Sample records for intermolecular dipole-dipole interactions

  1. Features of polymer chain dynamics as revealed by intermolecular nuclear magnetic dipole-dipole interaction: model calculations and field-cycling NMR relaxometry.

    PubMed

    Fatkullin, N; Gubaidullin, A; Stapf, S

    2010-03-01

    Proton NMR phenomena such as spin-lattice relaxation, free-induction decays, and solid echoes are analyzed with respect to contributions by intermolecular dipole-dipole interactions in polymer melts. The intermolecular dipole-dipole correlation function is calculated by taking into account the correlation hole effect characteristic for polymer melts. It is shown that the ratio between the intra- and intermolecular contributions to NMR measurands depends on the degree of isotropy of chain dynamics anticipated in different models. This, in particular, refers to the tube/reptation model that is intrinsically anisotropic in clear contrast to n-renormalized Rouse models, where no such restriction is implied. Due to anisotropy, the tube/reptation model predicts that the intramolecular contribution to the dipole-dipole correlation function increases with time relative to the intermolecular contribution. Therefore, the intramolecular contribution is expected to dominate NMR measurands by tendency at long times (or low frequencies). On the other hand, the isotropic nature of the n-renormalized Rouse model suggests that the intermolecular contribution tends to prevail on long-time scales (or low frequencies). Actually, theoretical estimations and the analysis of experimental spin-lattice relaxation data indicate that the intermolecular contribution to proton NMR measurands is no longer negligible for times longer than 10(-7) s-10(-6) s corresponding to frequencies below the megahertz regime. Interpretations not taking this fact into account need to be reconsidered. The systematic investigation of intermolecular interactions in long-time/low frequency proton NMR promises the revelation of the dynamic features of segment displacements relative to each other in polymer melts. PMID:20210412

  2. On the theory of the proton free induction decay and Hahn echo in polymer systems: the role of intermolecular magnetic dipole-dipole interactions and the modified Anderson-Weiss approximation.

    PubMed

    Fatkullin, N; Gubaidullin, A; Mattea, C; Stapf, S

    2012-12-14

    The influence of the intermolecular magnetic dipole-dipole interaction on the free induction decay (FID) as well as on the Hahn-echo of proton spins in polymer melts is investigated. It is shown that for isotropic models of polymer dynamics, when polymer segment displacements do not correlate with an initial chain conformation, the influence of the intermolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing more rapidly with evolution time than the corresponding influence of the intramolecular magnetic dipole-dipole interactions. On the other hand, the situation is inverted for the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing faster with time than the contribution from intermolecular interactions. A simple expression for the relative mean squared displacements of polymer segments from different chains is obtained from the intermolecular contribution to the FID. A modified Anderson-Weiss approximation, taking into account flip-flop transitions between different spins, is proposed and on that basis, the conditions for extracting the relative intermolecular mean squared displacements of polymer segments from the intermolecular contribution to the proton FID is established. Systematic investigations of intermolecular contributions, which were considered as an unimportant factor for FID and Hahn echo in polymer systems by most previous works, actually cannot be considered as negligible and opens a new dimension for obtaining information about polymer dynamics in the millisecond regime. PMID:23249032

  3. On the theory of the proton free induction decay and Hahn echo in polymer systems: The role of intermolecular magnetic dipole-dipole interactions and the modified Anderson-Weiss approximation

    NASA Astrophysics Data System (ADS)

    Fatkullin, N.; Gubaidullin, A.; Mattea, C.; Stapf, S.

    2012-12-01

    The influence of the intermolecular magnetic dipole-dipole interaction on the free induction decay (FID) as well as on the Hahn-echo of proton spins in polymer melts is investigated. It is shown that for isotropic models of polymer dynamics, when polymer segment displacements do not correlate with an initial chain conformation, the influence of the intermolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing more rapidly with evolution time than the corresponding influence of the intramolecular magnetic dipole-dipole interactions. On the other hand, the situation is inverted for the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions to the FID and Hahn echo is increasing faster with time than the contribution from intermolecular interactions. A simple expression for the relative mean squared displacements of polymer segments from different chains is obtained from the intermolecular contribution to the FID. A modified Anderson-Weiss approximation, taking into account flip-flop transitions between different spins, is proposed and on that basis, the conditions for extracting the relative intermolecular mean squared displacements of polymer segments from the intermolecular contribution to the proton FID is established. Systematic investigations of intermolecular contributions, which were considered as an unimportant factor for FID and Hahn echo in polymer systems by most previous works, actually cannot be considered as negligible and opens a new dimension for obtaining information about polymer dynamics in the millisecond regime.

  4. Self-assembly polymorphism of 2,7-bis-nonyloxy-9-fluorenone: solvent induced the diversity of intermolecular dipole-dipole interactions.

