Center

    Morrison-Love, David

    2014-01-01

    The ability of pre-service teachers (PSTs) to transfer learning between subjects and contexts when problem solving is critical for developing their capability as technologists and teachers of technology. However, a growing body of literature suggests this ability is often assumed or over-estimated, and rarely developed explicitly within courses or…

  17. Integrating dynamic stopping, transfer learning and language models in an adaptive zero-training ERP speller

    NASA Astrophysics Data System (ADS)

    Kindermans, Pieter-Jan; Tangermann, Michael; Müller, Klaus-Robert; Schrauwen, Benjamin

    2014-06-01

    Objective. Most BCIs have to undergo a calibration session in which data is recorded to train decoders with machine learning. Only recently zero-training methods have become a subject of study. This work proposes a probabilistic framework for BCI applications which exploit event-related potentials (ERPs). For the example of a visual P300 speller we show how the framework harvests the structure suitable to solve the decoding task by (a) transfer learning, (b) unsupervised adaptation, (c) language model and (d) dynamic stopping. Approach. A simulation study compares the proposed probabilistic zero framework (using transfer learning and task structure) to a state-of-the-art supervised model on n = 22 subjects. The individual influence of the involved components (a)-(d) are investigated. Main results. Without any need for a calibration session, the probabilistic zero-training framework with inter-subject transfer learning shows excellent performance—competitive to a state-of-the-art supervised method using calibration. Its decoding quality is carried mainly by the effect of transfer learning in combination with continuous unsupervised adaptation. Significance. A high-performing zero-training BCI is within reach for one of the most popular BCI paradigms: ERP spelling. Recording calibration data for a supervised BCI would require valuable time which is lost for spelling. The time spent on calibration would allow a novel user to spell 29 symbols with our unsupervised approach. It could be of use for various clinical and non-clinical ERP-applications of BCI.

  18. Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

    SciTech Connect

    Moreau, P.; Gregoire, S.; Lochegnies, D.; Cesar de Sa, J.

    2007-05-17

    Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication...). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutive contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.

  19. Integration Of Heat Transfer Coefficient In Glass Forming Modeling With Special Interface Element

    NASA Astrophysics Data System (ADS)

    Moreau, P.; César de Sá, J.; Grégoire, S.; Lochegnies, D.

    2007-05-01

    Numerical modeling of the glass forming processes requires the accurate knowledge of the heat exchange between the glass and the forming tools. A laboratory testing is developed to determine the evolution of the heat transfer coefficient in different glass/mould contact conditions (contact pressure, temperature, lubrication…). In this paper, trials are performed to determine heat transfer coefficient evolutions in experimental conditions close to the industrial blow-and-blow process conditions. In parallel of this work, a special interface element is implemented in a commercial Finite Element code in order to deal with heat transfer between glass and mould for non-meshing meshes and evolutive contact. This special interface element, implemented by using user subroutines, permits to introduce the previous heat transfer coefficient evolutions in the numerical modelings at the glass/mould interface in function of the local temperatures, contact pressures, contact time and kind of lubrication. The blow-and-blow forming simulation of a perfume bottle is finally performed to assess the special interface element performance.

  20. Transfer Advisement at One Community College: Integrating Technology, Initiatives and Programs for Increased Student Learning.

    ERIC Educational Resources Information Center

    DeWitt, Kristine; And Others

    In spring 1996, Maryland's Carroll Community College (CCC) began efforts to shift institutional focus and mission from that of a teaching institution to a learning-centered institution. The college's Counseling and Advising Services unit, responsible for advising and transfer, has adapted this educational shift to its unique position in the…

  1. CO-INJECTION RESIN TRANSFER MOLDING FOR OPTIMIZATION OF INTEGRAL ARMOR

    EPA Science Inventory

    To address the cost and performance barriers which hinder the introduction of composite materials for combat ground vehicle applications, Co-Injection Resin Transfer Molding (CIRTM) and Diffusion Enhanced Adhesion (DEA) have been recently invented and developed at the Army Resear...

  2. H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes.

    PubMed

    Higashi, Koichi; Tobe, Toru; Kanai, Akinori; Uyar, Ebru; Ishikawa, Shu; Suzuki, Yutaka; Ogasawara, Naotake; Kurokawa, Ken; Oshima, Taku

    2016-01-01

    Bacteria can acquire new traits through horizontal gene transfer. Inappropriate expression of transferred genes, however, can disrupt the physiology of the host bacteria. To reduce this risk, Escherichia coli expresses the nucleoid-associated protein, H-NS, which preferentially binds to horizontally transferred genes to control their expression. Once expression is optimized, the horizontally transferred genes may actually contribute to E. coli survival in new habitats. Therefore, we investigated whether and how H-NS contributes to this optimization process. A comparison of H-NS binding profiles on common chromosomal segments of three E. coli strains belonging to different phylogenetic groups indicated that the positions of H-NS-bound regions have been conserved in E. coli strains. The sequences of the H-NS-bound regions appear to have diverged more so than H-NS-unbound regions only when H-NS-bound regions are located upstream or in coding regions of genes. Because these regions generally contain regulatory elements for gene expression, sequence divergence in these regions may be associated with alteration of gene expression. Indeed, nucleotide substitutions in H-NS-bound regions of the ybdO promoter and coding regions have diversified the potential for H-NS-independent negative regulation among E. coli strains. The ybdO expression in these strains was still negatively regulated by H-NS, which reduced the effect of H-NS-independent regulation under normal growth conditions. Hence, we propose that, during E. coli evolution, the conservation of H-NS binding sites resulted in the diversification of the regulation of horizontally transferred genes, which may have facilitated E. coli adaptation to new ecological niches. PMID:26789284

  3. Thermodynamic Integration Networks and Their Application to Charge Transfer Reactions within the AauDyPI Fungal Peroxidase.

    PubMed

    Bauß, Anna; Langenmaier, Michael; Strittmatter, Eric; Plattner, Dietmar A; Koslowski, Thorsten

    2016-06-01

    We present a computer simulation study of the thermodynamics and kinetics of charge transfer reactions within the fungal peroxidase AauDyPI from Auricularia auriculae-judae. Driving forces and reorganization energies are obtained from a thermodynamic integration scheme based upon molecular dynamics simulations. To enhance the numerical accuracy, the free energies are analyzed within a least-squares scheme of a closely knit thermodynamic network. We identify Tyr147, Tyr229, and Trp105 as oxidative agents, and find Trp377 to be a long-lived reaction intermediate. The results are compared to recent experimental findings. PMID:27182684

  4. Influence of bias voltage and temperature on charge transfer states in organic photovoltaic and electroluminescent integrated device

    SciTech Connect

    Huang, Jiang; Wang, Hanyu; Qi, Yige; Yu, Junsheng

    2014-05-19

    Based on the organic photovoltaic (PV) and electroluminescent (EL) integrated device with a structure of SubPc/C{sub 60} heterojunction, both PV and EL properties of charge transfer states (CTSs) were simultaneously investigated. By means of infrared and visible isolating method, the EL characteristics of CTSs and singlet-triplet excitons were separated, and their properties dependence on bias voltage and temperature was analyzed by introducing modified diode models. From the simulation on the emissive photons from CTSs, the temperature independent parameters of CTSs were extracted, which have close relationship with thermal activation energy and effective emissive state number of CTSs at the SubPc/C{sub 60} interface.

  5. Proton Transfer Studied Using a Combined Ab Initio Reactive Potential Energy Surface with Quantum Path Integral Methodology

    PubMed Central

    Wong, Kim F.; Sonnenberg, Jason L.; Paesani, Francesco; Yamamoto, Takeshi; Vaníček, Jiří; Zhang, Wei; Schlegel, H. Bernhard; Case, David A.; Cheatham, Thomas E.; Miller, William H.; Voth, Gregory A.

    2010-01-01

    The rates of intramolecular proton transfer are calculated on a full-dimensional reactive electronic potential energy surface that incorporates high level ab initio calculations along the reaction path and by using classical Transition State theory, Path-Integral Quantum Transition State Theory, and the Quantum Instanton approach. The specific example problem studied is malonaldehyde. Estimates of the kinetic isotope effect using the latter two methods are found to be in reasonable agreement with each other. Improvements and extensions of this practical, yet chemically accurate framework for the calculations of quantized, reactive dynamics are also discussed. PMID:21116485

  6. T-DNA transfer and T-DNA integration efficiencies upon Arabidopsis thaliana root explant cocultivation and floral dip transformation.

    PubMed

    Ghedira, Rim; De Buck, Sylvie; Van Ex, Frédéric; Angenon, Geert; Depicker, Ann

    2013-12-01

    T-DNA transfer and integration frequencies during Agrobacterium-mediated root explant cocultivation and floral dip transformations of Arabidopsis thaliana were analyzed with and without selection for transformation-competent cells. Based on the presence or absence of CRE recombinase activity without or with the CRE T-DNA being integrated, transient expression versus stable transformation was differentiated. During root explant cocultivation, continuous light enhanced the number of plant cells competent for interaction with Agrobacterium and thus the number of transient gene expression events. However, in transformation competent plant cells, continuous light did not further enhance cotransfer or cointegration frequencies. Upon selection for root transformants expressing a first T-DNA, 43-69 % of these transformants showed cotransfer of another non-selected T-DNA in two different light regimes. However, integration of the non-selected cotransferred T-DNA occurred only in 19-46 % of these transformants, indicating that T-DNA integration in regenerating root cells limits the transformation frequencies. After floral dip transformation, transient T-DNA expression without integration could not be detected, while stable T-DNA transformation occurred in 0.5-1.3 % of the T1 seedlings. Upon selection for floral dip transformants with a first T-DNA, 8-34 % of the transformants showed cotransfer of the other non-selected T-DNA and in 93-100 % of them, the T-DNA was also integrated. Therefore, a productive interaction between the agrobacteria and the female gametophyte, rather than the T-DNA integration process, restricts the floral dip transformation frequencies. PMID:23975012

  7. Process for producing an activated carbon adsorbent with integral heat transfer apparatus

    NASA Technical Reports Server (NTRS)

    Jones, Jack A. (Inventor); Yavrouian, Andre H. (Inventor)

    1996-01-01

    A process for producing an integral adsorbent-heat exchanger apparatus useful in ammonia refrigerant heat pump systems. In one embodiment, the process wets an activated carbon particles-solvent mixture with a binder-solvent mixture, presses the binder wetted activated carbon mixture on a metal tube surface and thereafter pyrolyzes the mixture to form a bonded activated carbon matrix adjoined to the tube surface. The integral apparatus can be easily and inexpensively produced by the process in large quantities.

  8. Controlling electronic effects and intermolecular packing in contorted polyaromatic hydrocarbons (c-PAHs): towards high mobility field effect transistors.

    PubMed

    Bhattacharyya, Kalishankar; Mukhopadhyay, Titas Kumar; Datta, Ayan

    2016-06-01

    We have investigated the electronic and charge transport properties of two regioisomeric contorted polyaromatic hydrocarbons at the molecular level as well as in the crystalline state. Electron and hole transport is studied on the basis of an incoherent charge hopping model through DFT calculations. For trifluro-dibenzoperylene (CF3-DBP, ), which crystallizes as a herringbone network, the computed drift hole and electron mobilities are 0.234 and 0.008 cm(2) V(-1) S(-1), respectively. The greater hole mobility in the DBP crystal (μh/μe = 29) can be rationalized by its lower hole reorganization energy and higher hole transfer integral simultaneously. These calculations for the pristine DBP crystal differ from recent experiments indicating its preferential electron conductivity. This might be attributed to the interaction of the molecules with the gold source/drain electrodes. Its second regioisomer, , having a HOMO-LUMO gap of 3.2 eV and thus expectedly inefficient, can be converted into an effective OFET material by replacing the Ph-CF3 groups by oxo groups (>C[double bond, length as m-dash]O) in the 9 and 10 positions (9,10-dioxotribenzopyrene, ). has a suitable HOMO-LUMO gap of 2.18 eV. This bowl-shaped molecule is predicted to pack in a stacked orientation with preferential concaveconcave pairs having a short intermolecular distance of 4.15 Å and identical inter-chromophoric electron/hole coupling (th ∼ te). This creates an ambipolar charge transport behavior in . Clearly, fine tuning the structure-property relationship opens up the possibility of implanting tailored OFET properties in the existing library of molecules. PMID:27189183

  9. Magnetic Field Mapping and Integral Transfer Function Matching of the Prototype Dipoles for the NSLS-II at BNL

    SciTech Connect

    He, P.; Jain, A., Gupta, R., Skaritka, J., Spataro, C., Joshi, P., Ganetis, G., Anerella, M., Wanderer, P.

    2011-03-28

    The National Synchrotron Light Source-II (NSLS-II) storage ring at Brookhaven National Laboratory (BNL) will be equipped with 54 dipole magnets having a gap of 35 mm, and 6 dipoles having a gap of 90 mm. Each dipole has a field of 0.4 T and provides 6 degrees of bending for a 3 GeV electron beam. The large aperture magnets are necessary to allow the extraction of long-wavelength light from the dipole magnet to serve a growing number of users of low energy radiation. The dipoles must not only have good field homogeneity (0.015% over a 40 mm x 20 mm region), but the integral transfer functions and integral end harmonics of the two types of magnets must also be matched. The 35 mm aperture dipole has a novel design where the yoke ends are extended up to the outside dimension of the coil using magnetic steel nose pieces. This design increases the effective length of the dipole without increasing the physical length. These nose pieces can be tailored to adjust the integral transfer function as well as the homogeneity of the integrated field. One prototype of each dipole type has been fabricated to validate the designs and to study matching of the two dipoles. A Hall probe mapping system has been built with three Group 3 Hall probes mounted on a 2-D translation stage. The probes are arranged with one probe in the midplane of the magnet and the others vertically offset by {+-}10 mm. The field is mapped around a nominal 25 m radius beam trajectory. The results of measurements in the as-received magnets, and with modifications made to the nose pieces are presented.

  10. Reexamining surface-integral formulations for one-nucleon transfers to bound and resonance states

    NASA Astrophysics Data System (ADS)

    Escher, J. E.; Thompson, I. J.; Arbanas, G.; Elster, Ch.; Eremenko, V.; Hlophe, L.; Nunes, F. M.; Torus Collaboration

    2014-05-01

    One-nucleon transfer reactions, in particular (d ,p) reactions, have played a central role in nuclear structure studies for many decades. Present theoretical descriptions of the underlying reaction mechanisms are insufficient for addressing the challenges and opportunities that are opening up with new radioactive beam facilities. We investigate a theoretical approach that was proposed recently to address shortcomings in the description of transfers to resonance states. The method builds on ideas from the very successful R-matrix theory; in particular, it uses a similar separation of the coordinate space into interior and exterior regions and introduces a parametrization that can be related to physical observables, which, in principle, makes it possible to extract meaningful spectroscopic information from experiments. We carry out calculations, for a selection of isotopes and energies, to test the usefulness of the new approach.

  11. 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.

  12. Calculations of helical twisting powers from intermolecular torques.

    PubMed

    Earl, David J; Wilson, Mark R

    2004-05-22

    We present a Monte Carlo molecular simulation method that calculates the helical twisting power of a chiral molecule by sampling intermolecular torques. The approach is applied to an achiral nematic liquid crystalline system, composed of Gay-Berne particles, that is doped with chiral molecules. Calculations are presented for six chiral dopant molecules and the results show a good correlation with the sign and magnitude of experimentally determined helical twisting powers. PMID:15267981

  13. 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

  14. 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.

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

    PubMed

    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 5.2nm 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. PMID:27243966

  16. IR spectroscopy of monohydrated tryptamine cation: Rearrangement of the intermolecular hydrogen bond induced by photoionization

    NASA Astrophysics Data System (ADS)

    Sakota, Kenji; Kouno, Yuuki; Harada, Satoshi; Miyazaki, Mitsuhiko; Fujii, Masaaki; Sekiya, Hiroshi

    2012-12-01

    Rearrangement of intermolecular hydrogen bond in a monohydrated tryptamine cation, [TRA(H2O)1]+, has been investigated in the gas phase by IR spectroscopy and quantum chemical calculations. In the S0 state of TRA(H2O)1, a water molecule is hydrogen-bonded to the N atom of the amino group of a flexible ethylamine side chain [T. S. Zwier, J. Phys. Chem. A 105, 8827 (2001), 10.1021/jp011659+]. A remarkable change in the hydrogen-bonding motif of [TRA(H2O)]+ occurs upon photoionization. In the D0 state of [TRA(H2O)1]+, the water molecule is hydrogen-bonded to the NH group of the indole ring of TRA+, indicating that the water molecule transfers from the amino group to NH group. Quantum chemical calculations are performed to investigate the pathway of the water transfer. Two potential energy barriers emerge in [TRA(H2O)1]+ along the intrinsic reaction coordinate of the water transfer. The water transfer event observed in [TRA(H2O)1]+ is not an elementary but a complex process.

  17. Intermolecular interactions of thrombospondins drive their accumulation in extracellular matrix

    PubMed Central

    Kim, Dae Joong; Christofidou, Elena D.; Keene, Douglas R.; Hassan Milde, Marwah; Adams, Josephine C.

    2015-01-01

    Thrombospondins participate in many aspects of tissue organization in adult tissue homeostasis, and their dysregulation contributes to pathological processes such as fibrosis and tumor progression. The incorporation of thrombospondins into extracellular matrix (ECM) as discrete puncta has been documented in various tissue and cell biological contexts, yet the underlying mechanisms remain poorly understood. We find that collagen fibrils are disorganized in multiple tissues of Thbs1−/− mice. In investigating how thrombospondins become retained within ECM and thereby affect ECM organization, we find that accumulation of thrombospondin-1 or thrombospondin-5 puncta within cell-derived ECM is controlled by a novel, conserved, surface-exposed site on the thrombospondin L-type lectin domain. This site acts to recruit thrombospondin molecules into ECM by intermolecular interactions in trans. This mechanism is fibronectin independent, can take place extracellularly, and is demonstrated to be direct in vitro. The trans intermolecular interactions can also be heterotypic—for example, between thrombospondin-1 and thrombospondin-5. These data identify a novel concept of concentration-dependent, intermolecular “matrix trapping” as a conserved mechanism that controls the accumulation and thereby the functionality of thrombospondins in ECM. PMID:25995382

  18. Competing intramolecular vs. intermolecular hydrogen bonds in solution.

    PubMed

    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

  19. 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

  20. 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.

  1. Probing Intermolecular Interactions in Polycyclic Aromatic Hydrocarbons with 2D IR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Krummel, Amber

    2014-03-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment and impact geochemical processes that are critical to sustainable energy resources. For example, asphaltenes exist naturally in geologic formations and their aggregates heavily impact the petroleum economy. Unfortunately, the chemical dynamics that drive asphaltene nanoaggregation processes are still poorly understood. Solvent dynamics and intermolecular interactions such as π-stacking interactions play integral roles in asphaltene nanoaggregation. Linear and nonlinear vibrational spectroscopy including two-dimensional infrared spectroscopy (2DIR), are well suited to explore these fundamental interactions. Teasing apart the vibrational characteristics in PAHs that model asphaltenic compounds represents an important step towards utilizing 2D IR spectroscopy to understand the intermolecular interactions that are prevalent in asphaltene nanoaggregation. A solar dye, N,N'-Dioctyl-3,4,9,10-perylenedicarboximide, is used in this work to model aphaltenes. Carbonyl and ring vibrations are used to probe the nanoaggregates of the model compounds. However, the characteristics of these normal modes change as a function of the size of the conjugated ring system. Thus, in order to fully understand the nature of these normal modes, we include a systematic study of a series of quinones. Our investigation employs a combination of 2DIR spectroscopy and electronic structure calculations to explore vibrational coupling in quinones and PAHs. We compare the calculated vibrational characteristics to those extracted from 2DIR spectra. ATK acknowledges the Donors of the American Chemical Society Petroleum Research Fund for support of this research.

  2. Polar solvation and electron transfer

    SciTech Connect

    Not Available

    1993-04-13

    The report is divided into the following sections: completion of previous studies on solvation dynamics, dipole lattice studies, inertial components of solvation response, simple models of solvation dynamics, rotational dynamics and dielectric friction, intramolecular electron transfer reactions, and intermolecular donor-acceptor complexes.

  3. Permutationally invariant fitting of intermolecular potential energy surfaces: A case study of the Ne-C2H2 system

    NASA Astrophysics Data System (ADS)

    Li, Jun; Guo, Hua

    2015-12-01

    The permutation invariant polynomial-neural network (PIP-NN) approach is extended to fit intermolecular potential energy surfaces (PESs). Specifically, three PESs were constructed for the Ne-C2H2 system. PES1 is a full nine-dimensional PIP-NN PES directly fitted to ˜42 000 ab initio points calculated at the level of CCSD(T)-F12a/cc-pCVTZ-F12, while the other two consist of the six-dimensional PES for C2H2 [H. Han, A. Li, and H. Guo, J. Chem. Phys. 141, 244312 (2014)] and an intermolecular PES represented in either the PIP (PES2) or PIP-NN (PES3) form. The comparison of fitting errors and their distributions, one-dimensional cuts and two-dimensional contour plots of the PESs, as well as classical trajectory collisional energy transfer dynamics calculations shows that the three PESs are very similar. We conclude that full-dimensional PESs for non-covalent interacting molecular systems can be constructed efficiently and accurately by the PIP-NN approach for both the constituent molecules and intermolecular parts.

  4. Integrated titer plate-injector head for microdrop array preparation, storage and transfer

    DOEpatents

    Swierkowski, Stefan P.

    2000-01-01

    An integrated titer plate-injector head for preparing and storing two-dimensional (2-D) arrays of microdrops and for ejecting part or all of the microdrops and inserting same precisely into 2-D arrays of deposition sites with micrometer precision. The titer plate-injector head includes integrated precision formed nozzles with appropriate hydrophobic surface features and evaporative constraints. A reusable pressure head with a pressure equalizing feature is added to the titer plate to perform simultaneous precision sample ejection. The titer plate-injector head may be utilized in various applications including capillary electrophoresis, chemical flow injection analysis, microsample array preparation, etc.

  5. Full surface local heat transfer coefficient measurements in a model of an integrally cast impingement cooling geometry

    SciTech Connect

    Gillespie, D.R.H.; Wang, Z.; Ireland, P.T.; Kohler, S.T.

    1998-01-01

    Cast impingement cooling geometries offer the gas turbine designer higher structural integrity and improved convective cooling when compared to traditional impingement cooling systems, which rely on plate inserts. In this paper, it is shown that the surface that forms the jets contributes significantly to the total cooling. Local heat transfer coefficient distributions have been measured in a model of an engine wall cooling geometry using the transient heat transfer technique. The method employs temperature-sensitive liquid crystals to measure the surface temperature of large-scale perspex models during transient experiments. Full distributions of local Nusselt number on both surfaces of the impingement plate, and on the impingement target plate, are presented at engine representative Reynolds numbers. The relative effects of the impingement plate thermal boundary condition and the coolant supply temperature on the target plate heat transfer have been determined by maintaining an isothermal boundary condition at the impingement plate during the transient tests. The results are discussed in terms of the interpreted flow field.

  6. Integral Method for the Assessment of U-RANS Effectiveness in Non-Equilibrium Flows and Heat Transfer

    NASA Astrophysics Data System (ADS)

    Pond, Ian; Edabi, Alireza; Dubief, Yves; White, Christopher

    2015-11-01

    Reynolds Average Navier Stokes (RANS) modeling has established itself as a critical design tool in many engineering applications, thanks to its superior computational efficiency. The drawbacks of RANS models are well known, but not necessarily well understood: poor prediction of transition, non equilibrium flows, mixing and heat transfer, to name the ones relevant to our study. In the present study, we use a DNS of a reciprocating channel flow driven by an oscillating pressure gradient to test several low- and high-Reynolds RANS models. Temperature is introduced as a passive scalar to study heat transfer modeling. Low-Reynolds models manage to capture the overall physics of wall shear and heat flux well, yet with some phase discrepancies, whereas high Reynolds models fail. Under the microscope of the integral method for wall shear and wall heat flux, the qualitative agreement appears more serendipitous than driven by the ability of the models to capture the correct physics. The integral method is shown to be more insightful in the benchmarking of RANS models than the typical comparisons of statistical quantities. The authors acknowledges the support of NSF and DOE under grant NSF/DOE 1258697 (VT) and 1258702 (NH).

  7. An Investigation into the Process of Transference, through the Integration of Art with Science and Math Curricula, in a California Community College: A Case Study

    ERIC Educational Resources Information Center

    Rachford, Maryann Kvietkauskas

    2011-01-01

    The transference of learning from one discipline to another creates new knowledge between subjects. Students can connect and apply what they learn in one subject to previously existing knowledge. Art expression is an integral part of human nature and has been a means of communication throughout history. Through the integration of art with science…

  8. Active rc networks of low sensitivity for integrated circuit transfer function

    NASA Technical Reports Server (NTRS)

    Huelsman, L. P.; Kerwin, W. J.; Newcomb, R. W.

    1968-01-01

    Active RC network is capable of extremely high Q performance with exceptional stability and has independently adjustable zeros and poles. The circuit consists of two integrators and two summers that are interconnected to produce a complete second-order numerator and a second-order denominator.

  9. Clues to Coral Reef Health: Integrating Radiative Transfer Modeling and Hyperspectral Data

    NASA Technical Reports Server (NTRS)

    Guild, Liane; Ganapol, Barry; Kramer, Philip; Armstrong, Roy; Gleason, Art; Torres, Juan; Johnson, Lee; Garfield, Toby; Peterson, David L. (Technical Monitor)

    2002-01-01

    An important contribution to coral reef research is to improve spectral distinction between various health states of coral species in areas subject to harmful anthropogenic activity and climate change. New insights into radiative transfer properties of corals under healthy and stressed conditions can advance understandings of ecological processes on reefs and allow better assessments of the impacts of large-scale bleaching and disease events, Our objective was to examine the spectral and spatial properties of hyperspectral sensors that may be used to remotely sense changes in reef community health. We compare in situ reef environment spectra (healthy coral, stressed coral, dead coral, algae, and sand) with airborne hyperspectral data to identify important spectral characteristics and indices. Additionally, spectral measurements over a range of water depths, relief, and bottom types are compared to help quantify bottom-water column influences. In situ spectra were collected in July and August 2002 at the Long Rock site in the Andros Island, Bahamas coastal zone coral reef. Our primary emphasis was on Acropora palmata (or elkhorn coral), a major reef building coral, which is prevalent in the study area, but is suffering from white band disease. A. palmata is currently being, proposed as an endangered species because its populations have severely declined in many areas of the Caribbean. In addition to the A. palmata biotope, we have collected spectra of at least seven other coral biotopes that exist within the study area, each with different coral community composition, density of corals, relief, and size of corals. Coral spectral reflectance was then input into a radiative transfer model, CORALMOD (CM1), which is based on a leaf radiative transfer model. In CM1, input coral reflectance measurements produce modeled reflectance through an inversion at each visible wavelength to provide the absorption spectrum. Initially, we imposed a scattering baseline that is the

  10. Clues to Coral Reef Health: Integrating Radiative Transfer Modeling and Hyperspectral Data

    NASA Astrophysics Data System (ADS)

    Guild, L.; Ganapol, B.; Kramer, P.; Armstrong, R.; Gleason, A.; Torres, J.; Johnson, L.; Garfield, N.

    2002-12-01

    An important contribution to coral reef research is to improve spectral distinction between various health states of coral species in areas subject to harmful anthropogenic activity and climate change. New insights into radiative transfer properties of corals under healthy and stressed conditions can advance understandings of ecological processes on reefs and allow better assessments of the impacts of large-scale bleaching and disease events. Our objective is to examine the spectral and spatial properties of hyperspectral sensors that may be used to remotely sense changes in reef community health. We compare in situ reef environment spectra (healthy coral, stressed coral, dead coral, algae, and sand) with airborne hyperspectral data to identify important spectral characteristics and indices. Additionally, spectral measurements over a range of water depths, relief, and bottom types are compared to help quantify bottom-water column influences. In situ spectra was collected in July and August 2002 at the Long Rock site in the Andros Island, Bahamas coastal zone coral reef. Our primary emphasis is on Acropora palmata (or elkhorn coral), a major reef building coral, which is prevalent in the study area, but is suffering from white band disease. A. palmata is currently being proposed as an endangered species because its populations have severely declined in many areas of the Caribbean. In addition to the A. palmata biotope, we have collected spectra of at least seven other coral biotopes that exist within the study area, each with different coral community composition, density of corals, relief, and size of corals. Coral spectral reflectance is input into a radiative transfer model, CORALMOD (CM1), which is based on a leaf radiative transfer model. In CM1, input coral reflectance measurements produce modeled reflectance through an inversion at each visible wavelength to provide the absorption spectrum. Initially, we have imposed a scattering baseline that is the same

  11. Phosphorescence and Energy Transfer in Rigid Solutions.

    ERIC Educational Resources Information Center

    Enciso, E.; Cabello, A.

    1980-01-01

    Describes an experiment which illustrates the general aspects of intermolecular energy transfer between triplet states in rigid solutions of organic compounds solved in an ethanol-ether mixture. Measurements of quenching and energy transfer processes are made using the chemicals of benzophenone and naphthalene. (CS)

  12. State feedback with fractional integral control design based on the Bode's ideal transfer function

    NASA Astrophysics Data System (ADS)

    Al-Saggaf, U. M.; Mehedi, I. M.; Mansouri, R.; Bettayeb, M.

    2016-01-01

    State feedback technique through a gain matrix has been a well-known method for pole assignment of a linear system. The technique could encounter a difficulty in eliminating the steady-state errors in some states. Introducing an integral element can effectively eliminate these errors. State feedback with fractional integral control is proposed, in this work, for pole placement of a linear time invariant system. The proposed method yields simple gain formulae. The paper presents the derivation of the design formulae. The method is applied to stabilise an inherently unstable inverted pendulum-cart system. Simulation and experimental results show the effectiveness of the proposed method for set-point tracking, disturbance rejection and stabilising the inverted pendulum. Comparison with the results obtained from applying Achermann's formula is also presented.

  13. Data Transfer Software-SAS MetaData Server & Phoenix Integration Model Center

    Energy Science and Technology Software Center (ESTSC)

    2010-04-15

    This software is a plug-in that interfaces between the Phoenix Integration's Model Center and the Base SAS 9.2 applications. The end use of the plug-in is to link input and output data that resides in SAS tables or MS SQL to and from "legacy" software programs without recoding. The potential end users are users who need to run legacy code and want data stored in a SQL database.

  14. Enantioselective Intermolecular [2 + 2] Photocycloaddition Reactions of 2(1H)-Quinolones Induced by Visible Light Irradiation

    PubMed Central

    2016-01-01

    In the presence of a chiral thioxanthone catalyst (10 mol %) the title compounds underwent a clean intermolecular [2 + 2] photocycloaddition with electron-deficient olefins at λ = 419 nm. The reactions not only proceeded with excellent regio- and diastereoselectivity but also delivered the respective cyclobutane products with significant enantiomeric excess (up to 95% ee). Key to the success of the reactions is a two-point hydrogen bonding between quinolone and catalyst enabling efficient energy transfer and high enantioface differentiation. Preliminary work indicated that solar irradiation can be used for this process and that the substrate scope can be further expanded to isoquinolones. PMID:27268908

  15. Enantioselective Intermolecular [2 + 2] Photocycloaddition Reactions of 2(1H)-Quinolones Induced by Visible Light Irradiation.

    PubMed

    Tröster, Andreas; Alonso, Rafael; Bauer, Andreas; Bach, Thorsten

    2016-06-29

    In the presence of a chiral thioxanthone catalyst (10 mol %) the title compounds underwent a clean intermolecular [2 + 2] photocycloaddition with electron-deficient olefins at λ = 419 nm. The reactions not only proceeded with excellent regio- and diastereoselectivity but also delivered the respective cyclobutane products with significant enantiomeric excess (up to 95% ee). Key to the success of the reactions is a two-point hydrogen bonding between quinolone and catalyst enabling efficient energy transfer and high enantioface differentiation. Preliminary work indicated that solar irradiation can be used for this process and that the substrate scope can be further expanded to isoquinolones. PMID:27268908

  16. The Divergent Synthesis of Nitrogen Heterocycles by Rhodium(I)-Catalyzed Intermolecular Cycloadditions of Vinyl Aziridines and Alkynes.

    PubMed

    Feng, Jian-Jun; Lin, Tao-Yan; Zhu, Chao-Ze; Wang, Huamin; Wu, Hai-Hong; Zhang, Junliang

    2016-02-24

    Catalyst-controlled divergent intermolecular cycloadditions of vinylaziridines with alkynes have been developed. By using [Rh(NBD)2]BF4 as the catalyst, a [3 + 2] cycloaddition reaction was achieved with broad substrate scope and high stereoselectivity under mild reaction conditions. Moreover, the chirality of vinylaziridines can be completely transferred to the [3 + 2] cycloadducts. When the catalyst was changed to [Rh(η(6)-C10H8) (COD)]SbF6, the alternative [5 + 2] cycloadducts were selectively formed under otherwise identical conditions. PMID:26859710

  17. Time delay and integration array (TDI) using charge transfer device technology. Phase 2, volume 1: Technical

    NASA Technical Reports Server (NTRS)

    1977-01-01

    The 20x9 TDI array was developed to meet the LANDSAT Thematic Mapper Requirements. This array is based upon a self-aligned, transparent gate, buried channel process. The process features: (1) buried channel, four phase, overlapping gate CCD's for high transfer efficiency without fat zero; (2) self-aligned transistors to minimize clock feedthrough and parasitic capacitance; and (3) transparent tin oxide electrode for high quantum efficiency with front surface irradiation. The requirements placed on the array and the performance achieved are summarized. This data is the result of flat field measurements only, no imaging or dynamic target measurements were made during this program. Measurements were performed with two different test stands. The bench test equipment fabricated for this program operated at the 8 micro sec line time and employed simple sampling of the gated MOSFET output video signal. The second stand employed Correlated Doubled Sampling (CDS) and operated at 79.2 micro sec line time.

  18. Density-based Energy Decomposition Analysis for Intermolecular Interactions with Variationally Determined Intermediate State Energies

    SciTech Connect

    Wu, Q.; Ayers, P.W.; Zhang, Y.

    2009-10-28

    The first purely density-based energy decomposition analysis (EDA) for intermolecular binding is developed within the density functional theory. The most important feature of this scheme is to variationally determine the frozen density energy, based on a constrained search formalism and implemented with the Wu-Yang algorithm [Q. Wu and W. Yang, J. Chem. Phys. 118, 2498 (2003) ]. This variational process dispenses with the Heitler-London antisymmetrization of wave functions used in most previous methods and calculates the electrostatic and Pauli repulsion energies together without any distortion of the frozen density, an important fact that enables a clean separation of these two terms from the relaxation (i.e., polarization and charge transfer) terms. The new EDA also employs the constrained density functional theory approach [Q. Wu and T. Van Voorhis, Phys. Rev. A 72, 24502 (2005)] to separate out charge transfer effects. Because the charge transfer energy is based on the density flow in real space, it has a small basis set dependence. Applications of this decomposition to hydrogen bonding in the water dimer and the formamide dimer show that the frozen density energy dominates the binding in these systems, consistent with the noncovalent nature of the interactions. A more detailed examination reveals how the interplay of electrostatics and the Pauli repulsion determines the distance and angular dependence of these hydrogen bonds.

  19. Second Virial Coefficients and Transport Properties of Hexafluoride Gases from an Improved Intermolecular Potential

    NASA Astrophysics Data System (ADS)

    Coroiu, Ilioara; Demco, D. E.

    1997-10-01

    Second virial coefficients and a large number of Chapman-Cowling collision integrals were calculated for gases obeying an improved intermolecular potential proposed by Aziz et al. [J. Chem. Phys. 94, 1034 (1991)]. The results are tabulated for a large reduced temperature range, kT/ɛ from 0.1 to 100. The treatment was entirely classical, and no corrections for quantum effects were made. The higher approximations to the transport coefficients were also calculated and tabulated for the same temperature range. These results should be applicable to characterize the bulk properties of various spherical molecules, especially to predict gaseous transport properties. Evaluation of the potential parameters for uranium hexafluoride, together with fitting to second virial coefficient, viscosity, thermal conductivity and self-diffusion data are also presented. This potential appears to have the best overall predictive ability for gaseous hexafluoride data.

  20. 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.

  1. Computing free energy hypersurfaces for anisotropic intermolecular associations.

    PubMed

    Strümpfer, Johan; Naidoo, Kevin J

    2010-01-30

    We previously used an adaptive reaction coordinate force biasing method for calculating the free energy of conformation (Naidoo and Brady, J Am Chem Soc 1999, 121, 2244) and chemical reactions (Rajamani et al., J Comput Chem 2003, 24, 1775) amongst others. Here, we describe a generalized version able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces method. To illustrate it, we describe how we calculate a multidimensional intermolecular orientational free energy, which can be used to investigate complex systems such as protein conformation and liquids. This multidimensional intermolecular free energy W(r, theta(1), theta(2), phi) provides a measure of orientationally dependent interactions that are appropriate for applications in systems that inherently have molecular anisotropic features. It is a highly informative free energy volume, which can be used to parameterize key terms such as the Gay-Berne intermolecular potential in coarse grain simulations. To demonstrate the value of the information gained from the W(r, theta(1), theta(2), phi) hypersurfaces we calculated them for TIP3P, TIP4P, and TIP5P dimer water models in vacuum. A comparison with a commonly used one-dimensional distance free energy profile is made to illustrate the significant increase in configurational information. The W(r) plots show little difference between the three models while the W(r, theta(1), theta(2), phi) hypersurfaces reveal the underlying energetic reasons why these potentials reproduce tetrahedrality in the condensed phase so differently from each. PMID:19462397

  2. 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

  3. Photon Antibunching in Complex Intermolecular Fluorescence Quenching Kinetics.

    PubMed

    Sharma, Arjun; Enderlein, Jörg; Kumbhakar, Manoj

    2016-08-18

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

  4. Analysis of Hydrodynamics and Heat Transfer in a Thin Liquid Film Flowing over a Rotating Disk by Integral Method

    NASA Technical Reports Server (NTRS)

    Basu, S.; Cetegen, B. M.

    2005-01-01

    An integral analysis of hydrodynamics and heat transfer in a thin liquid film flowing over a rotating disk surface is presented for both constant temperature and constant heat flux boundary conditions. The model is found to capture the correct trends of the liquid film thickness variation over the disk surface and compare reasonably well with experimental results over the range of Reynolds and Rossby numbers covering both inertia and rotation dominated regimes. Nusselt number variation over the disk surface shows two types of behavior. At low rotation rates, the Nusselt number exhibits a radial decay with Nusselt number magnitudes increasing with higher inlet Reynolds number for both constant wall temperature and heat flux cases. At high rotation rates, the Nusselt number profiles exhibit a peak whose location advances radially outward with increasing film Reynolds number or inertia. The results also compare favorably with the full numerical simulation results from an earlier study as well as with the reported experimental results.

  5. A Small Molecule That Protects the Integrity of the Electron Transfer Chain Blocks the Mitochondrial Apoptotic Pathway.

    PubMed

    Jiang, Xian; Li, Li; Ying, Zhengxin; Pan, Chenjie; Huang, Shaoqiang; Li, Lin; Dai, Miaomiao; Yan, Bo; Li, Ming; Jiang, Hui; Chen, She; Zhang, Zhiyuan; Wang, Xiaodong

    2016-07-21

    In response to apoptotic stimuli, mitochondria in mammalian cells release cytochrome c and other apoptogenic proteins, leading to the subsequent activation of caspases and apoptotic cell death. This process is promoted by the pro-apoptotic members of the Bcl-2 family of proteins, such as Bim and Bax, which, respectively, initiate and execute cytochrome c release from the mitochondria. Here we report the discovery of a small molecule that efficiently blocks Bim-induced apoptosis after Bax is activated on the mitochondria. The cellular target of this small molecule was identified to be the succinate dehydrogenase subunit B (SDHB) protein of complex II of the mitochondrial electron transfer chain (ETC). The molecule protects the integrity of the ETC and allows treated cells to continue to proliferate after apoptosis induction. Moreover, this molecule blocked dopaminergic neuron death and reversed Parkinson-like behavior in a rat model of Parkinson's disease. PMID:27447985

  6. Integration of radiative transfer into satellite models of ocean primary production

    NASA Astrophysics Data System (ADS)

    Smyth, T. J.; Tilstone, G. H.; Groom, S. B.

    2005-10-01

    A major goal of ocean color observations from space is the determination of phytoplankton primary productivity (PP) and hence oceanic carbon uptake. Results of a PP model implemented to use satellite-derived fields of chlorophyll, photosynthetically available radiation (PAR) and sea-surface temperature (SST) are presented. The model gave a global estimate of PP of around 57 Gt C yr-1 and gives a low RMS (0.16) when compared with in situ data. However, as the model's in-water light field parameterization only considers attenuation by pure water and chlorophyll, PP is overestimated in case II waters where other optically important constituents such as colored dissolved organic matter (CDOM) and suspended particulate matter (SPM) are also present. This paper develops a novel technique to determine PP by coupling a radiative transfer code, which allows the inclusion of CDOM and SPM, to the original photosynthesis model. For the global calculations, a look-up table has been generated using chlorophyll, CDOM, SST, PAR and day length as inputs. The resultant 364,500 element look-up table has been applied to data from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate-Resolution Imaging Spectroradiometer (MODIS). PP retrievals are improved in case II waters and global estimates are reduced to between 52 and 55 Gt C yr-1.

  7. Space transfer vehicle concepts and requirements study. Volume 2, book 4: Integrated advanced technology development

    NASA Technical Reports Server (NTRS)

    Weber, Gary A.

    1991-01-01

    The Space Transfer Vehicle (STV) program provides both an opportunity and a requirement to increase our upper stage capabilities with the development and applications of new technologies. Issues such as man rating, space basing, reusability, and long lunar surface storage times drive the need for new technology developments and applications. In addition, satisfaction of mission requirements such as lunar cargo delivery capability and lunar landing either require new technology development or can be achieved in a more cost-effective manner with judicious applications of advanced technology. During the STV study, advanced technology development requirements and plans have been addressed by the Technology/Advanced Development Working Group composed of NASA and contractor representatives. This report discusses the results to date of this working group. The first section gives an overview of the technologies that have potential or required applications for the STV and identifies those technologies baselined for the STV. Figures are provided that list the technology categories and show the priority placed on those technology categories for either the space-based or ground-based options. The second section covers the plans and schedules for incorporating the technologies into the STV program.

  8. Zebrafish Class 1 Phosphatidylinositol Transfer Proteins: PITPβ and Double Cone Cell Outer Segment Integrity in Retina

    PubMed Central

    Ile, Kristina E.; Kassen, Sean; Cao, Canhong; Vihtehlic, Thomas; Shah, Sweety D.; Mousley, Carl J.; Alb, James G.; Huijbregts, Richard P.H.; Stearns, George W.; Brockerhoff, Susan E.; Hyde, David R.; Bankaitis, Vytas A.

    2010-01-01

    Phosphatidylinositol transfer proteins (PITPs) in yeast coordinate lipid metabolism with the activities of specific membrane trafficking pathways. The structurally unrelated metazoan-specific PITPs (mPITPs), on the other hand, are an under-investigated class of proteins. It remains unclear what biological activities mPITPs discharge, and the mechanisms by which these proteins function are also not understood. The soluble class 1 mPITPs include the PITPα and PITPβ isoforms. Of these, the β-isoforms are particularly poorly characterized. Herein, we report the use of zebrafish as a model vertebrate for the study of class 1 mPITP biological function. Zebrafish express PITPα and PITPβ-isoforms (Pitpna and Pitpnb, respectively) and a novel PITPβ-like isoform (Pitpng). Pitpnb expression is particularly robust in double cone cells of the zebrafish retina. Morpholino-mediated protein knockdown experiments demonstrate Pitpnb activity is primarily required for biogenesis/maintenance of the double cone photoreceptor cell outer segments in the developing retina. By contrast, Pitpna activity is essential for successful navigation of early developmental programs. This study reports the initial description of the zebrafish class 1 mPITP family, and the first analysis of PITPβ function in a vertebrate. PMID:20545905

  9. High performance organic integrated device with ultraviolet photodetective and electroluminescent properties consisting of a charge-transfer-featured naphthalimide derivative

    SciTech Connect

    Wang, Hanyu; Wang, Xu; Yu, Junsheng E-mail: jsyu@uestc.edu.cn; Zhou, Jie; Lu, Zhiyun E-mail: jsyu@uestc.edu.cn

    2014-08-11

    A high performance organic integrated device (OID) with ultraviolet photodetective and electroluminescent (EL) properties was fabricated by using a charge-transfer-featured naphthalimide derivative of 6-(3,5-bis-[9-(4-t-butylphenyl)-9H-carbazol-3-yl]-phenoxy)-2- (4-t-butylphenyl)-benzo[de]isoquinoline-1,3-dione (CzPhONI) as the active layer. The results showed that the OID had a high detectivity of 1.5 × 10{sup 11} Jones at −3 V under the UV-350 nm illumination with an intensity of 0.6 mW/cm{sup 2}, and yielded an exciplex EL light emission with a maximum brightness of 1437 cd/m{sup 2}. Based on the energy band diagram, both the charge transfer feature of CzPhONI and matched energy level alignment were responsible for the dual ultraviolet photodetective and EL functions of OID.

  10. Organic nanofibers integrated by transfer technique in field-effect transistor devices

    PubMed Central

    2011-01-01

    The electrical properties of self-assembled organic crystalline nanofibers are studied by integrating these on field-effect transistor platforms using both top and bottom contact configurations. In the staggered geometries, where the nanofibers are sandwiched between the gate and the source-drain electrodes, a better electrical conduction is observed when compared to the coplanar geometry where the nanofibers are placed over the gate and the source-drain electrodes. Qualitatively different output characteristics were observed for top and bottom contact devices reflecting the significantly different contact resistances. Bottom contact devices are dominated by contact effects, while the top contact device characteristics are determined by the nanofiber bulk properties. It is found that the contact resistance is lower for crystalline nanofibers when compared to amorphous thin films. These results shed light on the charge injection and transport properties for such organic nanostructures and thus constitute a significant step forward toward a nanofiber-based light-emitting device. PMID:21711821

  11. Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences.

    PubMed Central

    Mello, C C; Kramer, J M; Stinchcomb, D; Ambros, V

    1991-01-01

    We describe a dominant behavioral marker, rol-6(su-1006), and an efficient microinjection procedure which facilitate the recovery of Caenorhabditis elegans transformants. We use these tools to study the mechanism of C.elegans DNA transformation. By injecting mixtures of genetically marked DNA molecules, we show that large extrachromosomal arrays assemble directly from the injected molecules and that homologous recombination drives array assembly. Appropriately placed double-strand breaks stimulated homologous recombination during array formation. Our data indicate that the size of the assembled transgenic structures determines whether or not they will be maintained extrachromosomally or lost. We show that low copy number extrachromosomal transformation can be achieved by adjusting the relative concentration of DNA molecules in the injection mixture. Integration of the injected DNA, though relatively rare, was reproducibly achieved when single-stranded oligonucleotide was co-injected with the double-stranded DNA. Images PMID:1935914

  12. 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.

  13. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGESBeta

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

    2015-08-14

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

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

    PubMed

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

    2016-07-13

    Molecular orbital engineering is a key ingredient for the design of organic devices. Intermolecular hybridization promises efficient charge carrier transport but usually requires dense packing for significant wave function overlap. Here we use scanning tunneling spectroscopy to spatially resolve the electronic structure of a surface-confined nanoporous supramolecular sheet of a prototypical hydrocarbon compound featuring terminal alkyne (-CCH) groups. Surprisingly, localized nanopore orbitals are observed, with their electron density centered in the cavities surrounded by the functional moieties. Density functional theory calculations reveal that these new electronic states originate from the intermolecular hybridization of six in-plane π-orbitals of the carbon-carbon triple bonds, exhibiting significant electronic splitting and an energy downshift of approximately 1 eV. Importantly, these nanopore states are distinct from previously reported interfacial states. We unravel the underlying connection between the formation of nanopore orbital and geometric arrangements of functional groups, thus demonstrating the generality of applying related orbital engineering concepts in various types of porous organic structures. PMID:27253516

  15. 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

  16. Integration of energy and electron transfer processes in the photosynthetic membrane of Rhodobacter sphaeroides

    PubMed Central

    Cartron, Michaël L.; Olsen, John D.; Sener, Melih; Jackson, Philip J.; Brindley, Amanda A.; Qian, Pu; Dickman, Mark J.; Leggett, Graham J.; Schulten, Klaus; Hunter, C. Neil

    2014-01-01

    Photosynthesis converts absorbed solar energy to a protonmotive force, which drives ATP synthesis. The membrane network of chlorophyll–protein complexes responsible for light absorption, photochemistry and quinol (QH2) production has been mapped in the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides using atomic force microscopy (AFM), but the membrane location of the cytochrome bc1 (cytbc1) complexes that oxidise QH2 to quinone (Q) to generate a protonmotive force is unknown. We labelled cytbc1 complexes with gold nanobeads, each attached by a Histidine10 (His10)-tag to the C-terminus of cytc1. Electron microscopy (EM) of negatively stained chromatophore vesicles showed that the majority of the cytbc1 complexes occur as dimers in the membrane. The cytbc1 complexes appeared to be adjacent to reaction centre light-harvesting 1-PufX (RC-LH1-PufX) complexes, consistent with AFM topographs of a gold-labelled membrane. His-tagged cytbc1 complexes were retrieved from chromatophores partially solubilised by detergent; RC-LH1-PufX complexes tended to co-purify with cytbc1, whereas LH2 complexes became detached, consistent with clusters of cytbc1 complexes close to RC-LH1-PufX arrays, but not with a fixed, stoichiometric cytbc1-RC-LH1-PufX supercomplex. This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1-RC-PufX dimers & 2 RC-LH1-PufX monomers, 4 cytbc1 dimers and 2 ATP synthases. Simulation of the interconnected energy, electron and proton transfer processes showed a half-maximal ATP turnover rate for a light intensity equivalent to only 1% of bright sunlight. Thus, the photosystem architecture of the chromatophore is optimised for growth at low light intensities. PMID:24530865

  17. Integrated smartphone imaging of quantum dot photoluminescence and Förster resonance energy transfer

    NASA Astrophysics Data System (ADS)

    Petryayeva, Eleonora; Algar, W. Russ

    2015-06-01

    Smartphones and other mobile devices are emerging as promising analytical platforms for point-of-care diagnostics, particularly when combined with nanotechnology. For example, we have shown that the optical properties of semiconductor quantum dots (QDs) are well suited to photoluminescence (PL) detection with a smartphone camera. However, this previous work has utilized an external excitation source for interrogation of QD PL. In this proceeding, we demonstrate that the white-light LED photographic flashes built into smartphones can be optically filtered to yield blue light suitable for excitation of QD PL. Measurements were made by recording video with filtered flash illumination and averaging the frames of the video to obtain images with good signal-to-background ratios. These images permitted detection of green-emitting and red-emitting QDs at levels comparable to those possible with excitation using an external long-wave UV lamp. The optical properties of QDs proved to be uniquely suited to smartphone PL imaging, exhibiting emission that was 1-2 orders magnitude brighter than that of common fluorescent dyes under the same conditions. Excitation with the smartphone flash was also suitable for imaging of FRET between green-emitting QD donors and Alexa Fluor 555 (A555) fluorescent dye acceptors. No significant difference in FRET imaging capability was observed between excitation with the smartphone flash and a long-wave UV lamp. Although the smartphone flash did have some disadvantages compared to an external UV lamp, these disadvantages are potentially offset by the benefit of having excitation and detection integrated into the smartphone.

  18. Design, fabrication, and calibration of curved integral coils for measuring transfer function, uniformity, and effective length of LBL ALS (Lawrence Berkeley Laboratory Advanced Light Source) Booster Dipole Magnets

    SciTech Connect

    Green, M.I.; Nelson, D.; Marks, S.; Gee, B.; Wong, W.; Meneghetti, J.

    1989-03-01

    A matched pair of curved integral coils has been designed, fabricated and calibrated at Lawrence Berkeley Laboratory for measuring Advanced Light Source (ALS) Booster Dipole Magnets. Distinctive fabrication and calibration techniques are described. The use of multifilar magnet wire in fabrication integral search coils is described. Procedures used and results of AC and DC measurements of transfer function, effective length and uniformity of the prototype booster dipole magnet are presented in companion papers. 8 refs.

  19. Multiple Roles for Enterococcus faecalis Glycosyltransferases in Biofilm-Associated Antibiotic Resistance, Cell Envelope Integrity, and Conjugative Transfer

    PubMed Central

    Dale, Jennifer L.; Cagnazzo, Julian; Phan, Chi Q.; Barnes, Aaron M. T.

    2015-01-01

    The emergence of multidrug-resistant bacteria and the limited availability of new antibiotics are of increasing clinical concern. A compounding factor is the ability of microorganisms to form biofilms (communities of cells encased in a protective extracellular matrix) that are intrinsically resistant to antibiotics. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and also has the propensity to acquire resistance determinants via horizontal gene transfer. There is intense interest in the genetic basis for intrinsic and acquired antibiotic resistance in E. faecalis, since clinical isolates exhibiting resistance to multiple antibiotics are not uncommon. We performed a genetic screen using a library of transposon (Tn) mutants to identify E. faecalis biofilm-associated antibiotic resistance determinants. Five Tn mutants formed wild-type biofilms in the absence of antibiotics but produced decreased biofilm biomass in the presence of antibiotic concentrations that were subinhibitory to the parent strain. Genetic determinants responsible for biofilm-associated antibiotic resistance include components of the quorum-sensing system (fsrA, fsrC, and gelE) and two glycosyltransferase (GTF) genes (epaI and epaOX). We also found that the GTFs play additional roles in E. faecalis resistance to detergent and bile salts, maintenance of cell envelope integrity, determination of cell shape, polysaccharide composition, and conjugative transfer of the pheromone-inducible plasmid pCF10. The epaOX gene is located in a variable extended region of the enterococcal polysaccharide antigen (epa) locus. These data illustrate the importance of GTFs in E. faecalis adaptation to diverse growth conditions and suggest new targets for antimicrobial design. PMID:25918141

  20. Visualizing the orientational dependence of an intermolecular potential

    PubMed Central

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

    2016-01-01

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

  1. 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. PMID:7939660

  2. Visualizing the orientational dependence of an intermolecular potential

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  3. Intermolecular interactions in the crystalline state of some organotellurium antioxidants

    NASA Astrophysics Data System (ADS)

    Engman, L.; Kania, I.; Oleksyn, B. J.; Śliwiński, J.; Wojtoń, A.

    2002-05-01

    The X-ray crystal structure analysis was performed for single crystals of bis (4-aminophenyl) telluride ( 1), bis [4-( N, N-dimethylamino)phenyl] telluride ( 2) and bis (4-hydroxyphenyl) telluride hemihydrate ( 3). The molecules of the diaryl tellurides 1- 3 display two types of non-planar conformations: 'butterfly' and 'T-shaped'. They differ in the torsion angles around Te-C bonds. Intermolecular hydrogen bonds occur between water molecules and hydroxyl groups in compound 3 and also between phenyl rings and proton donors in compounds 2 and 3 with -H⋯π distances 2.56(8)-2.95(6) Å. Also, in compounds 1 and 2 short -H⋯π contacts (3.02(4)-3.29(5) Å) were observed.

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

    NASA Astrophysics Data System (ADS)

    Kannemann, Felix; Becke, Axel

    2010-03-01

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

  5. 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.

  6. 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.

  7. Definition, technology readiness, and development cost of the orbit transfer vehicle engine integrated control and health monitoring system elements

    NASA Technical Reports Server (NTRS)

    Cannon, I.; Balcer, S.; Cochran, M.; Klop, J.; Peterson, S.

    1991-01-01

    An Integrated Control and Health Monitoring (ICHM) system was conceived for use on a 20 Klb thrust baseline Orbit Transfer Vehicle (OTV) engine. Considered for space used, the ICHM was defined for reusability requirements for an OTV engine service free life of 20 missions, with 100 starts and a total engine operational time of 4 hours. Functions were derived by flowing down requirements from NASA guidelines, previous OTV engine or ICHM documents, and related contracts. The elements of an ICHM were identified and listed, and these elements were described in sufficient detail to allow estimation of their technology readiness levels. These elements were assessed in terms of technology readiness level, and supporting rationale for these assessments presented. The remaining cost for development of a minimal ICHM system to technology readiness level 6 was estimated. The estimates are within an accuracy range of minus/plus 20 percent. The cost estimates cover what is needed to prepare an ICHM system for use on a focussed testbed for an expander cycle engine, excluding support to the actual test firings.

  8. Integral cross section measurements and product recoil velocity distributions of Xe2+ + N2 hyperthermal charge-transfer collisions

    NASA Astrophysics Data System (ADS)

    Hause, Michael L.; Prince, Benjamin D.; Bemish, Raymond J.

    2016-07-01

    Charge exchange from doubly charged rare gas cations to simple diatomics proceeds with a large cross section and results in populations of many vibrational and electronic product states. The charge exchange between Xe2+ and N2, in particular, is known to create N2 + in both the A and B electronic states. In this work, we present integral charge exchange cross section measurements of the Xe2+ + N2 reaction as well as axial recoil velocity distributions of the Xe+ and N2 + product ions for collision energies between 0.3 and 100 eV in the center-of-mass (COM) frame. Total charge-exchange cross sections decrease from 70 Å2 to about 40 Å2 with increasing collision energy through this range. Analysis of the axial velocity distributions indicates that a Xe2+ - N2 complex exists at low collision energies but is absent by 17.6 eV COM. Analysis of the axial velocity distributions reveals evidence for complexes with lifetimes comparable to the rotational period at low collision energies. The velocity distributions are consistent with quasi-resonant single charge transfer at high collision energies.

  9. Integral cross section measurements and product recoil velocity distributions of Xe(2+) + N2 hyperthermal charge-transfer collisions.

    PubMed

    Hause, Michael L; Prince, Benjamin D; Bemish, Raymond J

    2016-07-28

    Charge exchange from doubly charged rare gas cations to simple diatomics proceeds with a large cross section and results in populations of many vibrational and electronic product states. The charge exchange between Xe(2+) and N2, in particular, is known to create N2 (+) in both the A and B electronic states. In this work, we present integral charge exchange cross section measurements of the Xe(2+) + N2 reaction as well as axial recoil velocity distributions of the Xe(+) and N2 (+) product ions for collision energies between 0.3 and 100 eV in the center-of-mass (COM) frame. Total charge-exchange cross sections decrease from 70 Å(2) to about 40 Å(2) with increasing collision energy through this range. Analysis of the axial velocity distributions indicates that a Xe(2+) - N2 complex exists at low collision energies but is absent by 17.6 eV COM. Analysis of the axial velocity distributions reveals evidence for complexes with lifetimes comparable to the rotational period at low collision energies. The velocity distributions are consistent with quasi-resonant single charge transfer at high collision energies. PMID:27475363

  10. 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.

  11. 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.

  12. 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…

  13. Toward Fast and Accurate Evaluation of Charge On-Site Energies and Transfer Integrals in Supramolecular Architectures Using Linear Constrained Density Functional Theory (CDFT)-Based Methods.

    PubMed

    Ratcliff, Laura E; Grisanti, Luca; Genovese, Luigi; Deutsch, Thierry; Neumann, Tobias; Danilov, Denis; Wenzel, Wolfgang; Beljonne, David; Cornil, Jérôme

    2015-05-12

    A fast and accurate scheme has been developed to evaluate two key molecular parameters (on-site energies and transfer integrals) that govern charge transport in organic supramolecular architecture devices. The scheme is based on a constrained density functional theory (CDFT) approach implemented in the linear-scaling BigDFT code that exploits a wavelet basis set. The method has been applied to model disordered structures generated by force-field simulations. The role of the environment on the transport parameters has been taken into account by building large clusters around the active molecules involved in the charge transfer. PMID:26574411

  14. Accompanying coordinate expansion and recurrence relation method using a transfer relation scheme for electron repulsion integrals with high angular momenta and long contractions

    SciTech Connect

    Hayami, Masao; Seino, Junji; Nakai, Hiromi

    2015-05-28

    An efficient algorithm for the rapid evaluation of electron repulsion integrals is proposed. The present method, denoted by accompanying coordinate expansion and transferred recurrence relation (ACE-TRR), is constructed using a transfer relation scheme based on the accompanying coordinate expansion and recurrence relation method. Furthermore, the ACE-TRR algorithm is extended for the general-contraction basis sets. Numerical assessments clarify the efficiency of the ACE-TRR method for the systems including heavy elements, whose orbitals have long contractions and high angular momenta, such as f- and g-orbitals.

  15. A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates

    NASA Astrophysics Data System (ADS)

    Shiga, Motoyuki; Fujisaki, Hiroshi

    2012-05-01

    We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer centroids in the imaginary-time path integral theory. This novel kind of reaction coordinate, which may be called the "centroid IRC," corresponds to the minimum free energy path connecting reactant and product states with a least amount of reversible work applied to the center of masses of the quantum nuclei, i.e., the centroids. We provide a numerical procedure to obtain the centroid IRC based on first principles by combining ab initio path integral simulation with the string method. This approach is applied to NH3 molecule and N2H_5^- ion as well as their deuterated isotopomers to study the importance of nuclear quantum effects in the intramolecular and intermolecular proton transfer reactions. We find that, in the intramolecular proton transfer (inversion) of NH3, the free energy barrier for the centroid variables decreases with an amount of about 20% compared to the classical one at the room temperature. In the intermolecular proton transfer of N2H_5^-, the centroid IRC is largely deviated from the "classical" IRC, and the free energy barrier is reduced by the quantum effects even more drastically.

  16. A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates

    SciTech Connect

    Shiga, Motoyuki; Fujisaki, Hiroshi

    2012-05-14

    We propose a generalization of the intrinsic reaction coordinate (IRC) for quantum many-body systems described in terms of the mass-weighted ring polymer centroids in the imaginary-time path integral theory. This novel kind of reaction coordinate, which may be called the ''centroid IRC,'' corresponds to the minimum free energy path connecting reactant and product states with a least amount of reversible work applied to the center of masses of the quantum nuclei, i.e., the centroids. We provide a numerical procedure to obtain the centroid IRC based on first principles by combining ab initio path integral simulation with the string method. This approach is applied to NH{sub 3} molecule and N{sub 2}H{sub 5}{sup -} ion as well as their deuterated isotopomers to study the importance of nuclear quantum effects in the intramolecular and intermolecular proton transfer reactions. We find that, in the intramolecular proton transfer (inversion) of NH{sub 3}, the free energy barrier for the centroid variables decreases with an amount of about 20% compared to the classical one at the room temperature. In the intermolecular proton transfer of N{sub 2}H{sub 5}{sup -}, the centroid IRC is largely deviated from the ''classical'' IRC, and the free energy barrier is reduced by the quantum effects even more drastically.

  17. Conjugal Transfer of Polychlorinated Biphenyl/Biphenyl Degradation Genes in Acidovorax sp. Strain KKS102, Which Are Located on an Integrative and Conjugative Element

    PubMed Central

    Ishibashi, Yoko; Naganawa, Hideaki; Hirokawa, Satoshi; Atobe, Satomi; Nagata, Yuji; Tsuda, Masataka

    2012-01-01

    A polychlorinated biphenyl (PCB)/biphenyl degradation gene cluster in Acidovorax sp. strain KKS102, which is very similar to that in Tn4371 from Cupriavidus oxalaticus A5, was transferred to several proteobacterial strains by conjugation. The mobilized DNA fragment consisted of 61,807 bp and carried genes for mating-pair formation (mpf), DNA transfer (dtr), integrase (int), and replication-partition proteins (rep-parAB). In the transconjugants, transferred DNA was integrated at ATTGCATCAG or similar sequences. The circular-form integrative and conjugative element (ICE) was detected by PCR, and quantitative PCR analyses revealed that, in KKS102 cells, the ratio of the circular form to the integrated form was very low (approximately 10−5). The circular form was not detected in a mutant of the int gene, which was located at the extreme left and transcribed in the inward direction, and the level of int transcriptional activity was much higher in the circular form than in the integrated form. These findings clearly demonstrated that the genes for PCB/biphenyl degradation in KKS102 cells are located on an ICE, which was named ICEKKS1024677. Comparisons of similar ICE-like elements collected from the public database suggested that those of beta- and gammaproteobacteria were distinguishable from other ICE-like elements, including those in alphaproteobacteria, with respect to the gene composition and gene organization. PMID:22685277

  18. New insights into the dual fluorescence of methyl salicylate: effects of intermolecular hydrogen bonding and solvation.

    PubMed

    Zhou, Panwang; Hoffmann, Mark R; Han, Keli; He, Guozhong

    2015-02-12

    In this paper, we propose a new and complete mechanism for dual fluorescence of methyl salicylate (MS) under different conditions using a combined experimental (i.e., steady-state absorption and emission spectra and time-resolved fluorescence spectra) and theoretical (i.e., time-dependent density function theory) study. First, our theoretical study indicates that the barrier height for excited state intramolecular proton transfer (ESIPT) reaction of ketoB depends on the solvent polarity. In nonpolar solvents, the ESIPT reaction of ketoB is barrierless; the barrier height will increase with increasing solvent polarity. Second, we found that, in alcoholic solvents, intermolecular hydrogen bonding plays a more important role. The ketoB form of MS can form two hydrogen bonds with alcoholic solvents; one will facilitate ESIPT and produce the emission band in the blue region; the other one precludes ESIPT and produces the emission band in the near-UV region. Our proposed new mechanism can well explain previous results as well as our new experimental results. PMID:24678946

  19. Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-21

    The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

  20. Intermolecular interaction of prednisolone with bovine serum albumin: Spectroscopic and molecular docking methods

    NASA Astrophysics Data System (ADS)

    Shi, Jie-hua; Zhu, Ying-Yao; Wang, Jing; Chen, Jun; Shen, Ya-Jing

    2013-02-01

    The intermolecular interaction of prednisolone with bovine serum albumin (BSA) was studied using fluorescence, circular dichroism (CD) and molecular docking methods. The experimental results showed that the fluorescence quenching of the BSA at 338 nm by prednisolone resulted from the formation of prednisolone-BSA complex. The number of binding sites (n) for prednisolone binding on BSA was approximately equal to 1. Base on the sign and magnitude of the enthalpy and entropy changes (ΔH0 = -149.6 kJ mol-1 and ΔS0 = -370.7 J mol-1 K-1) and the results of molecular docking, it could be suggested that the interaction forces were mainly Van der Waals and hydrogen bonding interactions. Moreover, in the binding process of BSA with prednisolone, prednisolone molecule can be inserted into the hydrophobic cavity of subdomain IIIA (site II) of BSA. The distance between prednisolone and Trp residue of BSA was calculated as 2.264 nm according to Forster's non-radiative energy transfer theory.

  1. Modelling past and future sediment transfer in catchment-lake systems using integrated records of environmental change

    NASA Astrophysics Data System (ADS)

    Smith, Hugh; Sellami, Haykel; Sangster, Heather; Riley, Mark; Chiverrell, Richard; Boyle, John

    2016-04-01

    Agricultural change has caused significant environmental impacts with the onset of modern practices and intensification over the past century. In response, many current policy and management initiatives aim to reduce soil erosion and river pollution by fine sediment. However, there is a lack of detailed, longer-term baseline information extending beyond the instrumental record against which to measure the success or otherwise of such efforts. Furthermore, future reductions in the magnitude of impacts on soil erosion achievable under a changing climate remain unclear. Here, we provide an overview of an integrated approach for reconstructing impacts from past agricultural change based on social and environmental records coupled with multi-model simulations of catchment erosion and lake sediment dating. We aim to model soil erosion and sediment transfer responses to climatic variability and land use changes spanning the last ca. 100 years using variants of the RUSLE and Morgan-Morgan-Finney models. The study focuses on six lake catchments in Britain which cover a range of agricultural environments from intensively-farmed lowlands to upland catchments subject to lower-intensity livestock grazing. Land use reconstructions are based on historic aerial photography (1940s-2000s) and satellite-derived land cover maps (1990-2007) in combination with annual parish-level agricultural census data (1890s-1970s) and farmer interviews. Radionuclide dating of lake sediments coupled with pollen analysis provides independent data on decadal sedimentation rates and vegetation cover for comparison with model outputs and land use reconstructions. This combination of social and environmental records, soil erosion modelling and dating of lake sedimentary archives forms a powerful platform from which to project impacts from future agricultural scenarios under a changing climate.

  2. Rous Sarcoma Virus Synaptic Complex Capable of Concerted Integration Is Kinetically Trapped by Human Immunodeficiency Virus Integrase Strand Transfer Inhibitors*

    PubMed Central

    Pandey, Krishan K.; Bera, Sibes; Korolev, Sergey; Campbell, Mary; Yin, Zhiqi; Aihara, Hideki; Grandgenett, Duane P.

    2014-01-01

    We determined conditions to produce milligram quantities of the soluble Rous sarcoma virus (RSV) synaptic complex that is kinetically trapped by HIV strand transfer inhibitors (STIs). Concerted integration catalyzed by RSV integrase (IN) is effectively inhibited by HIV STIs. Optimized assembly of the RSV synaptic complex required IN, a gain-of-function 3′-OH-recessed U3 oligonucleotide, and an STI under specific conditions to maintain solubility of the trapped synaptic complex at 4 °C. A C-terminal truncated IN (1–269 residues) produced a homogeneous population of trapped synaptic complex that eluted at ∼151,000 Da upon Superdex 200 size-exclusion chromatography (SEC). Approximately 90% of input IN and DNA are incorporated into the trapped synaptic complex using either the C-terminally truncated IN or wild type IN (1–286 residues). No STI is present in the SEC running buffer suggesting the STI-trapped synaptic complex is kinetically stabilized. The yield of the trapped synaptic complex correlates with the dissociative half-life of the STI observed with HIV IN-DNA complexes. Dolutegravir, MK-2048, and MK-0536 are equally effective, whereas raltegravir is ∼70% as effective. Without an STI present in the assembly mixture, no trapped synaptic complex was observed. Fluorescence and mass spectroscopy analyses demonstrated that the STI remains associated with the trapped complex. SEC-multiangle light scattering analyses demonstrated that wild type IN and the C-terminal IN truncation are dimers that acted as precursors to the tetramer. The purified STI-trapped synaptic complex contained a tetramer as shown by cross-linking studies. Structural studies of this three-domain RSV IN in complex with viral DNA may be feasible. PMID:24872410

  3. Femtosecond Fourier-transform spectroscopy of low-frequency intermolecular motions in weakly interacting liquids

    SciTech Connect

    Castner, E.W. Jr.; Chang, Y.J.; Melinger, J.S.; McMorrow, D.

    1993-07-01

    Recent work on the subject of solvation dynamics has concentrated on understanding the ultrafast dynamics of intermolecular interactions in strongly interacting, polar, and hydrogen-bonding solvents. In general, investigations into the effects of solvation dynamics on chemical reactions have concentrated on the highly polar liquids because it is in these solvents that the largest spectroscopic changes with solvent relaxation are observed. In these very polar liquids, however, the intermolecular dynamics are very complex, consisting of contributions from reorientational diffusion, inertially limited rotations, intermolecular vibrations involving both reorientational (librational) and translational degrees of freedom, and interaction-induced collisional effects. The role of collisional interaction-induced effects in shaping the intermolecular dynamics of molecular liquids has been a subject of considerable discussion. Molecular dynamics simulations have suggested that collisional effects can have a significant role in shaping the femtosecond dynamics and nonlinear-optical properties of molecular liquids. However, for anisotropic molecules, it is difficult to separate experimentally the collisional effects from other phenomena. In this paper the authors examine the intermolecular dynamics of the weakly interacting liquid carbon tetrachloride (CCl{sub 4}). Because carbon tetrachloride is a spherical top molecule (belonging to the T{sub d} point group), its intermolecular light-scattering spectrum is purely interaction-induced. By studying this purely collision-induced feature in CCl{sub 4}, the authors hope to gain insight on the lowest-frequency intermolecular vibrational behavior of more complex systems.

  4. Analysis of Intermolecular Interactions Using Calculated Molecular Properties: AN AB Initio Quantum Chemical Study

    NASA Astrophysics Data System (ADS)

    Brinck, Nils Tore

    The objective of this study has been to investigate the use of computed molecular properties in predicting and interpreting intermolecular interactions. The molecular properties have been calculated rigorously from ab initio wave functions. We have found the electrostatic potential to be a good tool for the analysis of nonbonding intermolecular interactions. It is demonstrated that the calculated electrostatic potentials around carbon-halogen bonds can be used to explain the directional preferences of halogen interactions in crystals. We also show that the orientation of the molecules in weak gas phase complexes between dihalogens and Lewis bases can be rationalized from their electrostatic potentials. However an analysis of the bonding in boron trifluoride and boron trichloride and their complexes with ammonia indicates that the relative stabilities of these complexes are dictated by charge transfer rather than electrostatics. The higher binding affinity for boron trichloride compared to boron trifluoride is explained by the higher charge capacity of the former. This is contrary to the commonly accepted explanation, which is based on backbonding. A local charge separation index has been defined from surface electrostatic potentials. This provides a measure of local polarity, even for molecules with zero dipole moments. Average local ionization energies computed on molecular surfaces permit predictions of relative reactivities of various sites toward electrophilic attack. There is a very good relationship between {rm p}K_{a} and minima in |{I}({bf r}), designated as |{I}_{S,min }, for a series of azines and azoles. Excellent correlations have also been found between { rm p}K_{a} values for a variety of carbon, oxygen and nitrogen acids and the |{I}_{S,min} of their conjugate bases. A study of the electrostatic potentials and average local ionization energies of the V-VII hydrides of the first three rows of the periodic table and their anions demonstrates the

  5. 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

  6. 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.

  7. Development of an optimized intermolecular potential for sulfur dioxide.

    PubMed

    Ketko, MaryBeth H; Kamath, Ganesh; Potoff, Jeffrey J

    2011-05-01

    A new force field for sulfur dioxide, capable of predicting accurately the vapor-liquid equilibria, critical properties, vapor pressure, and heats of vaporization is presented. The new force field reproduces the saturated liquid densities, vapor pressures and heats of vaporization to within 0.5, 2, and 2% of experiment, respectively. The predicted critical properties and the normal boiling point are in excellent agreement with experimental results. Pair distribution functions are calculated for the S-S, S-O, and O-O interactions are in close agreement with neutron and X-ray scattering experiments. In addition to the new force field, similar calculations are performed for four SO(2) intermolecular potentials proposed by Sokolic et al. (Sokolic, F.; Guissani, Y. and Guillot, B. J. Phys. Chem. 1985, 89, 3023], which show that these models work reasonably well near the state point where they were originally parametrized, but large errors in the predicted coexistence properties are displayed at higher and lower temperatures. Comparison of the radial distribution functions show the local structure is only weakly affected by the different force field parameters. PMID:21476503

  8. Intermolecular interactions of reduced nicotinamide adenine dinucleotide (NADH) in solution

    NASA Astrophysics Data System (ADS)

    Jasensky, Joshua; Junaid Farooqi, M.; Urayama, Paul

    2008-10-01

    Nicotinamide adenine dinucleotide (NAD^+/NADH) is a coenzyme involved in cellular respiration as an electron transporter. In aqueous solution, the molecule exhibits a folding transition characterized by the stacking of its aromatic moieties. A transition to an unfolded conformation is possible using chemical denaturants like methanol. Because the reduced NADH form is fluorescent, the folding transition can be monitored using fluorescence spectroscopy, e.g., via a blue-shift in the UV-excited emission peak upon methanol unfolding. Here we present evidence of interactions between NADH molecules in solution. We measure the excited-state emission from NADH at various concentrations (1-100 μM in MOPS buffer, pH 7.5; 337-nm wavelength excitation). Unlike for the folded form, the emission peak wavelength of the unfolded form is concentration dependent, exhibiting a red-shift with higher NADH concentration, suggesting the presence of intermolecular interactions. An understanding of NADH spectra in solution would assist in interpreting intercellular NADH measurements used for the in vivo monitoring cellular energy metabolism.

  9. Combined Electrostatics and Hydrogen Bonding Determine PIP2 Intermolecular Interactions

    PubMed Central

    Levental, Ilya; Cebers, Andrejs; Janmey, Paul A.

    2010-01-01

    Membrane lipids are active contributors to cell function as key mediators in signaling pathways of inflammation, apoptosis, migration, and proliferation. Recent work on multimolecular lipid structures suggests a critical role for lipid organization in regulating the function of both lipids and proteins. Of particular interest in this context are the polyphosphoinositides (PPI’s), specifically phosphatidylinositol (4,5) bisphosphate (PIP2). The cellular functions of PIP2 are numerous but the factors controlling targeting of PIP2 to specific proteins and organization of PIP2 in the inner leaflet of the plasma membrane remain poorly understood. To analyze the organization of PIP2 in a simplified planar system, we used Langmuir monolayers to study the effects of subphase conditions on monolayers of purified naturally derived PIP2 and other anionic or zwitterionic phospholipids. We report a significant molecular area expanding effect of subphase monovalent salts on PIP2 at biologically relevant surface densities. This effect is shown to be specific to PIP2 and independent of subphase pH. Chaotropic agents (e.g. salts, trehalose, urea, temperature) that disrupt water structure and the ability of water to mediate intermolecular hydrogen bonding also specifically expanded PIP2 monolayers. These results suggest a combination of water-mediated hydrogen bonding and headgroup charge in determining the organization of PIP2, and may provide an explanation for the unique functionality of PIP2 compared to other anionic phospholipids. PMID:18572937

  10. 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

  11. 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.

  12. 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).

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

    PubMed

    Lynch, Michael; Hagner, Kyle

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

  15. Evolutionary meandering of intermolecular interactions along the drift barrier

    PubMed Central

    Lynch, Michael; Hagner, Kyle

    2015-01-01

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

  16. Structurally dependent thermochromism of two iodoargentate hybrids based on the intermolecular charge transfer

    NASA Astrophysics Data System (ADS)

    Zhang, Caifeng; Shen, Junju; Guan, Qi; Yu, Tanlai; Fu, Yunlong

    2015-08-01

    Two iodoargentates directed by N-alkylated 3-cyanopyridiniums, [(EC) (Ag2I3)]n (1) and [(PC) (Ag5I6)]n (2) (EC = N-ethyl-3-cyanopyridinium, PC = N-propyl-3-cyanopyridinium) have been solvothermally synthesized. Structural analysis reveals that the variation of N-substituents on 3-cyanopyridinium is responsible for change of the inorganic moieties (belt-like chain for 1 and columnar chain for 2) and consequent packing modes, which further results in the shift of absorption edges and different thermochromic behavior (from yellow at room temperature to almost colorless for 1 and pale yellow for 2 at liquid nitrogen temperature), as proved by UV-vis spectra.

  17. Theoretical study of intermolecular interactions in CB4H8-HOX (X=F, Cl, Br, I) complexes.

    PubMed

    Derikvand, Zohreh; Zabardasti, Abedien; Azadbakht, Azadeh

    2015-11-01

    The molecular aggregation based on intermolecular interactions between CB4H8 and HOX (X=F, Cl, Br and I) with particular emphasis on their bonding characteristics have been investigated using second order Moller-Plesset perturbation (MP2) method with aug-cc-pVDZ basis set. Different kinds of interactions including hydrogen bond (HB; H⋯O, XH; H⋯X), dihydrogen bond (DiHB; H⋯H) and non-classical B-B⋯H interactions were found between CB4H8 and HOX molecules. The structures of complexes have been analyzed using AIM and natural bond orbital methodologies. Good correlations have been found between the interaction energies (SE), the second-order perturbation energies E((2)), and the charge transfer qCT in the studied systems. PMID:26103431

  18. The fragment spin difference scheme for triplet-triplet energy transfer coupling

    NASA Astrophysics Data System (ADS)

    You, Zhi-Qiang; Hsu, Chao-Ping

    2010-08-01

    To calculate the electronic couplings in both inter- and intramolecular triplet energy transfer (TET), we have developed the "fragment spin difference" (FSD) scheme. The FSD was a generalization from the "fragment charge difference" (FCD) method of Voityuk et al. [J. Chem. Phys. 117, 5607 (2002)] for electron transfer (ET) coupling. In FSD, the spin population difference was used in place of the charge difference in FCD. FSD is derived from the eigenstate energies and populations, and therefore the FSD couplings contain all contributions in the Hamiltonian as well as the potential overlap effect. In the present work, two series of molecules, all-trans-polyene oligomers and polycyclic aromatic hydrocarbons, were tested for intermolecular TET study. The TET coupling results are largely similar to those from the previously developed direct coupling scheme, with FSD being easier and more flexible in use. On the other hand, the Dexter's exchange integral value, a quantity that is often used as an approximate for the TET coupling, varies in a large range as compared to the corresponding TET coupling. To test the FSD for intramolecular TET, we have calculated the TET couplings between zinc(II)-porphyrin and free-base porphyrin separated by different numbers of p-phenyleneethynylene bridge units. Our estimated rate constants are consistent with experimentally measured TET rates. The FSD method can be used for both intermolecular and intramolecular TET, regardless of their symmetry. This general applicability is an improvement over most existing methodologies.

  19. A combined experimental and quantum chemical studies on molecular structure, spectral properties, intra and intermolecular interactions and first hyperpolarizability of 4-(benzyloxy)benzaldehyde thiosemicarbazone and its dimer

    NASA Astrophysics Data System (ADS)

    Kumar, Amit; Rawat, Poonam; Baboo, Vikas; Verma, Divya; Singh, R. N.; Saxena, Deepti; Gauniyal, H. M.; Pandey, Anoop Kumar; Pal, Harish

    2013-02-01

    In the present work, a detailed spectroscopic analysis of 4-(benzyloxy)benzaldehyde thiosemicarbazone (3) has been carried out using 1H NMR, 13C NMR, UV-Visible and FT-IR spectroscopic techniques. The quantum chemical calculations have been carried out using DFT level of theory, B3LYP functional and 6-31G(d,p) basis set. The calculated thermodynamic parameters show that the formation of 3 is an exothermic and spontaneous reaction at 25 °C. The vibrational analysis indicates the formation of dimer in the solid state by intermolecular hydrogen bonding (Nsbnd H⋯Sdbnd C) and the binding energy of dimer is calculated to be 11.2 kcal/mol, using DFT calculation. NBO analysis is carried out to investigate the charge transfer in various intra and intermolecular interactions involved in dimer. Topological parameters at bond critical points (BCPs) are calculated to analyze the strength and nature of various intra and intermolecular interactions in dimer by Bader's 'Atoms in molecules' AIM theory in detail. The local reactivity descriptors such as Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (ωk+, ωk-) analysis are performed to determine the reactive sites within molecule. Non linear optical (NLO) behavior of title compound is investigated by the computed value of first hyperpolarizability (β0).

  20. Non-covalent intermolecular carbon-carbon interactions in polyynes.

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-10-28

    Polyynes, the smaller analogues of one dimensional infinite chain carbon allotrope carbyne, have been studied for the type and strength of the intermolecular interactions in their dimer and tetramer complexes using density functional theory. The nature of end group functionalities and the chain length of the polyynes are varied to assess their role in modulating the non-covalent interaction energy. As seen in molecular electrostatic potential analysis, all the polyyne complexes showed a multitude of non-covalent CC interactions, resulting from complementary electrostatic interactions between relatively electron rich formal triple bond region of one monomer and the electron deficient formal single bond region of the other monomer. This type of paired (C[triple bond, length as m-dash]C)(C-C) bonding interaction, also characterized using quantum theory of atoms-in-molecules, increases with increase in the monomer chain length leading to substantial increase in interaction energy (Eint); -1.07 kcal mol(-1) for the acetylene dimer to -45.83 kcal mol(-1) for the 50yne dimer. The magnitude of Eint increases with substitutions at end positions of the polyyne and this effect persists even up to 50 triple bonds, the largest chain length analyzed in this paper. The role of CC interactions in stabilizing the polyyne dimers is also shown by sliding one monomer in a dimer over the other, which resulted in multiple minima with a reduced number of CC interactions and lower values of Eint. Furthermore, strong cooperativity in the CC bond strength in tetramers is observed as the interaction energy per monomer (Em) of the polyyne is 2.5-2.8 times higher compared to that of the dimer in a test set of four tetramers. The huge gain in energy observed in large polyyene dimers and tetramers predicts the formation of polyyne bundles which may find use in the design of new functional molecular materials. PMID:26412713

  1. An Operon of Three Transcriptional Regulators Controls Horizontal Gene Transfer of the Integrative and Conjugative Element ICEclc in Pseudomonas knackmussii B13

    PubMed Central

    Pradervand, Nicolas; Sulser, Sandra; Delavat, François; Miyazaki, Ryo; Lamas, Iker; van der Meer, Jan Roelof

    2014-01-01

    The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria. PMID:24945944

  2. 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)....

  3. The intermolecular vibrational dynamics of substituted benzene and cyclohexane liquids, studied by femtosecond OHD-RIKES

    SciTech Connect

    Castner, E.W. Jr.; Chang, Yong Joon

    1995-06-01

    By using the femtosecond optical-heterodyne detected, Raman-induced Kerr effect spectroscopy (OHD-RIKES), we have studied the intermolecular dynamics of toluene, benzyl alcohol, benzonitrile, cyclohexane, and methylcyclohexane in both the time and frequency domains.

  4. 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)

  5. The Raman and vibronic activity of intermolecular vibrations in aromatic-containing complexes and clusters

    SciTech Connect

    Maxton, P.M.; Schaeffer, M.W.; Ohline, S.M.; Kim, W.; Venturo, V.A.; Felker, P.M. )

    1994-11-15

    Theoretical and experimental results pertaining to the excitation of intermolecular vibrations in the Raman and vibronic spectra of aromatic-containing, weakly bound complexes and clusters are reported. The theoretical analysis of intermolecular Raman activity is based on the assumption that the polarizability tensor of a weakly bound species is given by the sum of the polarizability tensors of its constituent monomers. The analysis shows that the van der Waals bending fundamentals in aromatic--rare gas complexes may be expected to be strongly Raman active. More generally, it predicts strong Raman activity for intermolecular vibrations that involve the libration or internal rotation of monomer moieties having appreciable permanent polarizability anisotropies. The vibronic activity of intermolecular vibrations in aromatic-rare gas complexes is analyzed under the assumption that every vibronic band gains its strength from an aromatic-localized transition. It is found that intermolecular vibrational excitations can accompany aromatic-localized vibronic excitations by the usual Franck--Condon mechanism or by a mechanism dependent on the librational amplitude of the aromatic moiety during the course of the pertinent intermolecular vibration. The latter mechanism can impart appreciable intensity to bands that are forbidden by rigid-molecule symmetry selection rules. The applicability of such rules is therefore called into question. Finally, experimental spectra of intermolecular transitions, obtained by mass-selective, ionization-detected stimulated Raman spectroscopies, are reported for benzene--X (X=Ar, --Ar[sub 2], N[sub 2], HCl, CO[sub 2], and --fluorene), fluorobenzene--Ar and --Kr, aniline--Ar, and fluorene--Ar and --Ar[sub 2]. The results support the conclusions of the theoretical analyses and provide further evidence for the value of Raman methods in characterizing intermolecular vibrational level structures.

  6. A supramolecular photoswitch constructed by intermolecular hydrogen bond between BTEPy and TTF COOH

    NASA Astrophysics Data System (ADS)

    Feng, Yanli; Zhang, Qiong; Tan, Wenjuan; Zhang, Deqing; Tu, Yaoquan; Ågren, Hans; Tian, He

    2008-04-01

    A novel supramolecular photoswitch containing bisthienylethene-pyridine (BTEPy) and carboxyl attached tetrathiafluvalene (TTF-COOH) was constructed via intermolecular hydrogen bond. FT-IR spectra, XPS characterizations, 1H NMR and theoretical calculation were carried out to verify the formation of the intermolecular hydrogen bond. The supramolecular self-assemblies BTEPy · 2TTF show good photochromic properties. A molecular switch with UV/vis light as inputs and electrochemical signals as outputs was obtained.

  7. Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated.

    PubMed

    Ivanov, Sergei D; Grant, Ian M; Marx, Dominik

    2015-09-28

    With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure. PMID:26429008

  8. Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated

    SciTech Connect

    Ivanov, Sergei D. Grant, Ian M.; Marx, Dominik

    2015-09-28

    With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

  9. Quantum free energy landscapes from ab initio path integral metadynamics: Double proton transfer in the formic acid dimer is concerted but not correlated

    NASA Astrophysics Data System (ADS)

    Ivanov, Sergei D.; Grant, Ian M.; Marx, Dominik

    2015-09-01

    With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently and thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.

  10. Molecular dynamics study of solubilization of immiscible solutes by a micelle: Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method.

    PubMed

    Fujimoto, K; Yoshii, N; Okazaki, S

    2010-08-21

    Free energy of transfer, DeltaG(w-->m), from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated DeltaG(w-->m)'s are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol(-1) per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively. PMID:20726656

  11. Molecular dynamics study of solubilization of immiscible solutes by a micelle: Free energy of transfer of alkanes from water to the micelle core by thermodynamic integration method

    NASA Astrophysics Data System (ADS)

    Fujimoto, K.; Yoshii, N.; Okazaki, S.

    2010-08-01

    Free energy of transfer, ΔGw→m, from water phase to a sodium dodecyl sulfate (SDS) micelle core has been calculated for a series of hydrophobic solutes originally immiscible with water by thermodynamic integration method combined with molecular dynamics calculations. The calculated free energy of transfer is in good correspondence to the experiment as well as the theoretical free energy of transfer. The calculated ΔGw→m's are all negative, implying that the alkane molecules are more stable in the micelle than in the water phase. It decreases almost linearly as a function of the number of carbon atoms of the alkanes longer than methane with a decrement of 3.3 kJ mol-1 per one methylene group. The calculated free energy of transfer indicates that, for example, at the micelle concentration of 50 CMC (critical micelle concentration), about only 1 of 6 micelles or 1 of 32 000 micelles does not contain a solute methane or n-octane molecule, respectively.

  12. Intermolecular interactions and electrostatic properties of the β-hydroquinone apohost: implications for supramolecular chemistry.

    PubMed

    Clausen, Henrik F; Chen, Yu-Sheng; Jayatilaka, Dylan; Overgaard, Jacob; Koutsantonis, George A; Spackman, Mark A; Iversen, Bo B

    2011-11-17

    The crystal structure of the β-polymorph of hydroquinone (β-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/Å(2) (0.27 V/Å) 1 Å along the 3-fold axis and 0.0105 e/Å(2) (0.15 V/Å) 1 Å along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule. PMID:21809888

  13. Intermolecular Interactions and Electrostatic Properties of the [beta]-Hydroquinone Apohost: Implications for Supramolecular Chemistry

    SciTech Connect

    Clausen, Henrik F.; Chen, Yu-Sheng; Jayatilaka, Dylan; Overgaard, Jacob; Koutsantonis, George A.; Spackman, Mark A.; Iversen, Bo B.

    2012-02-07

    The crystal structure of the {beta}-polymorph of hydroquinone ({beta}-HQ), the apohost of a large family of clathrates, is reported with a specific focus on intermolecular interactions and the electrostatic nature of its cavity. Hirshfeld surface analysis reveals subtle close contacts between two interconnecting HQ networks, and the local packing and related close contacts were examined by breakdown of the fingerprint plot. An experimental multipole model containing anisotropic thermal parameters for hydrogen atoms has been successfully refined against 15(2) K single microcrystal synchrotron X-ray diffraction data. The experimental electron density model has been compared with a theoretical electron density calculated with the molecule embedded in its own crystal field. Hirshfeld charges, interaction energies and the electrostatic potential calculated for both models are qualitatively in good agreement, but small differences in the electrostatic potential persist due to charge transfer from all hydrogen atoms to the oxygen atoms in the theoretical model. The electrostatic potential in the center of the cavity is positive, very shallow and highly symmetric, suggesting that the inclusion of polar molecules in the void will involve a balance between opposing effects. The electric field is by symmetry zero in the center of the cavity, increasing to a value of 0.0185 e/{angstrom}{sup 2} (0.27 V/{angstrom}) 1 {angstrom} along the 3-fold axis and 0.0105 e/{angstrom}{sup 2} (0.15 V/{angstrom}) 1 {angstrom} along the perpendicular direction. While these values are substantial in a macroscopic context, they are quite small for a molecular cavity and are not expected to strongly polarize a guest molecule.

  14. The relationship between inadvertent ingestion and dermal exposure pathways: a new integrated conceptual model and a database of dermal and oral transfer efficiencies.

    PubMed

    Gorman Ng, Melanie; Semple, Sean; Cherrie, John W; Christopher, Yvette; Northage, Christine; Tielemans, Erik; Veroughstraete, Violaine; Van Tongeren, Martie

    2012-11-01

    Occupational inadvertent ingestion exposure is ingestion exposure due to contact between the mouth and contaminated hands or objects. Although individuals are typically oblivious to their exposure by this route, it is a potentially significant source of occupational exposure for some substances. Due to the continual flux of saliva through the oral cavity and the non-specificity of biological monitoring to routes of exposure, direct measurement of exposure by the inadvertent ingestion route is challenging; predictive models may be required to assess exposure. The work described in this manuscript has been carried out as part of a project to develop a predictive model for estimating inadvertent ingestion exposure in the workplace. As inadvertent ingestion exposure mainly arises from hand-to-mouth contact, it is closely linked to dermal exposure. We present a new integrated conceptual model for dermal and inadvertent ingestion exposure that should help to increase our understanding of ingestion exposure and our ability to simultaneously estimate exposure by the dermal and ingestion routes. The conceptual model consists of eight compartments (source, air, surface contaminant layer, outer clothing contaminant layer, inner clothing contaminant layer, hands and arms layer, perioral layer, and oral cavity) and nine mass transport processes (emission, deposition, resuspension or evaporation, transfer, removal, redistribution, decontamination, penetration and/or permeation, and swallowing) that describe event-based movement of substances between compartments (e.g. emission, deposition, etc.). This conceptual model is intended to guide the development of predictive exposure models that estimate exposure from both the dermal and the inadvertent ingestion pathways. For exposure by these pathways the efficiency of transfer of materials between compartments (for example from surfaces to hands, or from hands to the mouth) are important determinants of exposure. A database of

  15. The role of entropy and polarity in intermolecular contacts in protein crystals

    SciTech Connect

    Cieślik, Marcin; Derewenda, Zygmunt S.

    2009-05-01

    Logistic regression was used to study the amino-acid composition and structure of crystal contacts in monomeric proteins. Crystal contacts are generally depleted of large flexible amino acids and enriched in small and hydrophobic residues such as Gly and Leu; additionally, larger contacts have cores depleted of polar residues. The integrity and X-ray diffraction quality of protein crystals depend on the three-dimensional order of relatively weak but reproducible intermolecular contacts. Despite their importance, relatively little attention has been paid to the chemical and physical nature of these contacts, which are often regarded as stochastic and thus not different from randomly selected protein surface patches. Here, logistic regression was used to analyze crystal contacts in a database of 821 unambiguously monomeric proteins with structures determined to 2.5 Å resolution or better. It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces, which are typically small and hydrophobic, have been underestimated with respect to their contact-forming potential by earlier area-based calculations. For any given solvent-exposed surface, small and hydrophobic residues are more likely to be involved in crystal contacts than large and charged amino acids. Side-chain entropy is the single physicochemical property that is most negatively correlated with the involvement of amino acids in crystal contacts. It is also shown that crystal contacts with larger buried surfaces containing eight or more amino acids have cores that are depleted of polar amino acids.

  16. The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICEclc Controls both a Putative Efflux System and Initiation of ICE Transfer

    PubMed Central

    Pradervand, Nicolas; Delavat, François; Sulser, Sandra; Miyazaki, Ryo

    2014-01-01

    Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR. PMID:25182498

  17. Comment on 'Intermolecular interaction potentials of the methane dimer from the local density approximation'

    SciTech Connect

    Li, Arvin H.-T.; Chao, S.D.

    2006-01-15

    To verify the recently calculated intermolecular interaction potentials of the methane dimer within the density functional theory using the (Perdew) local density approximation (LDA) [Chen et al., Phys. Rev. A 69, 034701 (2004)], we have performed a parallel series of calculations using the LDA/6-311++G (3df, 3pd) level of theory with selected exchange functionals (B, G96, MPW, O, PBE, PW91, S, and XA). None of the above calculated intermolecular interaction potentials from the local density approximation reproduce the results reported in the commented paper. In addition, we point out the inappropriateness of using the Lennard-Jones function to model the long-range parts of the calculated intermolecular interaction potentials, as suggested positively by Chen et al.

  18. Integrating Communication into Engineering Curricula: An Interdisciplinary Approach to Facilitating Transfer at New Mexico Institute of Mining and Technology

    ERIC Educational Resources Information Center

    Ford, Julie Dyke

    2012-01-01

    This program profile describes a new approach towards integrating communication within Mechanical Engineering curricula. The author, who holds a joint appointment between Technical Communication and Mechanical Engineering at New Mexico Institute of Mining and Technology, has been collaborating with Mechanical Engineering colleagues to establish a…

  19. Integrating Metacognition into a Developmental Reading and Writing Course to Promote Skill Transfer: An Examination of Student Perceptions and Experiences

    ERIC Educational Resources Information Center

    Pacello, James

    2014-01-01

    This qualitative research study was aimed at examining the experiences and perceptions of students at a four-year college in New York City who were enrolled in an integrated reading and writing course designed to help students connect the literacy skills learned in the course to other contexts. Focusing on three students enrolled in the course,…

  20. Intermolecular potential functions and high resolution molecular spectroscopy of weakly bound complexes. Final progress report

    SciTech Connect

    Muenter, J.S.

    1997-04-01

    This report describes accomplishments over the past year in research supported by this grant. Two papers published in this period are briefly discussed. The general goal of the work is to consolidate the understanding of experimental results through a theoretical model of intermolecular potential energy surfaces. Progress in the experimental and theoretical phases of the program are presented and immediate goals outlined. The ability to construct analytic intermolecular potential functions that accurately predict the energy of interaction between small molecules will have great impact in many areas of chemistry, biochemistry, and biology.

  1. 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.

  2. Enantioselective intermolecular cross Rauhut-Currier reactions of activated alkenes with acrolein.

    PubMed

    Zhou, Wei; Chen, Peng; Tao, Mengna; Su, Xiao; Zhao, Qingjie; Zhang, Junliang

    2016-06-18

    The enantioselective intermolecular cross Rauhut-Currier reaction of acrolein with active olefins has been a long-standing challenge because of the competitive MBH reaction and polymerization. Herein a highly enantioselective intermolecular cross Rauhut-Currier reaction of acrolein with 3-acyl acrylates and 2-ene-1,4-diones, which is enabled by newly designed Peng-Phos catalysts. This method is scalable and highly enantioselective (up to 96% ee). Several transformations of the R-C products are carried out to showcase the synthetic utility. PMID:27225510

  3. 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.

  4. Modulation of the intermolecular interaction of myoglobin by removal of the heme

    PubMed Central

    Imamura, Hiroshi; Morita, Takeshi; Sumi, Tomonari; Isogai, Yasuhiro; Kato, Minoru; Nishikawa, Keiko

    2013-01-01

    Toward understanding intermolecular interactions governing self-association of proteins, the present study investigated a model protein, myoglobin, using a small-angle X-ray scattering technique. It has been known that removal of the heme makes myoglobin aggregation-prone. The interparticle interferences of the holomyoglobin and the apomyoglobin were compared in terms of the structure factor. Analysis of the structure factor using a model potential of Derjaguin–Laudau–Verwey–Overbeek (DLVO) suggests that the intermolecular interaction potential of apomyoglobin is more attractive than that of holomyoglobin at short range from the protein molecule. PMID:24121340

  5. Photoinduced electron transfer in binary blends of conjugated polymers

    SciTech Connect

    Jenekhe, A.A.; Paor, L.R. de; Chen, X.L.; Tarkka, R.M.

    1996-10-01

    The authors report observations concerning the intermolecular photoinduced electron transfer through blends of n-type/p-type {pi}-conjugated organic polymers. The results of transient absorption spectroscopy, fluorescence quenching analysis, and delocalized radical ion pair generation studies imply that these materials are supramolecular materials.

  6. Multifunctional Charge-Transfer Single Crystals through Supramolecular Assembly.

    PubMed

    Xu, Beibei; Luo, Zhipu; Wilson, Andrew J; Chen, Ke; Gao, Wenxiu; Yuan, Guoliang; Chopra, Harsh Deep; Chen, Xing; Willets, Katherine A; Dauter, Zbigniew; Ren, Shenqiang

    2016-07-01

    Centimeter-sized segregated stacking TTF-C60 single crystals are crystallized by a mass-transport approach combined with solvent-vapor evaporation for the first time. The intermolecular charge-transfer interaction in the long-range ordered superstructure enables the crystals to demonstrate external stimuli-controlled multifunctionalities and angle/electrical-potential-dependent luminescence. PMID:27146726

  7. A study on the integration of contactless energy transfer in the end teeth of a PM synchronous linear motor

    NASA Astrophysics Data System (ADS)

    Krop, D. C. J.; Lomonova, E. A.; Jansen, J. W.; Paulides, J. J. H.

    2009-04-01

    Linear motors find their utilization in an increasing number of industrial applications. Permanent magnet linear synchronous motors (PMLSMs) are favorable in many applications due to their servo characteristics, robustness, and high force density. The major disadvantage of moving coil type PMLSMs is the cable slab that energizes the coils from the fixed world to the moving parts of the machine. These cable slabs introduce extra wear and dynamical distortions. Moreover, in precision application the cable slab is supported by additional linear drives. These disadvantages can be eliminated if the coils could be powered wirelessly. In this paper two topologies are proposed that are capable of transferring 1 kW of power at most. The transformer part of the CET is characterized by means of two dimensional finite element analysis, and the influence of using additional capacitors to boost the output power is examined. Furthermore, an analysis of the core losses is conducted. Conclusions are drawn from the results.

  8. 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.

  9. Intermolecular hydroamination of vinylarenes by iminoanilide alkaline-earth catalysts: a computational scrutiny of mechanistic pathways.

    PubMed

    Tobisch, Sven

    2014-07-14

    A thorough computational exploration of the mechanistic intricacies of the intermolecular hydroamination (HA) of vinylarenes by a recently reported class of kinetically stabilised iminoanilide [{N^N}Ae{N(SiMe3)2}⋅(THF)n] alkaline-earth amido compounds (Ae = Ca, Sr, Ba) is presented. Two distinct mechanistic pathways for catalytic HA mediated by alkaline-earth and rare-earth compounds have emerged over the years that account equally well for the specific features of the process. On one hand, a concerted proton-assisted pathway to deliver the amine product in a single step can be invoked and, on the other, a stepwise σ-insertive pathway that comprises a rapid, reversible migratory olefin insertion step linked to a less facile, irreversible Ae-C alkyl bond aminolysis. The results of the study presented herein, which employed a heavily benchmarked and reliable DFT methodology, supports a stepwise σ-insertive pathway that involves fast and reversible migratory C=C bond insertion into the polar Ae-N pyrrolido σ bond. This proceeds with strict 2,1 regioselectivity via a highly polarised four-centre transition state (TS) structure, linked to irreversible intramolecular Ae-C bond aminolysis of the alkaline-earth alkyl intermediate as the energetically favourable mechanism. Turnover-limiting aminolysis is consistent with the significant KIE measured; the DFT-derived effective barrier matches the Eyring parameter empirically determined for the best-performing {N^N}Ba(NR2) catalyst gratifyingly well. It also predicts the observed trend in reactivity (Catransfer at the C=C linkage via a multi-centre TS structure. A detailed comparison of {N^N}Ae(NR2) catalysts revealed that the variation in

  10. Addressable test matrix for measuring analog transfer characteristics of test elements used for integrated process control and device evaluation

    NASA Technical Reports Server (NTRS)

    Buehler, Martin G. (Inventor)

    1988-01-01

    A set of addressable test structures, each of which uses addressing schemes to access individual elements of the structure in a matrix, is used to test the quality of a wafer before integrated circuits produced thereon are diced, packaged and subjected to final testing. The electrical characteristic of each element is checked and compared to the electrical characteristic of all other like elements in the matrix. The effectiveness of the addressable test matrix is in readily analyzing the electrical characteristics of the test elements and in providing diagnostic information.

  11. 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…

  12. Palladium-Catalyzed Intermolecular Aerobic Annulation of o-Alkenylanilines and Alkynes for Quinoline Synthesis.

    PubMed

    Zheng, Jia; Li, Zun; Huang, Liangbin; Wu, Wanqing; Li, Jianxiao; Jiang, Huanfeng

    2016-08-01

    A new approach to construct 2,3-disubstituted quinolines is described via Pd-catalyzed oxidative cyclization of o-vinylanilines and alkynes with molecular oxygen. This transformation is supposed to undergo intermolecular amination of alkyne, insertion of the olefin, and oxidative cleavage of C-C bond sequence. PMID:27418021

  13. Palladium(0)-Catalyzed Intermolecular Allylic Dearomatization of Indoles by a Formal [4+2] Cycloaddition Reaction.

    PubMed

    Gao, Run-Duo; Xu, Qing-Long; Zhang, Bo; Gu, Yiting; Dai, Li-Xin; You, Shu-Li

    2016-08-01

    Bridged indoline derivatives were synthesized by an intermolecular Pd-catalyzed allylic dearomatization reaction of substituted indoles. The reaction between indoles and allyl carbonates bearing a nucleophilic alcohol side-chain proceeds in a cascade fashion, providing bridged indolines in excellent enantioselectivity. PMID:27321285

  14. Copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides.

    PubMed

    Chen, Long; Xing, Haotian; Zhang, Huaibin; Jiang, Zhong-Xing; Yang, Zhigang

    2016-08-21

    A highly practical copper-catalyzed intermolecular chloroazidation of α,β-unsaturated amides has been described, giving a series of azidochlorides in good-to-excellent yields. The stable azidoiodine(iii) reagent and SOCl2 were used as azide and chlorine sources, respectively. The synthetic applications of this protocol were also explored by a variety of synthetically useful transformations. PMID:27462802

  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. PMID:26393532

  16. 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

  17. Rhodium(i)-catalysed intermolecular alkyne insertion into (2-pyridylmethylene)cyclobutenes.

    PubMed

    Matsuda, Takanori; Matsumoto, Takeshi

    2016-06-14

    Cyclobutenes with 2-pyridylmethylene groups at the 3 position underwent an intermolecular alkyne insertion reaction in the presence of a rhodium(i) catalyst at 170 °C to afford substituted benzenes. Among the different 2-pyridylmethylene groups examined, 3-methyl-2-pyridyl derivatives showed superior activity and readily coupled with various alkynes, including sterically demanding, heteroaromatic and terminal alkynes. PMID:27193826

  18. 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.

  19. Intermolecular forces and nonbonded interactions: Superoperator nonlinear time-dependent density-functional-theory response approach

    SciTech Connect

    Harbola, Upendra; Mukamel, Shaul

    2004-11-01

    Electrostatic and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge-density response functions of the isolated molecules, which in turn are expanded using the collective electronic oscillator (CEO) eigenmodes of linearized time-dependent density-functional theory. Closed expressions for the intermolecular energy are derived to sixth order in charge fluctuation amplitudes.

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

    PubMed

    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

  1. 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…

  2. 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…

  3. Intermolecular Cyclopropanation of Styrenes Using Iodine and Visible Light via Carbon-Iodine Bond Cleavage.

    PubMed

    Usami, Kaoru; Nagasawa, Yoshitomo; Yamaguchi, Eiji; Tada, Norihiro; Itoh, Akichika

    2016-01-01

    The intermolecular cyclopropanation of aromatic olefins with activated methylene compounds using iodine and visible light irradiation was described. This reaction proceeds under rare-metal-free conditions. Styrenes with various substituted groups (alkyl and electron-withdrawing groups) provided corresponding cyclopropanes in moderate to good yields. PMID:26654114

  4. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-01

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  5. THE INTERACTION OF PARAMAGNETIC RELAXATION REAGENTS WITH INTRA- AND INTERMOLECULAR HYDROGEN BONDED PHENOLS

    EPA Science Inventory

    Intermolecular electron-nuclear 13-C relaxation times (T(1)sup e's) from solutions containing the paramagnetic relaxation reagent (PARR), Cr(acac)3, used in conjunction with 13-C T(1)'s in diamagnetic solutions (intramolecular 13-C - (1)H dipolar T(1)'s) provide a significant inc...

  6. Instantaneous normal mode analysis for intermolecular and intramolecular vibrations of water from atomic point of view

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming

    2013-11-28

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given.

  7. Distance dependence of electron transfer from liposome-embedded (alkanephosphocholine-porphinato) zinc

    SciTech Connect

    Tsuchida, E.; Kaneko, M.; Nishide, H.; Hoshino, M.

    1986-05-22

    (Alkanephosphocholine-porphinato)zinc forms a geometrically well-defined bilayer liposome with phospholipid. Electron transfer from the liposome-embedded (porphinato)zincs with different alkyl chain lengths to methylviologen present in the outer bulk solution is measured by laser flash photolysis: the intermolecular electron transfer was observed only when the porphyrin plane is located within 12 A from the surface.

  8. 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.

  9. The role of charge-transfer integral in determining and engineering the carrier mobilities of 9,10-di(2-naphthyl)anthracene compounds

    NASA Astrophysics Data System (ADS)

    Tse, S. C.; So, S. K.; Yeung, M. Y.; Lo, C. F.; Wen, S. W.; Chen, C. H.

    2006-05-01

    The charge transporting properties of t-butylated 9,10-di(2-naphthyl)anthracene (ADN) compounds have been investigated experimentally and computationally in relation to their molecular structures. The ADN compounds are found to be ambipolar with both electron and hole mobilities in the range of 1-4 × 10 -7 cm 2 V -1 s -1 (electric field 0.5-0.8 MV/cm). As the degree of t-butylation increases, the carrier mobility decreases progressively. The mobility reduction was examined by Marcus theory of reorganization energies. All ADN compounds possess similar reorganization energies of ˜0.3 eV. The reduction of carrier mobilities with increasing t-butylation can be attributed to a decrease in the charge-transfer integral or the wavefunction overlap.

  10. A reduced-order integral formulation to account for the finite size effect of isotropic square panels using the transfer matrix method.

    PubMed

    Bonfiglio, Paolo; Pompoli, Francesco; Lionti, Riccardo

    2016-04-01

    The transfer matrix method is a well-established prediction tool for the simulation of sound transmission loss and the sound absorption coefficient of flat multilayer systems. Much research has been dedicated to enhancing the accuracy of the method by introducing a finite size effect of the structure to be simulated. The aim of this paper is to present a reduced-order integral formulation to predict radiation efficiency and radiation impedance for a panel with equal lateral dimensions. The results are presented and discussed for different materials in terms of radiation efficiency, sound transmission loss, and the sound absorption coefficient. Finally, the application of the proposed methodology for rectangular multilayer systems is also investigated and validated against experimental data. PMID:27106325

  11. Evaluation of the heat transfer module (FAHT) of Failure Analysis Nonlinear Thermal And Structural Integrated Code (FANTASTIC)

    NASA Technical Reports Server (NTRS)

    Keyhani, Majid

    1989-01-01

    The heat transfer module of FANTASTIC Code (FAHT) is studied and evaluated to the extend possible during the ten weeks duration of this project. A brief background of the previous studies is given and the governing equations as modeled in FAHT are discussed. FAHT's capabilities and limitations based on these equations and its coding methodology are explained in detail. It is established that with improper choice of element size and time step FAHT's temperature field prediction at some nodes will be below the initial condition. The source of this unrealistic temperature prediction is identified and a procedure is proposed for avoiding this phenomenon. It is further shown that the proposed procedure will converge to an accurate prediction upon mesh refinement. Unfortunately due to lack of time FAHT's ability to accurately account for pyrolysis and surface ablation has not been verified. Therefore, at the present time it can be stated with confidence that FAHT can accurately predict the temperature field for a transient multi-dimensional, orthotropic material with directional dependence, variable property, with nonlinear boundary condition. Such a prediction will provide an upper limit for the temperature field in an ablating decomposing nozzle liner. The pore pressure field, however, will not be known.

  12. Energy Transfer Involving Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Gibbons, John Paul

    A three-dimensional, Monte Carlo model for the calculation of vibrational energy relaxation and transfer rates for both diatomic-monatomic and diatomic-diatomic systems was developed, analyzed and implemented. Mediation by internal angular momentum was demonstrated to be important in these energy transfer processes. This was named the TLV mechanism for translation to vibration flow through changes in angular momentum. The equations for the component of vibrational energy change due to the TLV mechanism for the two extreme cases of very hard or very soft collisions were derived. Results of using these equations were compared with those obtained by direct integration of the differential equations of motion and in many cases were found to agree. This mechanism was incorporated into the model in order to achieve statistically significant results within reasonable computer running times. When this was done the variance of a result was frequently reduced by a factor of thirty to fifty or more with little or no increase in the computer times required. This made possible a meaningful study of the full three-dimensional diatomic-diatomic collisional processes and also permitted extension of the mono-diatomic model calculations to much lower temperatures than had been previously investigated. After this calculational procedure was developed for Ar - O(,2) collisions, it was also applied to He - O(,2) and to the near resonant vibration energy exchange process:. CO ((nu)=0)+N(,2)((nu)=1)(--->)CO((nu)=1)+N(,2)((nu)=0). These three processes were investigated at several temperatures between room temperature and 4000K. Exponential repulsive intermolecular potentials were used. The values for the coefficients and characteristic lengths for these potentials were obtained from independent sources both experimental and theoretical. In general, the results, when compared to experiment, are very consistent relative to their dependence on the potential parameters. In every case for all

  13. Intermolecular interactions in ternary solutions of some 1,2,4-triazolium ylids studied by spectral means

    NASA Astrophysics Data System (ADS)

    Closca, Valentina; Melniciuc-Puica, Nicoleta; Dorohoi, Dana Ortansa; Benchea, A. C.

    2014-08-01

    Triazolium ylids are dipolar molecules with separated charges in their ground electronic state; the positive charge is located on one Nitrogen atom belonging to the heterocycle and the negative charge is located near the ylid carbanion. The intramolecular charge transfer from the carbanion to heterocycle gives a visible electronic absorption band, very sensitive to the solvent nature. Its position in the wavenumber scale offers information about the intermolecular interactions in which the ylid molecules are engaged. The spectral study revealed the presence of both universal and specific interactions in solutions of 1,2,4-triazolium ylids with protic solvents. By choosing adequate binary solvents, the contribution of the specific interaction of the weak hydrogen bond between the -OH atomic group of the protic solvents and the ylid carbanion can be estimated. Ternary solutions of the studied ylids achieved with Methanol +Benzene, Water + Ethanol and 1,3 Propanediol + Dimethyl formamide binary solvents are analyzed from spectral point of view and the difference between the potential energies in molecular pairs of the types: 1,2,4-triazolium ylid-protic solvent and 1,2,4-triazolium ylid-non protic were estimated on the basis of the statistic cell model of ternary solutions.

  14. Impact of an integrated science and reading intervention (INSCIREAD) on bilingual students' misconceptions, reading comprehension, and transferability of strategies

    NASA Astrophysics Data System (ADS)

    Martinez, Patricia

    This thesis describes a research study that resulted in an instructional model directed at helping fourth grade diverse students improve their science knowledge, their reading comprehension, their awareness of the relationship between science and reading, and their ability to transfer strategies. The focus of the instructional model emerged from the intersection of constructs in science and reading literacy; the model identifies cognitive strategies that can be used in science and reading, and inquiry-based instruction related to the science content read by participants. The intervention is termed INSCIREAD (Instruction in Science and Reading). The GoInquire web-based system (2006) was used to develop students' content knowledge in slow landform change. Seventy-eight students participated in the study. The treatment group comprised 49 students without disabilities and 8 students with disabilities. The control group comprised 21 students without disabilities. The design of the study is a combination of a mixed-methods quasi-experimental design (Study 1), and a single subject design with groups as the unit of analysis (Study 2). The results from the quantitative measures demonstrated that the text recall data analysis from Study 1 yielded near significant statistical levels when comparing the performance of students without disabilities in the treatment group to that of the control group. Visual analyses of the results from the text recall data from Study 2 showed at least minimal change in all groups. The results of the data analysis of the level of the generated questions show there was a statistically significant increase in the scores students without disabilities obtained in the questions they generated from the pre to the posttest. The analyses conducted to detect incongruities, to summarize and rate importance, and to determine the number of propositions on a science and reading concept map data showed a statistically significant difference between students

  15. Accurate ab initio intermolecular potential energy surface for the quintet state of the O2(3Σg-)-O2(3Σg-) dimer

    NASA Astrophysics Data System (ADS)

    Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I.; Campos-Martínez, José; Hernandez-Lamoneda, Ramón

    2008-06-01

    A new potential energy surface (PES) for the quintet state of rigid O2(3Σg-)+O2(3Σg-) has been obtained using restricted coupled-cluster theory with singles, doubles, and perturbative triple excitations [RCCSD(T)]. A large number of relative orientations of the monomers (65) and intermolecular distances (17) have been considered. A spherical harmonic expansion of the interaction potential has been built from the ab initio data. It involves 29 terms, as a consequence of the large anisotropy of the interaction. The spherically averaged term agrees quite well with the one obtained from analysis of total integral cross sections. The absolute minimum of the PES corresponds to the crossed (D2d) structure (X shape) with an intermolecular distance of 6.224 bohrs and a well depth of 16.27 meV. Interestingly, the PES presents another (local) minimum close in energy (15.66 meV) at 6.50 bohrs and within a planar skewed geometry (S shape). We find that the origin of this second structure is due to the orientational dependence of the spin-exchange interactions which break the spin degeneracy and leads to three distinct intermolecular PESs with singlet, triplet, and quintet multiplicities. The lowest vibrational bound states of the O2-O2 dimer have been obtained and it is found that they reflect the above mentioned topological features of the PES: The first allowed bound state for the 16O isotope has an X structure but the next state is just 0.12 meV higher in energy and exhibits an S shape.

  16. Intermolecular carbon-carbon, nitrogen-nitrogen and oxygen-oxygen non-covalent bonding in dipolar molecules.

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-07-28

    Clear evidence for the existence of intermolecular carbon-carbon (C···C), nitrogen-nitrogen (N···N) and oxygen-oxygen (O···O) interactions between atoms in similar chemical environments in homogeneous dimers of organic dipolar molecules has been obtained from molecular orbital (MO), natural bond orbital (NBO) and atoms-in-molecule (AIM) electron density analyses at the M06L/6-311++G(d,p) level of density functional theory (DFT). These X···X type interactions are mainly the result of local polarization effects, causing segregation of electron-rich and electron-deficient regions in the X atoms, leading to complementary electrostatic interactions. NBO analysis provides evidence of charge transfer between the two X atoms. Even in symmetrical molecules such as acetylene, induced dipoles in the dimer create C···C bonding interactions. The strength of this type of interaction increases with increase in the dipole moment of the molecule. Energy decomposition analysis (EDA) shows that the electrostatic component of the interaction energy (Eint) is very high, up to 95.86%. The C···C interactions between similar carbon atoms are located for several crystal structures obtained from the literature. In addition, MO, AIM and electrostatic potential analyses support interactions between similar oxygen (O···O) and nitrogen (N···N) atoms in a variety of molecular dimers. Good prediction of Eint is achieved in terms of the total gain in electron density at non-covalently interacting intermolecular bonds (∑ρ) and the monomer dipole moment (μ). A rigorously tested QSAR equation has been derived to predict Eint for all dimer systems: Eint (kcal mol(-1)) = -138.395∑ρ(au) - 0.551μ (Debye). This equation suggests that the polarization-induced bonding interaction between atoms in a similar chemical environment could well be a general chemical phenomenon. The results have been further validated by different density functional methods and also by G3MP2 method

  17. Integrated test rig for tether hardware, real-time simulator and control algorithms: Robust momentum transfer validated

    NASA Astrophysics Data System (ADS)

    Kruijff, Michiel; van der Heide, Erik Jan

    2001-02-01

    In preparation of the ESA demonstration mission for a tethered sample return capability from ISS, a breadboard test has been performed to validate the robust StarTrack tether dynamics control algorithms in conjunction with the constructed hardware. The proposed mission will use hardware inherited from the YES mission (Kruijff, 1999). A tether spool is holding a 7 kg, 35 km Dyneema tether. A 45 kg re-entry capsule will be ejected by springs and then deployed by gravity gradient. The dynamics are solely controlled by a barberpole type friction brake, similar to the SEDS hardware. This hardware is integrated in a test rig, based on the TMM&M stand, that has been upgraded to accommodate both a Space Part (abruptly applied initial tether deployment speed, fine tensiometer, real-time space tether simulator using the tensiometer measurements as input, take-up roller deploying the tether at a simulator-controlled speed) and a Satellite Part (infra-red beams inside the tether canister, control computer estimating deployed length and required extra braking from the IRED interrupts, `barberpole' friction brake). So the set-up allows for a tether deployment with closed loop control, all governed by a real-time comprehensive tether dynamics simulation. The tether deployment is based on the two-stage StarTrack deployment. This scheme stabilizes the tether at an intermediate vertical stage (with 3 km deployed). When the orbit and landing site have synchronized, a high-speed deployment follows to a large angle. When the fully deployed 35-km tether swings to the vertical at approximately 40 m/s, it is cut at a prefixed time optimized for landing site accuracy. The paper discusses the tests performed to characterize the designed hardware, maturing of the developed algorithms with respect to the hardware noise levels and the difficulties and limitations of the test rig. It is found that the set-up can be applied to a variety of tether pre-mission tests. It is shown that the performed

  18. Rotational Energy Transfer in N2

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.

    1994-01-01

    Using the N2-N2 intermolecular potential of van der Avoird et al. rotational energy transfer cross sections have been calculated using both the coupled state (CS) and infinite order sudden (IOS) approximations. The rotational energy transfer rate constants at 300 K, calculated in the CS approximation, are in reasonable agreement with the measurements of Sitz and Farrow. The IOS approximation qualitatively reproduces the dependence of the rate constants on the rotational quantum numbers, but consistently overestimates their magnitudes. The treatment of exchange symmetry will be discussed.

  19. 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.

  20. Changes of microstructure characteristics and intermolecular interactions of preserved egg white gel during pickling.

    PubMed

    Zhao, Yan; Chen, Zhangyi; Li, Jianke; Xu, Mingsheng; Shao, Yaoyao; Tu, Yonggang

    2016-07-15

    Changes in gel microstructure characteristics and in intermolecular interactions of preserved egg whites during pickling were investigated. Spin-spin relaxation times of preserved egg whites significantly decreased in the first 8 days and remained unchanged after the 16th day. SEM images revealed a three-dimensional gel network, interwoven with a loose linear fibrous mesh structure. The protein gel mesh structure became more regular, smaller, and compacted with pickling time. Free sulfhydryl contents in the egg whites increased significantly, while total sulfhydryl contents dramatically decreased during pickling. The primary intermolecular forces in the preserved egg white gels were ionic and disulfide bonds. Secondary forces included hydrophobic interaction and relatively few hydrogen bonds. During the first 8 days, the proportion of ionic bonds sharply decreased, and that of disulfide bonds increased over the first 24 days. PMID:26948621

  1. Intramolecular and Intermolecular Interactions in Hybrid Organic-Inorganic Alucone Films Grown by Molecular Layer Deposition.

    PubMed

    Park, Yi-Seul; Kim, Hyein; Cho, Boram; Lee, Chaeyun; Choi, Sung-Eun; Sung, Myung Mo; Lee, Jin Seok

    2016-07-13

    Investigation of molecular interactions in polymeric films is crucial for understanding and engineering multiscale physical phenomena correlated to device function and performance, but this often involves a compromise between theoretical and experimental data, because of poor film uniformity. Here, we report the intramolecular and intermolecular interactions inside the ultrathin and conformal hybrid organic-inorganic alucone films grown by molecular layer deposition, based on sequential and self-limiting surface reactions. Varying the carbon chain length of organic precursors, which affects their molecular flexibility, caused intramolecular interactions such as double reactions by bending of the molecular backbone, resulting in formation of hole vacancies in the films. Furthermore, intermolecular interactions in alucone polymeric films are dependent on the thermal kinetics of molecules, leading to binding failures and cross-linking at low and high growth temperatures, respectively. We illustrate these key interactions and identify molecular geometries and potential energies by density functional theory calculations. PMID:27314844

  2. Influence of intermolecular potentials on rarefied gas flows: Fast spectral solutions of the Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Wu, Lei; Liu, Haihu; Zhang, Yonghao; Reese, Jason M.

    2015-08-01

    The Boltzmann equation with an arbitrary intermolecular potential is solved by the fast spectral method. As examples, noble gases described by the Lennard-Jones potential are considered. The accuracy of the method is assessed by comparing both transport coefficients with variational solutions and mass/heat flow rates in Poiseuille/thermal transpiration flows with results from the discrete velocity method. The fast spectral method is then applied to Fourier and Couette flows between two parallel plates, and the influence of the intermolecular potential on various flow properties is investigated. It is found that for gas flows with the same rarefaction parameter, differences in the heat flux in Fourier flow and the shear stress in Couette flow are small. However, differences in other quantities such as density, temperature, and velocity can be very large.

  3. 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.

  4. Study of intermolecular interactions in binary mixtures of ethanol in methanol

    NASA Astrophysics Data System (ADS)

    Maharolkar, Aruna P.; Khirade, P. W.; Murugkar, A. G.

    2016-05-01

    Present paper deals with study of physicochemical properties like viscosity, density and refractive index for the binary mixtures of ethanol and methanol over the entire concentration range were measured at 298.15 K. The experimental data further used to determine the excess properties viz. excess molar volume, excess viscosity, excess molar refraction. The values of excess properties further fitted with Redlich-Kister (R-K Fit) equation to calculate the binary coefficients and standard deviation. The resulting excess parameters are used to indicate the presence of intermolecular interactions and strength of intermolecular interactions between the molecules in the binary mixtures. Excess parameters indicate structure making factor in the mixture predominates in the system.

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

    PubMed Central

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

    2014-01-01

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

  6. 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.

  7. 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.

  8. Metal-free intermolecular formal cycloadditions enable an orthogonal access to nitrogen heterocycles

    PubMed Central

    Xie, Lan-Gui; Niyomchon, Supaporn; Mota, Antonio J.; González, Leticia; Maulide, Nuno

    2016-01-01

    Nitrogen-containing heteroaromatic cores are ubiquitous building blocks in organic chemistry. Herein, we present a family of metal-free intermolecular formal cycloaddition reactions that enable highly selective and orthogonal access to isoquinolines and pyrimidines at will. Applications of the products are complemented by a density functional theory mechanistic analysis that pinpoints the crucial factors responsible for the selectivity observed, including stoichiometry and the nature of the heteroalkyne. PMID:26975182

  9. Copper-catalyzed intermolecular oxyamination of olefins using carboxylic acids and O-benzoylhydroxylamines

    PubMed Central

    Hemric, Brett N

    2016-01-01

    Summary This paper reports a novel approach for the direct and facile synthesis of 1,2-oxyamino moieties via an intermolecular copper-catalyzed oxyamination of olefins. This strategy utilizes O-benzoylhydroxylamines as an electrophilic amine source and carboxylic acids as a nucleophilic oxygen source to achieve a modular difunctionalization of olefins. The reaction proceeded in a regioselective manner with moderate to good yields, exhibiting a broad scope of carboxylic acid, amine, and olefin substrates. PMID:26877805

  10. Comparison of interionic/intermolecular vibrational dynamics between ionic liquids and concentrated electrolyte solutions.

    PubMed

    Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki

    2009-12-28

    In this study, we have compared the interionic/intermolecular vibrational dynamics of ionic liquids (ILs) and concentrated electrolyte solutions measured by femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. A typical anion in ILs, bis(trifluoromethanesulfonyl)amide ([NTf(2)](-)), has been chosen as the anion for the sample ILs and concentrated electrolyte solutions. ILs used in this study are 1-butyl-3-methylimidazolium, 1-butylpyridinium, N-butyl-N,N,N-triethylammonium, and 1-butyl-1-methylpyrrolidinium with [NTf(2)](-). Li[NTf(2)] solutions (approximately 3.3 M) of water, methanol, propylene carbonate, and poly(ethylene glycol) have been selected as control samples. Kerr transients of the ILs and electrolyte solutions show intra- and interionic/intermolecular vibrational dynamics followed by slow picosecond overdamped relaxation. Fourier transform Kerr spectra have shown a difference in the relative intensities of intraionic vibrational bands of [NTf(2)](-) (280-350 cm(-1)) between the ILs and electrolyte solutions. The origin of the difference is attributed to the change in the conformational equilibrium between cisoid and transoid forms of [NTf(2)](-), which is caused by a favorable stabilization of dipolar cisoid form due to Li(+) and dipolar solvent molecules in the electrolyte solutions. Low-frequency Kerr spectra (0-200 cm(-1)) exhibit unique features with the variation of cation and solvent species. The aromatic ILs have a prominent high-frequency librational motion at about 100 cm(-1) in contrast to the case for the nonaromatic ones. The common structure of the spectra observed at about 20 cm(-1) likely comes from an interionic motion of [NTf(2)](-). The nonaromatic ILs allow a fair comparison with the electrolyte solutions of propylene carbonate and poly(ethylene glycol) because of the structural similarities. The comparison based on the first moment of the interionic/intermolecular vibrational spectrum suggests the

  11. Estimation of Some Parameters from Morse-Morse-Spline-Van Der Waals Intermolecular Potential

    SciTech Connect

    Coroiu, I.

    2007-04-23

    Some parameters such as transport cross-sections and isotopic thermal diffusion factor have been calculated from an improved intermolecular potential, Morse-Morse-Spline-van der Waals (MMSV) potential proposed by R.A. Aziz et al. The treatment was completely classical and no corrections for quantum effects were made. The results would be employed for isotope separations of different spherical and quasi-spherical molecules.

  12. Comparison of interionic/intermolecular vibrational dynamics between ionic liquids and concentrated electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki

    2009-12-01

    In this study, we have compared the interionic/intermolecular vibrational dynamics of ionic liquids (ILs) and concentrated electrolyte solutions measured by femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. A typical anion in ILs, bis(trifluoromethanesulfonyl)amide ([NTf2]-), has been chosen as the anion for the sample ILs and concentrated electrolyte solutions. ILs used in this study are 1-butyl-3-methylimidazolium, 1-butylpyridinium, N-butyl-N,N,N-triethylammonium, and 1-butyl-1-methylpyrrolidinium with [NTf2]-. Li[NTf2] solutions (˜3.3M) of water, methanol, propylene carbonate, and poly(ethylene glycol) have been selected as control samples. Kerr transients of the ILs and electrolyte solutions show intra- and interionic/intermolecular vibrational dynamics followed by slow picosecond overdamped relaxation. Fourier transform Kerr spectra have shown a difference in the relative intensities of intraionic vibrational bands of [NTf2]- (280-350 cm-1) between the ILs and electrolyte solutions. The origin of the difference is attributed to the change in the conformational equilibrium between cisoid and transoid forms of [NTf2]-, which is caused by a favorable stabilization of dipolar cisoid form due to Li+ and dipolar solvent molecules in the electrolyte solutions. Low-frequency Kerr spectra (0-200 cm-1) exhibit unique features with the variation of cation and solvent species. The aromatic ILs have a prominent high-frequency librational motion at about 100 cm-1 in contrast to the case for the nonaromatic ones. The common structure of the spectra observed at about 20 cm-1 likely comes from an interionic motion of [NTf2]-. The nonaromatic ILs allow a fair comparison with the electrolyte solutions of propylene carbonate and poly(ethylene glycol) because of the structural similarities. The comparison based on the first moment of the interionic/intermolecular vibrational spectrum suggests the stronger interionic/intermolecular interaction in

  13. Enantioselective Intermolecular Cyclopropanations for the Synthesis of Chiral Pyrimidine Carbocyclic Nucleosides.

    PubMed

    Xie, Ming-Sheng; Zhou, Peng; Niu, Hong-Ying; Qu, Gui-Rong; Guo, Hai-Ming

    2016-09-01

    A direct route to chiral cyclopropylpyrimidine carbocyclic nucleoside analogues has been reported via highly enantioselective intermolecular cyclopropanation reactions of N1-vinylpyrimidines with α-diazoesters. With chiral ruthenium(II)-phenyloxazoline complex (2 mol %) as the catalyst, cyclopropyl pyrimidine nucleoside analogues could be obtained in good yields (71-96% yields) with high levels of diastereo- and enantioselectivities (10:1 to >20:1 dr and 96-99% ee) in 1 min. PMID:27526779

  14. 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. PMID:24328234

  15. 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.

  16. Temperature-dependent intermolecular force measurement of poly(N-isopropylacrylamide) grafted surface with protein.

    PubMed

    Cho, Eun Chul; Kim, Yong Deuk; Cho, Kilwon

    2005-06-15

    We have investigated the temperature dependence of the intermolecular force between poly(N-isopropylacrylamide) (PNiPAM) grafted surface and bovine serum albumin (BSA) in phosphate buffer (pH 7.4) using atomic force microscopy at the nanonewton scale. These observations show that the interaction force is nearly zero below the phase transition temperature of PNiPAM and that it increases steeply during the phase transition. Since the PNiPAM chains are grafted onto the aminosilane (gamma-aminopropyltriethoxysilane)-treated silicon wafer, we measured the force-distance curve of BSA-immobilized tips for the bare and the aminosilane-treated silicon wafer. These surfaces show no temperature dependence and their values are different from those of the PNiPAM-grafted surfaces at 30 degrees C. The results indicate that the measured adhesion force is between the PNiPAM-grafted surface and the BSA-immobilized tip. Our studies on the intermolecular force between other surfaces (CH(3)- and COOH-terminated self-assembled monolayers) and the BSA-immobilized tip indicate that the variation in the intermolecular force between the PNiPAM surface and BSA with temperature can be attributed to the changes in the properties of the PNiPAM chains. From consideration of the PNiPAM phase transition mechanism, it is speculated that the intermolecular force between the PNiPAM-grafted surface and BSA would be affected by changes in the arrangement of the bound water molecules around the PNiPAM chain and by changes in the conformation (i.e., in the chain mobility) of the PNiPAM chain during the phase transition. PMID:15897061

  17. Cupric-Superoxo Mediated Inter-Molecular C-H Activation Chemistry

    PubMed Central

    Peterson, Ryan L.; Himes, Richard A.; Kotani, Hiroaki; Suenobu, Tomoyoshi; Tian, Li; Siegler, Maxime A.; Solomon, Edward I.; Fukuzumi, Shunichi; Karlin, Kenneth D.

    2011-01-01

    A new cupric-superoxo complex [LCuII(O2•−)]+, which possesses particularly strong O–O and Cu–O bonding, is capable of intermolecular C-H activation of the NADH analogue 1-benzyl-1,4-dihydronicotinamide (BNAH). Kinetic studies indicate a first-order dependence on both the Cu-complex and BNAH with a deuterium kinetic isotope effect (KIE) of 12.1, similar to that observed for certain copper monooxygenases. PMID:21265534

  18. Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR

    PubMed Central

    Bayro, Marvin J.; Debelouchina, Galia T.; Eddy, Matthew T.; Birkett, Neil R.; MacPhee, Catherine E.; Rosay, Melanie; Maas, Werner E.; Dobson, Christopher M.

    2011-01-01

    We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range 13C-13C correlation spectra and a third based on the identification of intermolecular interactions in 13C-15N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3), that efficient 13C-13C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The 13C-13C experiments are corroborated by 15N-13C correlation spectrum obtained from a mixed [15N,12C]/[14N,13C] sample which directly quantifies interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular 15N-13C constraints present in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total the experiments provide 111 intermolecular 13C-13C and 15N-13C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril. PMID:21774549

  19. Construction integrity assessment report (ETN-98-0005) S-Farm overground transfer (OGT) system valve pit 241-S-B to valve pit 241-S-D

    SciTech Connect

    HICKS, D.F.

    1999-08-12

    The S-Farm overground transfer (OGT) line will bypass the existing line(s), between valve pits 241-S-B and 241-S-D that no longer meet system requirements. The new OGT line will provide a waste transfer pipeline between these valve pits in support of saltwell pumping activities. The length of the OGT line is approximately 180 ft from pit to pit. The primary pipe is nominal 1-in. diameter stainless steel (SST) braided Ethylene-propylene Diene Monomer (EPDM) hose. The encasement pipe is a nominal 3-in., flanged, SST pipe made up of several different length pipe spool pieces (drawing H-2-829564, sh. 1 and sh. 2). The OGT line slopes from valve pit 241-S-B toward valve pit 241-S-D. At each end, the primary and encasement pipe connect to a pit entry spool piece. The pit entry spool pieces are constructed of prefabricated SST materials. These spool pieces allow for the separation of the primary and encasement pipelines after the pipes have entered the valve pits (drawing H-2-818280, sh. 2). The pit entry spool pieces also allow for leak detection of the encasement pipe at each end (drawing H-2-829564, sh. 2). The OGT encasement pipeline is supported above ground by adjustable height unistrut brackets and precast concrete bases (drawing H-2-829654, sh. 1). The pipeline is heat-traced and insulated. The heat tracing and insulation supply and retain latent heat that prevents waste solidification during transfers and provides freeze protection. The total length of the pipeline is above ground, thereby negating the need for cathodic corrosion protection. This Construction Integrity Assessment Report (CIAR) is prepared by Fluor Daniel Northwest for Numatec Hanford Corporation/Lockheed Martin Hanford Corporation, the operations contractor, and the U. S. Department of Energy, the system owner. The CIAR is intended to verify that construction was performed in accordance with the provisions of Washington Administrative Code, WAC-173-303-640 (3) (c), (e), (f) and (h).

  20. 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.

  1. 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

  2. Stereodynamics in the Collisional Autoionization of Water, Ammonia, and Hydrogen Sulfide with Metastable Rare Gas Atoms: Competition Between Intermolecular Halogen and Hydrogen Bonds.

    PubMed

    Falcinelli, Stefano; Bartocci, Alessio; Cavalli, Simonetta; Pirani, Fernando; Vecchiocattivi, Franco

    2016-01-11

    Recent experiments on the title subject, performed with a high-resolution crossed-beam apparatus, have provided the total ionization cross sections as a function of the collision energy between noble gas atoms, electronically excited in their metastable states (Ng*), and H2 O, H2 S, and NH3 reagents, as well as the emitted electron energy spectra. This paper presents a rationalization of all the experimental findings in a unifying picture to cast light on the basic chemical properties of Ng* under conditions of great relevance both from a fundamental and from an applied point of view. The importance of this investigation is that it isolates the selective role of the intermolecular halogen and hydrogen bonds, to assess their anisotropic effects on the stereodynamics of the promoted ionization reactions, and to model energy transfer and reactivity in systems of applied interest, such as planetary atmospheres, plasmas, lasers, and flames. PMID:26633846

  3. S- to N-Palmitoyl Transfer During Proteomic Sample Preparation

    NASA Astrophysics Data System (ADS)

    Ji, Yuhuan; Bachschmid, Markus M.; Costello, Catherine E.; Lin, Cheng

    2016-04-01

    N-palmitoylation has been reported in a number of proteins and suggested to play an important role in protein localization and functions. However, it remains unclear whether N-palmitoylation is a direct enzyme-catalyzed process, or results from intramolecular S- to N-palmitoyl transfer. Here, using the S-palmitoyl peptide standard, GCpalmLGNAK, as the model system, we observed palmitoyl migration from the cysteine residue to either the peptide N-terminus or the lysine side chain during incubation in both neutral and slightly basic buffers commonly used in proteomic sample preparation. Palmitoyl transfer can take place either intra- or inter-molecularly, with the peptide N-terminus being the preferred migration site, presumably because of its lower basicity. The extent of intramolecular palmitoyl migration was low in the system studied, as it required the formation of an entropically unfavored macrocycle intermediate. Intermolecular palmitoyl transfer, however, remained a tangible problem, and may lead to erroneous reporting of in vivo N-palmitoylation. It was found that addition of the MS-compatible detergent RapiGest could significantly inhibit intermolecular palmitoyl transfer, as well as thioester hydrolysis and DTT-induced thioester cleavage. Finally, palmitoyl transfer from the cysteine residue to the peptide N-terminus can also occur in the gas phase, during collision-induced dissociation, and result in false identification of N-palmitoylation. Therefore, one must be careful with both sample preparation and interpretation of tandem mass spectra in the study of N-palmitoylation.

  4. Evaluating the integrity of the reinforced concrete structure repaired by epoxy injection using simulated transfer function of impact-echo response

    SciTech Connect

    Cheng, Chia-Chi; Yu, Chih-peng; Wu, Jiunn-Hong; Hsu, Keng-Tsan; Ke, Ying-Tsu

    2014-02-18

    Cracks and honeycombs are often found inside reinforced concrete (RC) structure caused by excessive external force, or improper casting of concrete. The repairing method usually involves epoxy injection. The impact-echo method, which is a sensitive for detecting of the interior voids, may not be applicable to assess the integrity of the repaired member as both air and epoxy are less in acoustic impedances. In this study, the repaired RC structure was evaluated by the simulated transfer function of the IE displacement waveform where the R-wave displacement waveform is used as a base of a simulated force-time function. The effect of different thickness of the epoxy layer to the amplitude corresponding to the interface is studied by testing on specimen containing repaired naturally delaminated cracks with crack widths about 1 mm, 3 mm and 5 mm. The impact-echo responses were compared with the drilling cores at the test positions. The results showed the cracks were not fully filled with epoxy when the peak amplitude corresponding to the interface dropped less than 20%. The peak corresponding to the thicker epoxy layer tends to be larger in amplitude. A field study was also performed on a column damaged by earthquake before and after repairing.

  5. Fully Integrated On-Chip Coil in 0.13 μm CMOS for Wireless Power Transfer Through Biological Media.

    PubMed

    Zargham, Meysam; Gulak, P Glenn

    2015-04-01

    Delivering milliwatts of wireless power at centimeter distances is advantageous to many existing and emerging biomedical applications. It is highly desirable to fully integrate the receiver on a single chip in standard CMOS with no additional post-processing steps or external components. This paper presents a 2 × 2.18 mm(2) on-chip wireless power transfer (WPT) receiver (Rx) coil fabricated in 0.13 μm CMOS. The WPT system utilizes a 14.5 × 14.5 mm(2) transmitter (Tx) coil that is fabricated on a standard FR4 substrate. The on-chip power harvester demonstrates a peak WPT efficiency of -18.47 dB , -20.96 dB and -20.15 dB at 10 mm of separation through air, bovine muscle and 0.2 molar NaCl, respectively. The achieved efficiency enables the delivery of milliwatts of power to application circuits while staying below safe power density and electromagnetic (EM) exposure limits. PMID:25099630

  6. Analysis and calculation by integral methods of laminar compressible boundary-layer with heat transfer and with and without pressure gradient

    NASA Technical Reports Server (NTRS)

    Morduchow, Morris

    1955-01-01

    A survey of integral methods in laminar-boundary-layer analysis is first given. A simple and sufficiently accurate method for practical purposes of calculating the properties (including stability) of the laminar compressible boundary layer in an axial pressure gradient with heat transfer at the wall is presented. For flow over a flat plate, the method is applicable for an arbitrarily prescribed distribution of temperature along the surface and for any given constant Prandtl number close to unity. For flow in a pressure gradient, the method is based on a Prandtl number of unity and a uniform wall temperature. A simple and accurate method of determining the separation point in a compressible flow with an adverse pressure gradient over a surface at a given uniform wall temperature is developed. The analysis is based on an extension of the Karman-Pohlhausen method to the momentum and the thermal energy equations in conjunction with fourth- and especially higher degree velocity and stagnation-enthalpy profiles.

  7. Transfer and partitioning of energy and mass through seafloor hydrothermal systems: comparative studies at the Ridge2000 Integrated Study Sites (ISS) (Invited)

    NASA Astrophysics Data System (ADS)

    Tivey, M. K.

    2010-12-01

    Seafloor hydrothermal systems are major players in the transfer of mass and energy from the mantle and crust to the ocean and biosphere. Over the past thirty years, much has been learned about this transfer to the ocean, but considerably less is known about the transfer to the biosphere. Study of hydrothermal systems in a diverse range of geologic settings has shown relationships between spreading rate and hydrothermal heat flux, substrate composition (including rock geochemistry, presence/absence of sediment) and hydrothermal fluid composition, and magmatic/tectonic events and temporal variability of fluid composition (e.g., German and Von Damm, Treatise On Geochemistry, 2004; Baker et al. AGU Monograph Series 91, 1995). Studies in arc and back-arc settings are documenting the effects of magmatic acid volatiles on fluid-rock reaction and fluid and vent deposit compositions (e.g., Ishibashi and Urabe, Backarc Basins: Tectonics and Magmatism, 1995). These comparative studies in a wide range of geologic settings, including at the three Ridge2000 ISS, have provided a fairly good understanding of the flux of heat and many elements to the ocean associated with high temperature seafloor hydrothermal systems. Considerably less is known, however, about the partitioning of heat and mass (particularly metals and sulfur) in hydrothermal systems. The deposits that form at vent sites are intimately linked within paths of energy and mass transport from the mantle and crust to the oceans. Transport differs greatly through different types of deposits (e.g., black smokers, white smokers/diffusers, flanges). Estimates of heat flux from measured temperatures of flow (unless integrated over and around an entire vent field) require an understanding of the partitioning of flow between focused black smokers and more diffuse flow from diffusers, flanges, and surfaces of deposits, and from the igneous substrate. Estimates of mass flux into the ocean require an understanding of the

  8. Motivational Influences on Transfer

    ERIC Educational Resources Information Center

    Pugh, Kevin J.; Bergin, David A.

    2006-01-01

    Both transfer and motivation are important constructs accompanied by extensive bodies of literature. However, there is a lack of integration of the 2 constructs. This article analyzes the potential indirect influence of motivational factors on transfer by reviewing studies that examine the influence of motivation on cognitive processes related to…

  9. Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases.

    PubMed

    Bartocci, Alessio; Belpassi, Leonardo; Cappelletti, David; Falcinelli, Stefano; Grandinetti, Felice; Tarantelli, Francesco; Pirani, Fernando

    2015-05-14

    The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl4 and CF4. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl4 and Ng-CF4 and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF4, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl4, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the

  10. Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

    SciTech Connect

    Bartocci, Alessio; Cappelletti, David; Pirani, Fernando; Belpassi, Leonardo; Falcinelli, Stefano; Grandinetti, Felice; Tarantelli, Francesco

    2015-05-14

    The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl{sub 4} and CF{sub 4}. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl{sub 4} and Ng-CF{sub 4} and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF{sub 4}, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl{sub 4}, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential

  11. Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases

    NASA Astrophysics Data System (ADS)

    Bartocci, Alessio; Belpassi, Leonardo; Cappelletti, David; Falcinelli, Stefano; Grandinetti, Felice; Tarantelli, Francesco; Pirani, Fernando

    2015-05-01

    The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl4 and CF4. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl4 and Ng-CF4 and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF4, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl4, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the

  12. A quantum chemical insight to intermolecular hydrogen bonding interaction between cytosine and nitrosamine: Structural and energetic investigations

    NASA Astrophysics Data System (ADS)

    Khalili, Behzad

    2016-03-01

    Hydrogen bond interactions which are formed during complex formation between cytosine and nitrosamine have been fully investigated using B3LYP, B3PW91 and MP2 methods in conjunction with various basis sets including 6-311++G (d,p), 6-311++G (2d,2p), 6-311++G (df,pd) and AUG-cc-pVDZ. Three regions around the most stable conformer of cytosine in the gas phase with six possible double H-bonded interactions were considered. Two intermolecular hydrogen bonds of type NC-N-HNA and O-H(N-H)C-ONA were found on the potential energy surface in a cyclic system with 8-member in CN1, CN3, CN5 and 7-member in CN2, CN4, CN6 systems. Results of binding energy calculation at all applied methods reveal that the CN1 structure is the most stable one which is formed by interaction of nitrosamine with cytosine in S1 region. The BSSE-corrected binding energy for six complex system is ranging from -23.8 to -43.6 kJ/mol at MP2/6-311++G (df,pd) level and the stability order is as CN1 > CN2 > CN3 > CN4 > CN5 > CN6 in all studied levels of theories. The NBO results reveal that the charge transfer occurred from cytosine to nitrosamine in CN1, CN3, CN5 and CN6 whereas this matter in the case of CN2 and CN4 was reversed. The relationship between BEs with red shift of H-bond involved bonds vibrational frequencies, charge transfer energies during complex formation and electron densities at H-bond BCPs were discussed. In addition activation energetic properties related to the proton transfer process between cytosine and nitrosamine have been calculated at MP2/6-311++G (df,pd) level. AIM results imply that H-bond interactions are electrostatic with partially covalent characteristic in nature.

  13. Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids.

    PubMed

    Tan, Samuel Y S; Izgorodina, Ekaterina I

    2016-06-14

    The effective fragment potential (EFP) method that decomposes the interaction energy as a sum of the five fundamental forces-electrostatic, exchange-repulsion, polarization, dispersion, and charge transfer-was applied to a large test set of ionic liquid ion pairs and compared against the state-of-the-art method, Symmetry-Adapted Perturbation Theory (SAPT). The ion pairs include imidazolium and pyrrolidinium cations combined with anions that are routinely used in the field of ionic liquids. The aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(d,p) basis sets were used for EFP, while SAPT2+3/aug-cc-pVDZ provided the benchmark energies. Differences between the two methods were found to be large, and strongly dependent on the anion type. For the aug-cc-pVTZ basis set, which produced the least errors, average relative errors were between 2.3% and 18.4% for pyrrolidinium ion pairs and between 2.1% and 27.7% for imidazolium ion pairs for each individual energetic component (excluding charge transfer), as well as the total interaction energy. Charge transfer gave the largest relative errors: 56% and 63% on average for pyrrolidinium- and imidazolium-based ion pairs, respectively. Scaling of the EFP components against SAPT2+3 showed improvement for polarization (induction) and dispersion terms, thus indicating potential for the development of cost-effective alternatives for intermolecular induction and dispersion potentials for ionic liquids. PMID:27116302

  14. Using corresponding state theory to obtain intermolecular potentials to calculate pure liquid shock Hugoniots

    SciTech Connect

    Hobbs, M.L.

    1997-12-01

    Determination of product species, equations-of-state (EOS) and thermochemical properties of high explosives and pyrotechnics remains a major unsolved problem. Although, empirical EOS models may be calibrated to replicate detonation conditions within experimental variability (5--10%), different states, e.g. expansion, may produce significant discrepancy with data if the basic form of the EOS model is incorrect. A more physically realistic EOS model based on intermolecular potentials, such as the Jacobs Cowperthwaite Zwisler (JCZ3) EOS, is needed to predict detonation states as well as expanded states. Predictive capability for any EOS requires a large species data base composed of a wide variety of elements. Unfortunately, only 20 species have known JCZ3 molecular force constants. Of these 20 species, only 10 have been adequately compared to experimental data such as molecular scattering or shock Hugoniot data. Since data in the strongly repulsive region of the molecular potential is limited, alternative methods must be found to deduce force constants for a larger number of species. The objective of the present study is to determine JCZ3 product species force constants by using a corresponding states theory. Intermolecular potential parameters were obtained for a variety of gas species using a simple corresponding states technique with critical volume and critical temperature. A more complex, four parameter corresponding state method with shape and polarity corrections was also used to obtain intermolecular potential parameters. Both corresponding state methods were used to predict shock Hugoniot data obtained from pure liquids. The simple corresponding state method is shown to give adequate agreement with shock Hugoniot data.

  15. 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.

  16. Real-space identification of intermolecular bonding with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Qiu, Xiaohui

    2014-03-01

    A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms, whose formation and breaking result in chemical reactions and the production of new substances. Distinct from the covalent bond, the intermolecular interactions are often a vague concept elusive in experimental observations. Nevertheless, intermolecular interactions virtually affect all physical and chemical properties of substances in the condensed phases. The interactions between molecules, particularly the hydrogen bond, are responsible for the structural transformations and functions of biological molecules. Because most of the molecular characterization techniques are more sensitive to the covalent structures of the molecules, it remains a challenge to quantitatively study the weak interactions between molecules despite the tremendous efforts toward this goal. Here we report a real-space identification of the formation of hydrogen bonding between molecules adsorbed on metal substrate using a non-contact atomic force microscope (nc-AFM). The atomically resolved molecular structures with unprecedented details enable a precise determination of the characteristics of the hydrogen bond network, including bonding sites, orientations and lengths. The observed bond contrast was interpreted by ab initio density functional calculations that indicate the electron density contribution from the hybridized electronic state of hydrogen bond. Given the extensively discussion on the nature of hydrogen bonding and the recent redefinition by IUPAC, the observation of hydrogen bonding in real-space may be a stimulating evidence for theoretical chemistry. Meanwhile, the direct identification of local bonding configurations by nc-AFM would advance the understanding of intermolecular interactions in complex molecules with multiple active sites, offering complementary structural information essential for various applications in materials and biological sciences.

  17. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  18. Electron collisions with phenol: Total, integral, differential, and momentum transfer cross sections and the role of multichannel coupling effects on the elastic channel

    SciTech Connect

    Costa, Romarly F. da; Oliveira, Eliane M. de; Lima, Marco A. P.; Bettega, Márcio H. F.; Varella, Márcio T. do N.; Jones, Darryl B.; Brunger, Michael J.; Blanco, Francisco; Colmenares, Rafael; and others

    2015-03-14

    We report theoretical and experimental total cross sections for electron scattering by phenol (C{sub 6}H{sub 5}OH). The experimental data were obtained with an apparatus based in Madrid and the calculated cross sections with two different methodologies, the independent atom method with screening corrected additivity rule (IAM-SCAR), and the Schwinger multichannel method with pseudopotentials (SMCPP). The SMCPP method in the N{sub open}-channel coupling scheme, at the static-exchange-plus-polarization approximation, is employed to calculate the scattering amplitudes at impact energies ranging from 5.0 eV to 50 eV. We discuss the multichannel coupling effects in the calculated cross sections, in particular how the number of excited states included in the open-channel space impacts upon the convergence of the elastic cross sections at higher collision energies. The IAM-SCAR approach was also used to obtain the elastic differential cross sections (DCSs) and for correcting the experimental total cross sections for the so-called forward angle scattering effect. We found a very good agreement between our SMCPP theoretical differential, integral, and momentum transfer cross sections and experimental data for benzene (a molecule differing from phenol by replacing a hydrogen atom in benzene with a hydroxyl group). Although some discrepancies were found for lower energies, the agreement between the SMCPP data and the DCSs obtained with the IAM-SCAR method improves, as expected, as the impact energy increases. We also have a good agreement among the present SMCPP calculated total cross section (which includes elastic, 32 inelastic electronic excitation processes and ionization contributions, the latter estimated with the binary-encounter-Bethe model), the IAM-SCAR total cross section, and the experimental data when the latter is corrected for the forward angle scattering effect [Fuss et al., Phys. Rev. A 88, 042702 (2013)].

  19. Assimilation of SMOS-derived soil moisture in a fully integrated hydrological and soil-vegetation-atmosphere transfer model in Western Denmark

    NASA Astrophysics Data System (ADS)

    Ridler, Marc-Etienne; Madsen, Henrik; Stisen, Simon; Bircher, Simone; Fensholt, Rasmus

    2014-11-01

    Real surface soil moisture retrieved from the Soil Moisture and Ocean Salinity (SMOS) satellite is downscaled and assimilated in a fully integrated hydrological and soil-vegetation-atmosphere transfer (MIKE SHE SW-ET) model using a bias aware ensemble transform Kalman filter (Bias-ETKF). Satellite-derived soil moisture assimilation in a catchment scale model is typically restricted by two challenges: (1) passive microwave is too coarse for direct assimilation and (2) the data tend to be biased. The solution proposed in this study is to disaggregate the SMOS bias using a higher resolution land cover classification map that was derived from Landsat thermal images. Using known correlations between SMOS bias and vegetation type, the assimilation filter is adapted to calculate biases online, using an initial bias estimate. Real SMOS-derived soil moisture is assimilated in a precalibrated catchment model in Denmark. The objective is to determine if any additional gains can be achieved by SMOS surface soil moisture assimilation beyond the optimized model. A series of assimilation experiments were designed to (1) determine how effectively soil moisture corrections propagate downward in the soil column, (2) compare the efficacy of in situ versus SMOS assimilation, and (3) determine how soil moisture assimilation affects fluxes and discharge in the catchment. We find that assimilation of SMOS improved R2 soil moisture correlations in the upper 5 cm compared to a network of 30 in situ sensors for most land cover classes. Assimilation also brought modest gains in R2 at 25 cm depth but slightly degraded the correlation at 50 cm depth. Assimilation overcorrected discharge peaks.

  20. Copper-catalyzed intermolecular trifluoromethylarylation of alkenes: mutual activation of arylboronic acid and CF3+ reagent.

    PubMed

    Wang, Fei; Wang, Dinghai; Mu, Xin; Chen, Pinhong; Liu, Guosheng

    2014-07-23

    A novel copper-catalyzed intermolecular trifluoromethylarylation of alkenes is developed using less active ether-type Togni's reagent under mild reaction conditions. Various alkenes and diverse arylboronic acids are compatible with these conditions. Preliminary mechanistic studies reveal that a mutual activation process between arylboronic acid and CF3(+) reagent is essential. In addition, the reaction might involve a rate-determining transmetalation, and the final aryl C-C bond is derived from reductive elimination of the aryl(alkyl)Cu(III) intermediate. PMID:24983408

  1. Structure and intermolecular interactions of glipizide from laboratory X-ray powder diffraction.

    PubMed

    Burley, Jonathan C

    2005-12-01

    The crystal structure of glipizide, used as a major treatment of type-2 diabetes, has been determined ab initio using variable-temperature laboratory X-ray powder diffraction combined with a direct-space Monte Carlo/simulated annealing methodology. The strengths of the intermolecular interactions (van der Waals, pi-pi stacking, hydrogen bonding and steric interlock) were quantitatively estimated using the thermal expansion data, which were collected in the same set of experiments as those used to determine the structure. PMID:16306678

  2. Studies of interdiffusion, chemical bonding, and intermolecular interactions in fiber-matrix adhesion

    SciTech Connect

    Chou, Chiate.

    1990-01-01

    A study of the key factors involved in adhesion was conducted to determine a quantitative relation between the underlying physicochemical mechanisms of adhesion and the adhesive performance at the fiber-matrix interface. Aramid fiber was modified by attaching pendent chains to its surface to change the nature of its interaction with matrix materials. The relative importance of the three fundamental factors of adhesion (interdiffusion, intermolecular interactions, and chemical bonding) was studied by evaluating the fiber-matrix adhesive performance of these modified fiber-matrix systems.

  3. Intermolecular Interactions between Eosin Y and Caffeine Using (1)H-NMR Spectroscopy.

    PubMed

    Okuom, Macduff O; Wilson, Mark V; Jackson, Abby; Holmes, Andrea E

    2013-12-31

    DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using (1)H-NMR, (1)H-COSY, and (1)H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed. PMID:25018772

  4. Intermolecular interactions in photodamaged DNA from density functional theory symmetry-adapted perturbation theory.

    PubMed

    Sadeghian, Keyarash; Bocola, Marco; Schütz, Martin

    2011-05-01

    The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry-adapted perturbation theory (DFT-SAPT) and compared to the original (or repaired) case with pyrimidines (TpT) instead of CPD. The CPD aggregation is on average destabilized by about 6 kcal mol(-1) relative to that involving TpT. The effect of destabilization is asymmetric, that is, it involves a single H-bonding (Watson-Crick (WC) type) base-pair interaction. PMID:21452189

  5. Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.

    2006-09-20

    Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

  6. Iron(II)-Catalyzed Intermolecular Aminofluorination of Unfunctionalized Olefins Using Fluoride Ion.

    PubMed

    Lu, Deng-Fu; Zhu, Cheng-Liang; Sears, Jeffrey D; Xu, Hao

    2016-09-01

    We herein report a new catalytic method for intermolecular olefin aminofluorination using earth-abundant iron catalysts and nucleophilic fluoride ion. This method tolerates a broad range of unfunctionalized olefins, especially nonstyrenyl olefins that are incompatible with existing olefin aminofluorination methods. This new iron-catalyzed process directly converts readily available olefins to internal vicinal fluoro carbamates with high regioselectivity (N vs F), many of which are difficult to prepare using known methods. Preliminary mechanistic studies demonstrate that it is possible to exert asymmetric induction using chiral iron catalysts and that both an iron-nitrenoid and carbocation species may be reactive intermediates. PMID:27529196

  7. Modification of PEGylated enzyme with glutaraldehyde can enhance stability while avoiding intermolecular crosslinking†

    PubMed Central

    McShane, M. J.

    2015-01-01

    We demonstrate an enzyme stabilization approach whereby a model enzyme is PEGylated, followed by controlled chemical modification with glutaraldehyde. Using this stabilization strategy, size increases and aggregation due to intermolecular crosslinking are avoided. Immediately following synthesis, the PEGylated enzyme with and without glutaraldehyde modification possessed specific activities of 372.9 ± 20.68 U/mg and 373.9 ± 15.14 U/mg, respectively (vs. 317.7 ± 19.31 U/mg for the native enzyme). The glutaraldehyde-modified PEGylated enzyme retains 73% original activity after 4 weeks at 37 °C (vs. 2% retention for control). PMID:26052433

  8. 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

  9. Regiodivergent Intermolecular [3+2] Cycloadditions of Vinyl Aziridines and Allenes: Stereospecific Synthesis of Chiral Pyrrolidines.

    PubMed

    Lin, Tao-Yan; Zhu, Chao-Ze; Zhang, Peichao; Wang, Yidong; Wu, Hai-Hong; Feng, Jian-Jun; Zhang, Junliang

    2016-08-26

    The first rhodium-catalyzed intermolecular [3+2] cycloaddition reaction of vinyl aziridines and allenes for the synthesis of enantioenriched functionalized pyrrolidines was realized. [3+2] cycloaddition with the proximal C=C bond of N-allenamides gave 3-methylene-pyrrolidines in high regio- and diastereoselectivity, whereas, 2-methylene-pyrrolidines were obtained as the major products by the cycloadditions of vinyl aziridines with the distal C=C bond of allenes. Use of readily available starting materials, a broad substrate scope, high selectivity, mild reaction conditions, as well as versatile functionalization of the cycloadducts make this approach very practical and attractive. PMID:27485044

  10. Buried waste integrated demonstration technology integration process

    SciTech Connect

    Ferguson, J.S.; Ferguson, J.E.

    1992-04-01

    A Technology integration Process was developed for the Idaho National Energy Laboratories (INEL) Buried Waste Integrated Demonstration (BWID) Program to facilitate the transfer of technology and knowledge from industry, universities, and other Federal agencies into the BWID; to successfully transfer demonstrated technology and knowledge from the BWID to industry, universities, and other Federal agencies; and to share demonstrated technologies and knowledge between Integrated Demonstrations and other Department of Energy (DOE) spread throughout the DOE Complex. This document also details specific methods and tools for integrating and transferring technologies into or out of the BWID program. The document provides background on the BWID program and technology development needs, demonstrates the direction of technology transfer, illustrates current processes for this transfer, and lists points of contact for prospective participants in the BWID technology transfer efforts. The Technology Integration Process was prepared to ensure compliance with the requirements of DOE's Office of Technology Development (OTD).

  11. Buried waste integrated demonstration technology integration process

    SciTech Connect

    Ferguson, J.S.; Ferguson, J.E.

    1992-04-01

    A Technology integration Process was developed for the Idaho National Energy Laboratories (INEL) Buried Waste Integrated Demonstration (BWID) Program to facilitate the transfer of technology and knowledge from industry, universities, and other Federal agencies into the BWID; to successfully transfer demonstrated technology and knowledge from the BWID to industry, universities, and other Federal agencies; and to share demonstrated technologies and knowledge between Integrated Demonstrations and other Department of Energy (DOE) spread throughout the DOE Complex. This document also details specific methods and tools for integrating and transferring technologies into or out of the BWID program. The document provides background on the BWID program and technology development needs, demonstrates the direction of technology transfer, illustrates current processes for this transfer, and lists points of contact for prospective participants in the BWID technology transfer efforts. The Technology Integration Process was prepared to ensure compliance with the requirements of DOE`s Office of Technology Development (OTD).

  12. The integrity of the alpha-helical domain of intestinal fatty acid binding protein is essential for the collision-mediated transfer of fatty acids to phospholipid membranes.

    PubMed

    Franchini, G R; Storch, J; Corsico, B

    2008-04-01

    Intestinal FABP (IFABP) and liver FABP (LFABP), homologous proteins expressed at high levels in intestinal absorptive cells, employ markedly different mechanisms of fatty acid transfer to acceptor model membranes. Transfer from IFABP occurs during protein-membrane collisional interactions, while for LFABP transfer occurs by diffusion through the aqueous phase. In addition, transfer from IFABP is markedly faster than from LFABP. The overall goal of this study was to further explore the structural differences between IFABP and LFABP which underlie their large functional differences in ligand transport. In particular, we addressed the role of the alphaI-helix domain in the unique transport properties of intestinal FABP. A chimeric protein was engineered with the 'body' (ligand binding domain) of IFABP and the alphaI-helix of LFABP (alpha(I)LbetaIFABP), and the fatty acid transfer properties of the chimeric FABP were examined using a fluorescence resonance energy transfer assay. The results showed a significant decrease in the absolute rate of FA transfer from alpha(I)LbetaIFABP compared to IFABP. The results indicate that the alphaI-helix is crucial for IFABP collisional FA transfer, and further indicate the participation of the alphaII-helix in the formation of a protein-membrane "collisional complex". Photo-crosslinking experiments with a photoactivable reagent demonstrated the direct interaction of IFABP with membranes and further support the importance of the alphaI helix of IFABP in its physical interaction with membranes. PMID:18284926

  13. Photo-induced electron transfer between dendritic zinc(II) phthalocyanine bearing carboxylic terminal groups and methyl viologen

    NASA Astrophysics Data System (ADS)

    Wang, Yuhua; Chen, Jiangxu; Huang, Lishan; Xie, Shusen; Yang, Hongqin; Peng, Yiru

    2012-12-01

    The intermolecular electron transfer between carboxylic dendritic zinc(II) phthalocyanine bearing carboxylic terminal groups(G1-ZnPc(COOH)8) and methyl viologens (MV2+) was studied by steady-state fluorescence and UV/Vis spectroscopy. The effect of different concentrations of MV2+ on intermolecular electron transfer was investigated. The results show that the fluorescence emission of this dendritic phthalocyanine could be greatly quenched with an increasing amount of MV2+ upon excitation at 610 nm. Our study suggests that this novel dendritic phthalocyanine is an effective new electron donor and transmission complex and could be used as a potential biosensor conjugated with suitable fluorescence quencher.

  14. An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics.

    PubMed

    Pyzer-Knapp, Edward O; Thompson, Hugh P G; Day, Graeme M

    2016-08-01

    We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%. PMID:27484370

  15. 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.

  16. Intermolecular associations determine the dynamics of the circadian KaiABC oscillator

    PubMed Central

    Qin, Ximing; Byrne, Mark; Mori, Tetsuya; Zou, Ping; Williams, Dewight R.; Mchaourab, Hassane; Johnson, Carl Hirschie

    2010-01-01

    Three proteins from cyanobacteria (KaiA, KaiB, and KaiC) can reconstitute circadian oscillations in vitro. At least three molecular properties oscillate during this reaction, namely rhythmic phosphorylation of KaiC, ATP hydrolytic activity of KaiC, and assembly/disassembly of intermolecular complexes among KaiA, KaiB, and KaiC. We found that the intermolecular associations determine key dynamic properties of this in vitro oscillator. For example, mutations within KaiB that alter the rates of binding of KaiB to KaiC also predictably modulate the period of the oscillator. Moreover, we show that KaiA can bind stably to complexes of KaiB and hyperphosphorylated KaiC. Modeling simulations indicate that the function of this binding of KaiA to the KaiB•KaiC complex is to inactivate KaiA's activity, thereby promoting the dephosphorylation phase of the reaction. Therefore, we report here dynamics of interaction of KaiA and KaiB with KaiC that determine the period and amplitude of this in vitro oscillator. PMID:20679240

  17. 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.

  18. 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.

  19. Non-continuum correlated intermolecular dynamical displacements in entangled biopolymer solutions

    NASA Astrophysics Data System (ADS)

    Schweizer, Kenneth S.; Dell, Zachary E.; Tsang, Boyce; Jiang, Lingxiang; Granick, Steve

    Understanding correlated intermolecular motion is important in biology and of fundamental interest in polymer physics. We performed real space measurements of the correlated dynamical displacements of a pair of biopolymers in entangled F-actin solutions over mesoscopic and continuum length scales, and on time scales beyond the entanglement crossover but much shorter than the reptation time. A microscopic theory is constructed based on generalizing a recent force-level statistical mechanical approach for predicting the separation-dependent, non-hydrodynamic relative friction of a pair of colloids in polymer melts and in dense suspensions. In the mesoscopic time regime, individual biopolymers move by reptation, and the dynamically-emergent intermolecular correlation hole is proposed as the mechanism for inducing non-hydrodynamic collective Fickian motion. Non-continuum cross correlations are predicted to dominate for inter-polymer separations up to the rod length (~15 microns), beyond which a crossover to hydrodynamic behavior occurs. The theoretical results agree well with our measurements at different observation times and physical mesh values.

  20. 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

  1. Structural changes and intermolecular interactions of filled ice Ic structure for hydrogen hydrate under high pressure

    NASA Astrophysics Data System (ADS)

    Machida, S.; Hirai, H.; Kawamura, T.; Yamamoto, Y.; Yagi, T.

    2010-03-01

    High-pressure experiments of hydrogen hydrate were performed using a diamond anvil cell under conditions of 0.1-44.2 GPa and at room temperature. Also, high pressure Raman studies of solid hydrogen were performed in the pressure range of 0.1-43.7 GPa. X-ray diffractometry (XRD) for hydrogen hydrate revealed that a known high-pressure structure, filled ice Ic structure, of hydrogen hydrate transformed to a new high-pressure structure at approximately 35-40 GPa. A comparison of the Raman spectroscopy of a vibron for hydrogen molecules between hydrogen hydrate and solid hydrogen revealed that the extraction of hydrogen molecules from hydrogen hydrate occurred above 20 GPa. Also, the Raman spectra of a roton revealed that the rotation of hydrogen molecules in hydrogen hydrate was suppressed at around 20 GPa and that the rotation recovered under higher pressure. These results indicated that remarkable intermolecular interactions in hydrogen hydrate between neighboring hydrogen molecules and between guest hydrogen molecules and host water molecules might occur. These intermolecular interactions could produce the stability of hydrogen hydrate.

  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. Intermolecular stabilization of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) compressed to 20 GPa.

    PubMed

    Chellappa, Raja S; Dattelbaum, Dana M; Coe, Joshua D; Velisavljevic, Nenad; Stevens, Lewis L; Liu, Zhenxian

    2014-08-01

    The room temperature stability of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) has been investigated using synchrotron far-infrared, mid-infrared, Raman spectroscopy, and synchrotron X-ray diffraction (XRD) up to 20 GPa. The as-loaded DAAF samples exhibited subtle pressure-induced ordering phenomena (associated with positional disorder of the azoxy "O" atom) resulting in doubling of the a-axis, to form a superlattice similar to the low-temperature polymorph. Neither high pressure synchrotron XRD, nor high pressure infrared or Raman spectroscopies indicated the presence of structural phase transitions up to 20 GPa. Compression was accommodated in the unit cell by a reduction of the c-axis between the planar DAAF layers, distortion of the β-angle of the monoclinic lattice, and an increase in intermolecular hydrogen bonding. Changes in the ring and -NH2 deformation modes and increased intermolecular hydrogen bonding interactions with compression suggest molecular reorganizations and electronic transitions at ∼ 5 GPa and ∼ 10 GPa that are accompanied by a shifting of the absorption band edge into the visible. A fourth-order Birch-Murnaghan fit to the room temperature isotherm afforded an estimate of the zero-pressure isothermal bulk modulus, K0 = 12.4 ± 0.6 GPa and its pressure derivative K0' = 7.7 ± 0.3. PMID:25011055

  4. 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

  5. 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

  6. Physical properties and intermolecular dynamics of an ionic liquid compared with its isoelectronic neutral binary solution.

    PubMed

    Shirota, Hideaki; Castner, Edward W

    2005-10-27

    In this study, we address the following question about room-temperature ionic liquids (RTILs). Are the properties of a RTIL more dependent on the charges of the molecular ions or on the fact that the liquid is a complex mixture of two species, one or both of which are asymmetric? To address this question and to better understand the interactions and dynamics in RTILs, we have prepared the organic ionic liquid 1-methoxyethylpyridinium dicyanoamide (MOEPy(+)/DCA(-)) and compared this RTIL with the analogous isoelectronic binary solution, comprised of equal parts of 1-methoxyethylbenzene (MOEBz) and dicyanomethane (DCM). In essence, we have created a RTIL and a nearly identical neutral pair in which we have effectively turned off the charges. To understand the intermolecular interactions in both of these liquids, we have characterized the bulk density and shear viscosity. Using femtosecond optical Kerr effect spectroscopy, we have also characterized the intermolecular vibrational dynamics and diffusive reorientation. To verify that the shape, polarizability, and electronic structure of the RTIL ions and the components of the neutral pair are truly quite similar, we have carried out density functional theory calculations on the individual molecular ion and neutral species. PMID:16866386

  7. 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

  8. Pressure and temperature effects on intermolecular vibrational dynamics of ionic liquids.

    PubMed

    Penna, Tatiana C; Faria, Luiz F O; Matos, Jivaldo R; Ribeiro, Mauro C C

    2013-03-14

    Low frequency Raman spectra of ionic liquids have been obtained as a function of pressure up to ca. 4.0 GPa at room temperature and as a function of temperature along the supercooled liquid and glassy state at atmospheric pressure. Intermolecular vibrations are observed at ~20, ~70, and ~100 cm(-1) at room temperature in ionic liquids based on 1-alkyl-3-methylimidazolium cations. The component at ~100 cm(-1) is assigned to librational motion of the imidazolium ring because it is absent in non-aromatic ionic liquids. There is a correspondence between the position of intermolecular vibrational modes in the normal liquid state and the spectral features that the Raman spectra exhibit after partial crystallization of samples at low temperatures or high pressures. The pressure-induced frequency shift of the librational mode is larger than the other two components that exhibit similar frequency shifts. The lowest frequency vibration observed in a glassy state corresponds to the boson peak observed in light and neutron scattering spectra of glass-formers. The frequency of the boson peak is not dependent on the length scale of polar∕non-polar heterogeneity of ionic liquids, it depends instead on the strength of anion-cation interaction. As long as the boson peak is assigned to a mixing between localized modes and transverse acoustic excitations of high wavevectors, it is proposed that the other component observed in Raman spectra of ionic liquids has a partial character of longitudinal acoustic excitations. PMID:23514505

  9. Optimization of intermolecular potential parameters for the CO2/H2O mixture.

    PubMed

    Orozco, Gustavo A; Economou, Ioannis G; Panagiotopoulos, Athanassios Z

    2014-10-01

    Monte Carlo simulations in the Gibbs ensemble were used to obtain optimized intermolecular potential parameters to describe the phase behavior of the mixture CO2/H2O, over a range of temperatures and pressures relevant for carbon capture and sequestration processes. Commonly used fixed-point-charge force fields that include Lennard-Jones 12-6 (LJ) or exponential-6 (Exp-6) terms were used to describe CO2 and H2O intermolecular interactions. For force fields based on the LJ functional form, changes of the unlike interactions produced higher variations in the H2O-rich phase than in the CO2-rich phase. A major finding of the present study is that for these potentials, no combination of unlike interaction parameters is able to adequately represent properties of both phases. Changes to the partial charges of H2O were found to produce significant variations in both phases and are able to fit experimental data in both phases, at the cost of inaccuracies for the pure H2O properties. By contrast, for the Exp-6 case, optimization of a single parameter, the oxygen-oxygen unlike-pair interaction, was found sufficient to give accurate predictions of the solubilities in both phases while preserving accuracy in the pure component properties. These models are thus recommended for future molecular simulation studies of CO2/H2O mixtures. PMID:25198539

  10. Intermolecular interactions in solid-state metalloporphyrins and their impacts on crystal and molecular structures.

    PubMed

    Hunter, Seth C; Smith, Brenda A; Hoffmann, Christina M; Wang, Xiaoping; Chen, Yu-Sheng; McIntyre, Garry J; Xue, Zi-Ling

    2014-11-01

    A variable-temperature (VT) crystal structure study of [Fe(TPP)Cl] (TPP(2-) = meso-tetraphenylporphyrinate) and Hirshfeld surface analyses of its structures and previously reported structures of [M(TPP)(NO)] (M = Fe, Co) reveal that intermolecular interactions are a significant factor in structure disorder in the three metalloporphyrins and phase changes in the nitrosyl complexes. These interactions cause, for example, an 8-fold disorder in the crystal structures of [M(TPP)(NO)] at room temperature that obscures the M-NO binding. Hirshfeld analyses of the structure of [Co(TPP)(NO)] indicate that the phase change from I4/m to P1 leads to an increase in void-volume percentage, permitting additional structural compression through tilting of the phenyl rings to offset the close-packing interactions at the interlayer positions in the crystal structures with temperature decrease. X-ray and neutron structure studies of [Fe(TPP)Cl] at 293, 143, and 20 K reveal a tilting of the phenyl groups away from being perpendicular to the porphyrin ring as a result of intermolecular interactions. Structural similarities and differences among the three complexes are identified and described by Hirshfeld surface and void-volume calculations. PMID:25338536

  11. Polar solvation and electron transfer. Annual progress report, July 1, 1992--June 30, 1993

    SciTech Connect

    Not Available

    1993-04-13

    The report is divided into the following sections: completion of previous studies on solvation dynamics, dipole lattice studies, inertial components of solvation response, simple models of solvation dynamics, rotational dynamics and dielectric friction, intramolecular electron transfer reactions, and intermolecular donor-acceptor complexes.

  12. Electron transfer control in soluble methane monooxygenase.

    PubMed

    Wang, Weixue; Iacob, Roxana E; Luoh, Rebecca P; Engen, John R; Lippard, Stephen J

    2014-07-01

    The hydroxylation or epoxidation of hydrocarbons by bacterial multicomponent monooxygenases (BMMs) requires the interplay of three or four protein components. How component protein interactions control catalysis, however, is not well understood. In particular, the binding sites of the reductase components on the surface of their cognate hydroxylases and the role(s) that the regulatory proteins play during intermolecular electron transfer leading to the hydroxylase reduction have been enigmatic. Here we determine the reductase binding site on the hydroxylase of a BMM enzyme, soluble methane monooxygenase (sMMO) from Methylococcus capsulatus (Bath). We present evidence that the ferredoxin domain of the reductase binds to the canyon region of the hydroxylase, previously determined to be the regulatory protein binding site as well. The latter thus inhibits reductase binding to the hydroxylase and, consequently, intermolecular electron transfer from the reductase to the hydroxylase diiron active site. The binding competition between the regulatory protein and the reductase may serve as a control mechanism for regulating electron transfer, and other BMM enzymes are likely to adopt the same mechanism. PMID:24937475

  13. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water.

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

    Full classical molecular dynamics (MD) simulations of two-dimensional (2D) infrared-Raman and 2D Raman spectroscopies of liquid water were carried out to elucidate a mode-mode coupling mechanism using a polarizable water model for intermolecular and intramolecular vibrational spectroscopy (POLI2VS). This model is capable of describing both infrared and Raman spectra. Second-order response functions, which consist of one molecular polarizability and two molecular dipole moments for 2D IR-Raman and three molecular polarizabilities for 2D Raman spectroscopies, were calculated using an equilibrium-non-equilibrium hybrid MD approach. The obtained signals were analyzed using a multi-mode Brownian oscillator (BO) model with nonlinear system-bath interactions representing the intramolecular OH stretching, intramolecular HOH bending, hydrogen bonded (HB)-intermolecular librational motion and HB-intermolecular vibrational (translational) motion of liquid water. This model was applied through use of hierarchal Fokker-Planck equations. The qualitative features of the peak profiles in the 2D spectra obtained from the MD simulations are accurately reproduced with the BO model. This indicates that this model captures the essential features of the intermolecular and intramolecular motion. We elucidate the mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling, the nonlinearities of the polarizability and dipole moment, and the vibrational dephasing processes of liquid water even in the case that the 2D spectral peaks obtained from the MD simulation overlap or are unclear. The mode coupling peaks caused by electrical anharmonic coupling (EAHC) and mechanical anharmonic coupling (MAHC) are observed in all of the 2D spectra. We find that the strength of the MAHC between the OH-stretching and HB-intermolecular vibrational modes is comparable to that between the OH-stretching and HOH bending modes. Moreover, we find that this OH-stretching and HB-intermolecular

  14. Squeezing water clusters between graphene sheets: energetics, structure, and intermolecular interactions.

    PubMed

    McKenzie, S; Kang, H C

    2014-12-21

    The behavior of water confined at the nanoscale between graphene sheets has attracted much theoretical and experimental attention recently. However, the interactions, structure, and energy of water at the molecular scale underpinning the behavior of confined water have not been characterized by first-principles calculations. In this work we consider small water clusters up to the hexamer adsorbed between graphene sheets using density functional theory calculations with van der Waals corrections. We investigate the effects on structure, energy, and intermolecular interactions due to confinement between graphene sheets. For interlayer distances of about one nanometer or more, the cluster adsorption energy increases approximately linearly with the cluster size by 0.1 eV per molecule in the cluster. As the interlayer distance decreases, the cluster adsorption energy reaches a maximum at 6 to 7 Å with approximately 0.16 eV stabilization energy relative to large interlayer distances. This suggests the possibility of controlling the amount of adsorption in graphene nanomaterials by varying the interlayer distance. We also quantify the intermolecular hydrogen bonding in the clusters by calculating the dissociation energy required to remove one molecule from each cluster. For each cluster size, this is constant for interlayer distances larger than approximately 6 to 8 Å. For smaller distances the intermolecular interaction decreases rapidly thus leading to weaker cohesion between molecules in a squeezed cluster. We expect a mechanism of concerted motion for hydrogen-bonded water molecules confined between graphene sheets, as has been observed for water confined within the carbon nanotubes. Thus, the decrease in the dissociation energy we observed here is consistent with experimental results for water transport through graphene and related membranes that are of interest in nanofiltration. We also calculate the corrugation in the interaction potential between graphene

  15. Photoinduced intermolecular cross-linking of gas phase triacylglycerol lipid ions.

    PubMed

    Nie, Shuai; Pham, Huong T; Blanksby, Stephen J; Reid, Gavin E

    2015-01-01

    Complex mixtures of plant derived triglycerol (TG) lipids are commonly used as feedstock components for the production of industrial polymers. However, there remains a need for the development of analytical strategies to investigate the intrinsic intermolecular cross-linking reactivity of individual TG molecules within these mixtures as a function of their structures and physicochemical properties, and for the characterization of the resultant products. Here, to address this need, we describe a novel multistage tandem mass spectrometry based method for intermolecular cross-linking and subsequent structural characterization of TG lipid ions in the gas phase. Cross-linking reactions were initiated using 266 nm ultraviolet photodissociation tandem mass spectrometry (UVPD-MS/MS) of saturated or unsaturated TG dimers introduced via electrospray ionization into a linear ion trap mass spectrometer as noncovalent complexes with protonated 3,4-, 2,4- or 3,5- diiodoaniline (diIA). UVPD resulted in the initial formation of an anilinyl biradical via the sequential loss of two iodine radicals, which underwent further reaction to yield multiple cross-linked TG products along with competing noncross-linking processes. These chemistries are proposed to occur via sequential combinations of hydrogen abstraction (H-abstraction), radical addition and radical recombination. Multistage collision induced dissociation tandem mass spectrometry (CID-MS(n)) was used to obtain evidence for the structures and mechanisms of formation for these products, as a function of both the TG lipid and diIA ion structures. The efficiency of the UVPD reaction was shown to be dependent on the number of unsaturation sites present within the TG lipids. However, when unsaturation sites were present, formation of the cross-linked and noncross-linked product ions via H-abstraction and radical addition mechanisms was found to be competitive. Finally, the identity of the anilinyl biradical (e.g., 3,4- versus 2

  16. Electron transfer activity of a de novo designed copper center in a three-helix bundle fold.

    PubMed

    Plegaria, Jefferson S; Herrero, Christian; Quaranta, Annamaria; Pecoraro, Vincent L

    2016-05-01

    In this work, we characterized the intermolecular electron transfer (ET) properties of a de novo designed metallopeptide using laser-flash photolysis. α3D-CH3 is three helix bundle peptide that was designed to contain a copper ET site that is found in the β-barrel fold of native cupredoxins. The ET activity of Cuα3D-CH3 was determined using five different photosensitizers. By exhibiting a complete depletion of the photo-oxidant and the successive formation of a Cu(II) species at 400nm, the transient and generated spectra demonstrated an ET transfer reaction between the photo-oxidant and Cu(I)α3D-CH3. This observation illustrated our success in integrating an ET center within a de novo designed scaffold. From the kinetic traces at 400nm, first-order and bimolecular rate constants of 10(5)s(-1) and 10(8)M(-1)s(-1) were derived. Moreover, a Marcus equation analysis on the rate versus driving force study produced a reorganization energy of 1.1eV, demonstrating that the helical fold of α3D requires further structural optimization to efficiently perform ET. This article is part of a Special Issue entitled Biodesign for Bioenergetics - the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. PMID:26427552

  17. ICESluvan, a 94-Kilobase Mosaic Integrative Conjugative Element Conferring Interspecies Transfer of VanB-Type Glycopeptide Resistance, a Novel Bacitracin Resistance Locus, and a Toxin-Antitoxin Stabilization System

    PubMed Central

    Bjørkeng, Eva K.; Hjerde, Erik; Pedersen, Torunn; Sundsfjord, Arnfinn

    2013-01-01

    A 94-kb integrative conjugative element (ICESluvan) transferable to Enterococcus faecium and Enterococcus faecalis from an animal isolate of Streptococcus lutetiensis consists of a mosaic of genetic fragments from different Gram-positive bacteria. A variant of ICESluvan was confirmed in S. lutetiensis from a patient. A complete Tn5382/Tn1549 with a vanB2 operon is integrated into a streptococcal ICESde3396-like region harboring a putative bacteriophage exclusion system, a putative agglutinin receptor precursor, and key components of a type IV secretion system. Moreover, ICESluvan encodes a putative MobC family mobilization protein and a relaxase and, thus, in total has all genetic components essential for conjugative transfer. A 9-kb element within Tn5382/Tn1549 encodes, among others, putative proteins similar to the TnpX site-specific recombinase in Faecalibacterium and VanZ in Paenibacillus, which may contribute to the detected low-level teicoplanin resistance. Furthermore, ICESluvan encodes a novel bacitracin resistance locus that is associated with reduced susceptibility to bacitracin when transferred to E. faecium. The expression of a streptococcal pezAT toxin-antitoxin-encoding operon of ICESluvan in S. lutetiensis, E. faecium, and E. faecalis was confirmed by reverse transcription (RT)-PCR, indicating an active toxin-antitoxin system which may contribute to stabilizing ICESluvan within new hosts. Junction PCR and DNA sequencing confirmed that ICESluvan excised to form a circular intermediate in S. lutetiensis, E. faecalis, and E. faecium. Transfer between E. faecalis cells was observed in the presence of helper plasmid pIP964. Sequence analysis of the original S. lutetiensis donor and enterococcal transconjugants showed that ICESluvan integrates in a site-specific manner into the C-terminal end of the chromosomal tRNA methyltransferase gene rumA. PMID:24078615

  18. Single Molecule Electron Transfer Process of Ruthenium Complexes.

    SciTech Connect

    Hu, Dehong; Lu, H PETER.

    2006-03-01

    Transition metal complexes such as ruthenium complexes, having metal-to-ligand charge transfer states, are extensively used in solar energy conversion and electron transfer in biological systems and at interfaces. The dynamics of metal-to-ligand charge transfer and subsequent intermolecular, intramolecular, and interfacial electron transfer processes can be highly complex and inhomogeneous, especially when molecules are involved in interactions and perturbations from heterogeneous local environments and gated by conformation fluctuations. We have employed the single-molecule spectroscopy, a powerful approach for inhomogeneous systems to study the electron transfer dynamics of ruthenium complexes. We have applied a range of statistical analysis methods to reveal nonclassical photon emission behavior of the single ruthenium complex, i.e., photon antibunching, and photophysical ground-state recovering dynamics on a microsecond time scale. The use of photon antibunching to measure phosphorescence lifetimes and single-molecule electron transfer dynamics at room temperature is demonstrated.

  19. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

    SciTech Connect

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-07

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

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

    PubMed

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

    2015-10-01

    The recognition properties of heteroditopic hemicryptophane hosts towards anions, cations, and neutral pairs, combining both cation-π and anion-π interaction sites, were investigated to probe the complexity of interfering weak intermolecular interactions. It is suggested from NMR experiments, and supported by CASSCF/CASPT2 calculations, that the binding constants of anions can be modulated by a factor of up to 100 by varying the fluorination sites on the electron-poor aromatic rings. Interestingly, this subtle chemical modification can also reverse the sign of cooperativity in ion-pair recognition. Wavefunction calculations highlight how short- and long-range interactions interfere in this recognition process, suggesting that a disruption of anion-π interactions can occur in the presence of a co-bound cation. Such molecules can be viewed as prototypes for examining complex processes controlled by the competition of weak interactions. PMID:26401973

  1. Intermolecular hydrogen bonded and self-assembled β-pleated sheet structures of β-sulfidocarbonyls

    NASA Astrophysics Data System (ADS)

    Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

    2007-06-01

    The three crystal structures of β-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to β-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

  2. Metal-Free Intermolecular Azide-Alkyne Cycloaddition Promoted by Glycerol.

    PubMed

    Rodríguez-Rodríguez, Marta; Gras, Emmanuel; Pericàs, Miquel A; Gómez, Montserrat

    2015-12-14

    Metal-free intermolecular Huisgen cycloadditions using nonactivated internal alkynes have been successfully performed in neat glycerol, both under thermal and microwave dielectric heating. In sharp contrast, no reaction occurs in other protic solvents, such as water, ethanol, or diols. DFT calculations have shown that the BnN3/glycerol adduct promotes a more important stabilization of the corresponding LUMO than that produced in the analogous BnN3/alcohol adducts, favoring the reactivity with the alkyne in the first case. The presence of copper salts in the medium did not change the reaction pathway (Cu(I) acts as spectator), except for disubstituted silylalkynes, for which desilylation takes place in contrast to the metal-free system. PMID:26541267

  3. Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

    NASA Astrophysics Data System (ADS)

    Gu, Quanli; Trindle, Carl; Knee, J. L.

    2012-09-01

    Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.

  4. Cobalt-catalysed site-selective intra- and intermolecular dehydrogenative amination of unactivated sp3 carbons

    PubMed Central

    Wu, Xuesong; Yang, Ke; Zhao, Yan; Sun, Hao; Li, Guigen; Ge, Haibo

    2015-01-01

    Cobalt-catalysed sp2 C–H bond functionalization has attracted considerable attention in recent years because of the low cost of cobalt complexes and interesting modes of action in the process. In comparison, much less efforts have been devoted to the sp3 carbons. Here we report the cobalt-catalysed site-selective dehydrogenative cyclization of aliphatic amides via a C–H bond functionalization process on unactivated sp3 carbons with the assistance of a bidentate directing group. This method provides a straightforward synthesis of monocyclic and spiro β- or γ-lactams with good to excellent stereoselectivity and functional group tolerance. In addition, a new procedure has been developed to selectively remove the directing group, which enables the synthesis of free β- or γ-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp3 carbons is also realized. PMID:25753366

  5. Inhibition of tau aggregation by a rosamine derivative that blocks tau intermolecular disulfide cross-linking.

    PubMed

    Haque, Md Mamunul; Kim, Dohee; Yu, Young Hyun; Lim, Sungsu; Kim, Dong Jin; Chang, Young-Tae; Ha, Hyung-Ho; Kim, Yun Kyung

    2014-09-01

    Abnormal tau aggregates are presumed to be neurotoxic and are an important therapeutic target for multiple neurodegenerative disorders including Alzheimer's disease. Growing evidence has shown that tau intermolecular disulfide cross-linking is critical in generating tau oligomers that serve as a building block for higher-order aggregates. Here we report that a small molecule inhibitor prevents tau aggregation by blocking the generation of disulfide cross-linked tau oligomers. Among the compounds tested, a rosamine derivative bearing mild thiol reactivity selectively labeled tau and effectively inhibited oligomerization and fibrillization processes in vitro. Our data suggest that controlling tau oxidation status could be a new therapeutic strategy for prevention of abnormal tau aggregation. PMID:24919397

  6. Intermolecular interactions during complex coacervation of pea protein isolate and gum arabic.

    PubMed

    Liu, Shuanghui; Cao, Yuan-Long; Ghosh, Supratim; Rousseau, Dérick; Low, Nicholas H; Nickerson, Michael T

    2010-01-13

    The nature of intermolecular interactions during complexation between pea protein isolate (PPI) and gum arabic (GA) was investigated as a function of pH (4.30-2.40) by turbidimetric analysis and confocal scanning microscopy in the presence of destabilizing agents (100 mM NaCl or 100 mM urea) and at different temperatures (6-60 degrees C). Complex formation followed two pH-dependent structure-forming events associated with the formation of soluble and insoluble complexes and involved interactions between GA and PPI aggregates. Complex formation was driven by electrostatic attractive forces between complementary charged biopolymers, with secondary stabilization by hydrogen bonding. Hydrophobic interactions were found to enhance complex stability at lower pH (pH 3.10), but not with its formation. PMID:19938857

  7. Always look on the bright site of Rho: structural implications for a conserved intermolecular interface.

    PubMed

    Dvorsky, Radovan; Ahmadian, Mohammad Reza

    2004-12-01

    The signalling functions of Rho-family GTPases are based on the formation of distinctive protein-protein complexes. Invaluable insights into the structure-function relationships of the Rho GTPases have been obtained through the resolution of several of their structures in complex with regulators and downstream effectors. In this review, we use these complexes to compare the binding and specificity-determining sites of the Rho GTPases. Although the properties that characterize these sites are diverse, some fundamental conserved principles that govern their intermolecular interactions have emerged. Notably, all of the interacting partners of the Rho GTPases, irrespective of their function, bind to a common set of conserved amino acids that are clustered on the surface of the switch regions. This conserved region and its specific structural characteristics exemplify the convergence of the Rho GTPases on a consensus binding site. PMID:15577926

  8. 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. PMID:26673196

  9. 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.

  10. Intermolecular control of thermoswitching and photoswitching phenomena in two spin-crossover polymorphs

    NASA Astrophysics Data System (ADS)

    Buron-Le Cointe, M.; Hébert, J.; Baldé, C.; Moisan, N.; Toupet, L.; Guionneau, P.; Létard, J. F.; Freysz, E.; Cailleau, H.; Collet, E.

    2012-02-01

    We discuss here the important role of intermolecular coupling for the thermal- and light-induced molecular state switching in the solid state. Investigations were performed on the two crystalline polymorphs of the spin-crossover [Fe-(PM-BIA)2(NCS)2] material. In addition to structural studies at thermal equilibrium, light-induced phenomena were investigated through photocrystallography, photomagnetic, and dynamical optical measurements. Strong similarities between the thermal-equilibrium and the out-of-equilibrium light-induced transformations are observed in each polymorph: strong cooperative phenomena in one polymorph versus weak cooperative ones in the second polymorph. These different responses of the two crystalline forms of the compound to external perturbations are discussed at the microscopic level in terms of Ising-like model and two-mode description of on-site molecular potentials.

  11. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    SciTech Connect

    Crusius, Johann-Philipp Hassel, Egon; Hellmann, Robert Bich, Eckard

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  12. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

    NASA Astrophysics Data System (ADS)

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-01

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π-π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.

  13. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines.

    PubMed

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-01

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π-π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface. PMID:26450327

  14. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    SciTech Connect

    Karayel, A. E-mail: yccaoh@hotmail.com; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  15. Genetic analysis of response regulator activation in bacterial chemotaxis suggests an intermolecular mechanism

    PubMed Central

    Re, Sandra Da; Tolstykh, Tatiana; Wolanin, Peter M.; Stock, Jeffry B.

    2002-01-01

    Response regulator proteins of two-component systems are usually activated by phosphorylation. The phosphorylated response regulator protein CheY∼P mediates the chemotaxis response in Escherichia coli. We performed random mutagenesis and selected CheY mutants that are constitutively active in the absence of phosphorylation. Although a single amino acid substitution can lead to constitutive activation, no single DNA base change can effect such a transition. Numerous different sets of mutations that activate in synergy were selected in several different combinations. These mutations were all located on the side of CheY defined by α4, β5, α5, and α1. Our findings argue against the two-state hypothesis for response regulator activation. We propose an alternative intermolecular mechanism that involves a dynamic interplay between response regulators and their effector targets. PMID:12381847

  16. Interfacial and intermolecular interactions determining the rotational orientation of C60 adsorbed on Au(111)

    NASA Astrophysics Data System (ADS)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

    Close-packed monolayers of fullerenes on metallic substrates are very rich systems with respect to their rotational degrees of freedom and possible interactions with different adsorption sites or next neighbours. In this connection, we report in detail on the (2√3 × 2√3)R30°-superstructure of C60 with respect to the Au(111)-surface. We use molecular orbital imaging in systematic UHV-STM studies to reveal the delicate balance of interfacial and intermolecular interactions in this system. Thus, bright C60-molecules in 5:6-top and 6:6-top geometries are observed depending on the respective next neighbours. Moreover, tiny changes in the appearance of the unoccupied molecular orbitals of dim C60-molecules in hex-vac positions are identified which are caused by the respective interaction with the facets surrounding the Au-vacancy.

  17. A structural study of the intermolecular interactions of tyramine in the solid state and in solution

    NASA Astrophysics Data System (ADS)

    Quevedo, Rodolfo; Nuñez-Dallos, Nelson; Wurst, Klaus; Duarte-Ruiz, Álvaro

    2012-12-01

    The nature of the interactions between tyramine units was investigated in the solid state and in solution. Crystals of tyramine in its free base form were analyzed by Fourier transform infrared (FT-IR) spectroscopy and single-crystal X-ray diffraction (XRD). The crystal structure shows a linear molecular organization held together by "head-to-tail" intermolecular hydrogen bonds between the amino groups and the phenolic hydroxyl groups. These chains are arranged in double layers that can geometrically favor the formation of templates in solution, which may facilitate macrocyclization reactions to form azacyclophane-type compounds. Computational calculations using the PM6-DH+ method and electrospray ionization mass spectrometry (ESI-HRMS) reveal that the formation of a hydrogen-bonded tyramine dimer is favored in solution.

  18. New mechanism for the ring-opening polymerization of lactones? Uranyl aryloxide-induced intermolecular catalysis.

    PubMed

    Walshe, Aurora; Fang, Jian; Maron, Laurent; Baker, Robert J

    2013-08-01

    The uranyl aryloxide [UO2(OAr)2(THF)2] (Ar = 2,6-(t)Bu2-C6H2) is an active catalyst for the ring-opening cyclo-oligomerization of ε-caprolactone and δ-valerolactone but not for β-butyrolactone, γ-butyrolactone, and rac-lactide. (1)H EXSY measurements give the thermodynamic parameters for exchange of monomer and coordinated THF, and rates of polymerization have been determined. A comprehensive theoretical examination of the mechanism is discussed. From both experiment and theory, the initiation step is intramolecular and in keeping with the accepted mechanism, while computational studies indicate that propagation can go via an intermolecular pathway, which is the first time this has been observed. The lack of polymerization for the inactive monomers has been investigated theoretically and C-H···π interactions stabilize the coordination of the less rigid monomers. PMID:23879703

  19. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

    PubMed

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data. PMID:26133428

  20. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    NASA Astrophysics Data System (ADS)

    Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-01

    The crystal structures of 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  1. Manifestation of structure and intermolecular interactions of biologically active brassinosteroids in infrared spectra

    NASA Astrophysics Data System (ADS)

    Borisevich, N. A.; Skornyakov, I. V.; Khripach, V. A.; Tolstorozhev, G. B.; Zhabinskii, V. N.

    2007-09-01

    We have analyzed the IR spectra obtained for steroidal phytohormones 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, and 28-homocastasterone. The characteristic frequencies of the stretching vibrations of the hydrocarbon groups CH3, CH2, and CH and also the C=O groups in the spectra of brassinolides are higher than in the spectra of castasterones, which makes it possible to identify them from the IR spectra. Study of the spectra of these brassinosteroids in different media (pressed samples in KBr, films, solutions in CHCl3 and CDCl3) allowed us to establish the presence of intermolecular interactions in which C=O and OH groups, OH-OH groups participate, and also the possible formation of intramolecular hydrogen bonds between the OH groups of the molecules.

  2. Influence of intermolecular contacts on the structure of recombinant prolidase from Thermococcus sibiricus

    PubMed Central

    Trofimov, A. A.; Slutskaya, E. A.; Polyakov, K. M.; Dorovatovskii, P. V.; Gumerov, V. M.; Popov, V. O.

    2012-01-01

    Prolidases are peptidases that are specific for dipeptides with proline as the second residue. The structure of recombinant prolidase from the hyperthermophilic archaeon Thermococcus sibiricus (Tsprol) was determined at 2.6 Å resolution. The homodimer of Tsprol is characterized by a complete lack of interactions between the N- and C-terminal domains of the two subunits and hence can be considered to be the most open structure when compared with previously structurally studied prolidases. This structure exists owing to intermolecular coordination bonds between cadmium ions derived from the crystallization solution and histidine residues of a His tag and aspartate and glutamate residues, which link the dimers to each other. This linking leads to the formation of a crystal with a loose packing of protein molecules and low resistance to mechanical influence and temperature increase. PMID:23143231

  3. Intermolecular symmetry-adapted perturbation theory study of large organic complexes

    SciTech Connect

    Heßelmann, Andreas; Korona, Tatiana

    2014-09-07

    Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

  4. Projectile containing metastable intermolecular composites and spot fire method of use

    DOEpatents

    Asay, Blaine W.; Son, Steven F.; Sanders, V. Eric; Foley, Timothy; Novak, Alan M.; Busse, James R.

    2012-07-31

    A method for altering the course of a conflagration involving firing a projectile comprising a powder mixture of oxidant powder and nanosized reductant powder at velocity sufficient for a violent reaction between the oxidant powder and the nanosized reductant powder upon impact of the projectile, and causing impact of the projectile at a location chosen to draw a main fire to a spot fire at such location and thereby change the course of the conflagration, whereby the air near the chosen location is heated to a temperature sufficient to cause a spot fire at such location. The invention also includes a projectile useful for such method and said mixture preferably comprises a metastable intermolecular composite.

  5. Bile salt–induced intermolecular disulfide bond formation activates Vibrio cholerae virulence

    PubMed Central

    Yang, Menghua; Liu, Zhi; Hughes, Chambers; Stern, Andrew M.; Wang, Hui; Zhong, Zengtao; Kan, Biao; Fenical, William; Zhu, Jun

    2013-01-01

    To be successful pathogens, bacteria must often restrict the expression of virulence genes to host environments. This requires a physical or chemical marker of the host environment as well as a cognate bacterial system for sensing the presence of a host to appropriately time the activation of virulence. However, there have been remarkably few such signal–sensor pairs identified, and the molecular mechanisms for host-sensing are virtually unknown. By directly applying a reporter strain of Vibrio cholerae, the causative agent of cholera, to a thin layer chromatography (TLC) plate containing mouse intestinal extracts, we found two host signals that activate virulence gene transcription. One of these was revealed to be the bile salt taurocholate. We then show that a set of bile salts cause dimerization of the transmembrane transcription factor TcpP by inducing intermolecular disulfide bonds between cysteine (C)-207 residues in its periplasmic domain. Various genetic and biochemical analyses led us to propose a model in which the other cysteine in the periplasmic domain, C218, forms an inhibitory intramolecular disulfide bond with C207 that must be isomerized to form the active C207–C207 intermolecular bond. We then found bile salt–dependent effects of these cysteine mutations on survival in vivo, correlating to our in vitro model. Our results are a demonstration of a mechanism for direct activation of the V. cholerae virulence cascade by a host signal molecule. They further provide a paradigm for recognition of the host environment in pathogenic bacteria through periplasmic cysteine oxidation. PMID:23341592

  6. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization

    SciTech Connect

    Christensen, Anders S. E-mail: cui@chem.wisc.edu; Cui, Qiang E-mail: cui@chem.wisc.edu; Elstner, Marcus

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets.

  7. A Colloidal Description of Intermolecular Interactions Driving Fibril-Fibril Aggregation of a Model Amphiphilic Peptide.

    PubMed

    Owczarz, Marta; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

    2015-07-14

    We apply a kinetic analysis platform to study the intermolecular interactions underlying the colloidal stability of dispersions of charged amyloid fibrils consisting of a model amphiphilic peptide (RADA 16-I). In contrast to the aggregation mechanisms observed in the large majority of proteins and peptides, where several elementary reactions involving both monomers and fibrils are present simultaneously, the system selected in this work allows the specific investigation of the fibril-fibril aggregation process. We examine the intermolecular interactions driving the aggregation reaction at pH 2.0 by changing the buffer composition in terms of salt concentration, type of ion as well as type and concentration of organic solvent. The aggregation kinetics are followed by dynamic light scattering, and the experimental data are simulated by Smoluchowski population balance equations, which allow to estimate the energy barrier between two colliding fibrils in terms of the Fuchs stability ratio (W). When normalized on a dimensionless time weighted on the Fuchs stability ratio, the aggregation profiles under a broad range of conditions collapse on a single master curve, indicating that the buffer composition modifies the aggregation kinetics without affecting the aggregation mechanism. Our results show that the aggregation process does not occur under diffusion-limited conditions. Rather, the reaction rate is limited by the presence of an activation energy barrier that is largely dominated by electrostatic repulsive interactions. Such interactions could be reduced by increasing the concentration of salt, which induces charge screening, or the concentration of organic solvent, which affects the dielectric constant. It is remarkable that the dependence of the activation energy on the ionic strength can be described quantitatively in terms of charge screening effects in the frame of the DLVO theory, although specific anion and cation effects are also observed. While anion

  8. Intermolecular Association Provides Specific Optical and NMR Signatures for Serotonin at Intravesicular Concentrations

    PubMed Central

    Nag, Suman; Balaji, J.; Madhu, P. K.; Maiti, S.

    2008-01-01

    Neurotransmitter vesicles contain biomolecules at extraordinarily high concentrations (hundreds of millimoles/liter). Such concentrations can drive intermolecular associations, which may affect vesicular osmolarity and neuronal signaling. Here we investigate whether aqueous serotonin (a monoamine neurotransmitter) forms oligomers at intravesicular concentrations and whether these oligomers have specific spectroscopic signatures that can potentially be used for monitoring neuronal storage and release. We report that, as serotonin concentration is increased from 60 μM to 600 mM, the normalized fluorescence spectrum of serotonin displays a growing long-wavelength tail, with an isoemissive point at 376 nm. The fluorescence decay is monoexponential with a lifetime of 4 ns at low concentrations but is multiexponential with an average lifetime of 0.41 ns at 600 mM. A 600 mM serotonin solution has 30% less osmolarity than expected for monomeric serotonin, indicating oligomer formation. The proton NMR chemical shifts move upfield by as much as 0.3 ppm at 600 mM compared to those at 10 mM, indicating a stacking of the serotonin indole moieties. However, no intermolecular crosspeak is evident in the two-dimensional NMR rotating frame Overhauser effect spectroscopy spectrum even at 600 mM, suggesting that oligomeric structures are possibly weakly coupled. The appearance of a single peak for each proton suggests that the rate of interconversion between the monomeric and the oligomeric structures is faster than 240 Hz. A stopped-flow kinetic experiment also confirms that the rate of dissociation is faster than 100 ms. We conclude that serotonin forms oligomers at intravesicular concentrations but becomes monomeric quickly on dilution. NMR signatures of the oligomers provide potential contrast agents for monitoring the activity of serotonergic neurons in vivo. PMID:18234835

  9. Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5.

    PubMed

    Pradhan, Lagnajeet; Gopal, Sunil; Li, Shichang; Ashur, Shayan; Suryanarayanan, Saai; Kasahara, Hideko; Nam, Hyun-Joo

    2016-03-29

    Heart development in mammalian systems is controlled by combinatorial interactions of master cardiac transcription factors such as TBX5 and NKX2.5. They bind to promoters/enhancers of downstream targets as homo- or heteromultimeric complexes. They physically interact and synergistically regulate their target genes. To elucidate the molecular basis of the intermolecular interactions, a heterodimer and a homodimer of NKX2.5 and TBX5 were studied using X-ray crystallography. Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA and a crystal structure of TBX5 homodimer. The ternary complex structure of NKX2.5 and TBX5 with the target DNA shows physical interactions between the two proteins through Lys158 (NKX2.5), Asp140 (TBX5), and Pro142 (TBX5), residues that are highly conserved in TBX and NKX families across species. Extensive homodimeric interactions were observed between the TBX5 proteins in both crystal structures. In particular, in the crystal structure of TBX5 protein that includes the N-terminal and DNA binding domains, intermolecular interactions were mediated by the N-terminal domain of the protein. The N-terminal domain of TBX5 was predicted to be "intrinsically unstructured", and in one of the two molecules in an asymmetric unit, the N-terminal domain assumes a β-strand conformation bridging two β-sheets from the two molecules. The structures reported here may represent general mechanisms for combinatorial interactions among transcription factors regulating developmental processes. PMID:26926761

  10. Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.

    PubMed

    Zhang, Zhiyong; Sanbonmatsu, Karissa Y; Voth, Gregory A

    2011-10-26

    The ribosome is a very large complex that consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, intermolecular interactions in the Escherichia coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins and to capture functional motions in the ribosome, and then the CG sites are connected by harmonic springs, and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, and they are in good agreement with various experimental data. Nearly all the bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has minimal CG interactions with the rest of the subunit; however, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the intermolecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models. PMID:21910449

  11. Anomalous Reactivity and Selectivity in the Intermolecular Diels-Alder Reactions of Multisubstituted Acyclic Dienes with Geometrical Isomers of Enals.

    PubMed

    Zhou, Jia-Hui; Cai, Sai-Hu; Xu, Yun-He; Loh, Teck-Peng

    2016-05-20

    A Lewis-acid catalyzed intermolecular Diels-Alder reaction between multisubstituted acyclic dienes and the E and Z isomers of α,β-enals was studied. It was found that the diene reacted selectively with the Z-isomer of the α,β-enal. PMID:27132468

  12. A Hands-On Activity to Build Mastery of Intermolecular Forces and Its Impacts on Student Learning

    ERIC Educational Resources Information Center

    Bruck, Laura B.

    2016-01-01

    The intermolecular forces activity presented in this article is designed to foster concept-building through students' use of concrete, manipulative objects, and it was developed to be pedagogically sound. Data analysis via pre- and posttesting and subsequent exam questions indicated that students who had the opportunity to participate in the…

  13. Intermolecular Interactions and Cooperative Effects from Electronic Structure Calculations: An Effective Means for Developing Interaction Potentials for Condensed Phase Simulations

    SciTech Connect

    Xantheas, Sotiris S.

    2004-05-01

    The modeling of the macroscopic properties of homogeneous and inhomogeneous systems via atomistic simulations such as molecular dynamics (MD) or Monte Carlo (MC) techniques is based on the accurate description of the relevant solvent-solute and solvent-solvent intermolecular interactions. The total energy (U) of an n-body molecular system can be formally written as [1,2,3

  14. Comparison of CNES spherical and NASA hemispherical large aperture integrating sources. I - Using a laboratory transfer spectroradiometer. II - Using the SPOT-2 satellite instruments

    NASA Technical Reports Server (NTRS)

    Guenther, B.; Mclean, J.; Leroy, M.; Henry, P.

    1990-01-01

    CNES spherical and NASA hemispherical large aperture calibration sources are examined using a laboratory transfer spectroradiometer and SPOT-2 instruments. The sources, collected at Matra in France during October 1987, are compared in terms of absolute calibration, linearity, and uniformity. The laboratory transfer spectroradiometer data reveal that the calibration results correspond to within about 7 percent absolute accuracy level and the linearity of the CNES source with lamp level is good. It is observed using the satellite data that both sources have an excellent uniformity over a 4 deg field of view.

  15. Strategic directions and mechanisms in technology transfer

    NASA Technical Reports Server (NTRS)

    Mackin, Robert

    1992-01-01

    An outline summarizing the Working Panel discussion related to strategic directions for technology transfer is presented. Specific topics addressed include measuring success, management of technology, innovation and experimentation in the tech transfer process, integration of tech transfer into R&D planning, institutionalization of tech transfer, and policy/legislative resources.

  16. Summary Report on Information Technology Integration Activities For project to Enhance NASA Tools for Coastal Managers in the Gulf of Mexico and Support Technology Transfer to Mexico

    SciTech Connect

    Gulbransen, Thomas C.

    2009-04-27

    Deliverable to NASA Stennis Space Center summarizing summarizes accomplishments made by Battelle and its subcontractors to integrate NASA's COAST visualization tool with the Noesis search tool developed under the Gulf of Mexico Regional Collaborative project.

  17. Pragmatic Transfer.

    ERIC Educational Resources Information Center

    Kasper, Gabriele

    1992-01-01

    Attempting to clarify the concept of pragmatic transfer, this article proposes as a basic distinction Leech/Thomas' dichotomy of sociopragmatics versus pragmalinguistics, presenting evidence for transfer at both levels. Issues discussed include pragmatic universals in speech act realization, conditions for pragmatic transfer, communicative…

  18. Photo-induced electron transfer between a dendritic zinc(II) phthalocyanine and methyl viologen

    NASA Astrophysics Data System (ADS)

    Wang, Yuhua; Chen, Jiangxu; Huang, Lishan; Xie, Shusen; Yang, Hongqin; Peng, Yiru

    2013-01-01

    The intermolecular electron transfer between the carboxylic dendritic zinc(II) phthalocyanines [G1-ZnPc( and G2-ZnPc(] and methyl viologen (MV) is studied by steady-state fluorescence and UV/Vis absorption spectroscopic method. The effect of dendron generation of this series of dendritic phthalocyanines on intermolecular electron transfer is investigated. The results show that the fluorescence emission of these dendritic phthalocyanines could be greatly quenched by MV upon excitation at 610 nm. The Stern-Volmer constant (KSV) of electron transfer is decreased with increasing dendron generations. Our study suggests that these dendritic phthalocyanines are an effective new electron donor and transmission complex and could be used as a potential artificial photosynthesis system.

  19. Theoretical study of vibrational energy transfer of free OH groups at the water-air interface

    NASA Astrophysics Data System (ADS)

    Zheng, Renhui; Wei, Wenmei; Sun, Yuanyuan; Song, Kai; Shi, Qiang

    2016-04-01

    Recent experimental studies have shown that the vibrational dynamics of free OH groups at the water-air interface is significantly different from that in bulk water. In this work, by performing molecular dynamics simulations and mixed quantum/classical calculations, we investigate different vibrational energy transfer pathways of free OH groups at the water-air interface. The calculated intramolecular vibrational energy transfer rate constant and the free OH bond reorientation time scale agree well with the experiment. It is also found that, due to the small intermolecular vibrational couplings, the intermolecular vibrational energy transfer pathway that is very important in bulk water plays a much less significant role in the vibrational energy relaxation of the free OH groups at the water-air interface.

  20. Theoretical study of vibrational energy transfer of free OH groups at the water-air interface.

    PubMed

    Zheng, Renhui; Wei, Wenmei; Sun, Yuanyuan; Song, Kai; Shi, Qiang

    2016-04-14

    Recent experimental studies have shown that the vibrational dynamics of free OH groups at the water-air interface is significantly different from that in bulk water. In this work, by performing molecular dynamics simulations and mixed quantum/classical calculations, we investigate different vibrational energy transfer pathways of free OH groups at the water-air interface. The calculated intramolecular vibrational energy transfer rate constant and the free OH bond reorientation time scale agree well with the experiment. It is also found that, due to the small intermolecular vibrational couplings, the intermolecular vibrational energy transfer pathway that is very important in bulk water plays a much less significant role in the vibrational energy relaxation of the free OH groups at the water-air interface. PMID:27083739