    PubMed

    Cui, Lihua; Miao, Xinrui; Xu, Li; Hu, Yi; Deng, Wenli

    2015-02-01

    In this present work, a scanning tunneling microscope (STM) operated under ambient conditions was utilized to probe the self-assembly behavior of 2,7-bis-nonyloxy-9-fluorenone (F-OC9) at the liquid-solid (l/s) interface. On the highly oriented pyrolytic graphite (HOPG) surface, two-dimensional (2D) polymorphism with diversity of intermolecular dipole interactions induced by solvent was found. Solvents ranged from hydrophilic solvating properties with high polarity, such as viscous alkylated acids, to nonpolar alkylated aromatics and alkanes. 1-Octanol and dichloromethane were used to detect the assembly of F-OC9 at the gas-solid (g/s) interface. The opto-electronic properties of F-OC9 were determined by UV-vis and fluorescence spectroscopy in solution. Our results showed that there were tremendous solvent-dependent self-assemblies in 2D ordering for the surface-confined target molecules. When a homologous series of alkanoic acids ranging from heptanoic to nonanoic acid were employed as solvents, the self-assembled monolayer evolved from low-density coadsorbed linear lamellae to a semi-circle-like pattern at relatively high concentrations, which was proven to be the thermodynamic state as it was the sole phase observed at the g/s interface after the evaporation of solvent. Moreover, by increasing the chain length of the alkylated acids, the weight of the carboxylic group, also being the group responsible for the dielectric properties, diminished from heptanoic to nonanoic acid, which could make the easier/earlier appearance of a linear coadsorption effect. However, this was not the case for nonpolar 1-phenyloctane and n-tetradecane: no concentration effect was detected. It showed a strong tendency to aggregate to generate coexistence of separate domains of different phases due to the fast nucleation sites. Furthermore, thermodynamic calculations indicated that the stable structural coexistence of the fluorenone derivative was attributed to synergistic intermolecular dipole-dipole and van der Waals (vdWs) forces at l/s interface. It is believed that the results are of significance to the fields of solvent induced polymorphism assembly and surface science. PMID:25554245

  5. Molecular near-field antenna effect in resonance hyper-Raman scattering: Intermolecular vibronic intensity borrowing of solvent from solute through dipole-dipole and dipole-quadrupole interactions

    SciTech Connect

    Shimada, Rintaro; Hamaguchi, Hiro-o, E-mail: hhama@nctu.edu.tw [Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Road, Hsinchu 30010, Taiwan (China)

    2014-05-28

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solute–solvent dipole–dipole and dipole–quadrupole interactions. It is shown that the infrared active modes arise from the dipole–dipole interaction, whereas Raman active modes from the dipole–quadrupole interaction. It is also shown that vibrations that give strongly polarized Raman bands are weak in the HR molecular near-field effect. The observed solvent HR spectra are simulated with the help of quantum chemical calculations for various orientations and distances of a solvent molecule with respect to the solute. The observed spectra are best simulated with random orientations of the solvent molecule at an intermolecular distance of 10 Å.

  6. Observation of Stueckelberg oscillations in dipole-dipole interactions

    SciTech Connect

    Ditzhuijzen, C. S. E. van; Tauschinsky, Atreju; Van Linden van den Heuvell, H. B. [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands)

    2009-12-15

    We have observed Stueckelberg oscillations in the dipole-dipole interaction between Rydberg atoms with an externally applied radio-frequency field. The oscillating rf field brings the interaction between cold Rydberg atoms in two separated volumes into resonance. We observe multiphoton transitions when varying the amplitude of the rf field and the static electric field offset. The angular momentum states we use show a quadratic Stark shift, which leads to a fundamentally different behavior than linearly shifting states. Both cases are studied theoretically using the Floquet approach and are compared. The amplitude of the sidebands, related to the interaction strength, is given by the Bessel function in the linearly shifting case and by the generalized Bessel function in the quadratically shifting case. The oscillatory behavior of both functions corresponds to Stueckelberg oscillations, an interference effect described by the semiclassical Landau-Zener-Stueckelberg model. The measurements prove coherent dipole-dipole interaction during at least 0.6 mus.

  7. Magnetic Field of a Dipole and the Dipole-Dipole Interaction

    ERIC Educational Resources Information Center

    Kraftmakher, Yaakov

    2007-01-01

    With a data-acquisition system and sensors commercially available, it is easy to determine magnetic fields produced by permanent magnets and to study the dipole-dipole interaction for different separations and angular positions of the magnets. For sufficiently large distances, the results confirm the 1/R[superscript 3] law for the magnetic field…

  8. Artificial Abelian gauge potentials induced by dipole-dipole interactions between Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Cesa, A.; Martin, J.

    2013-12-01

    We analyze the influence of dipole-dipole interactions between Rydberg atoms on the generation of Abelian artificial gauge potentials and fields. When two Rydberg atoms are driven by a uniform laser field, we show that the combined atom-atom and atom-field interactions give rise to nonuniform, artificial gauge potentials. We identify the mechanism responsible for the emergence of these gauge potentials. Analytical expressions for the latter indicate that the strongest artificial magnetic fields are reached in the regime intermediate between the dipole blockade regime and the regime in which the atoms are sufficiently far apart such that atom-light interaction dominates over atom-atom interactions. We discuss the differences and similarities of artificial gauge fields originating from resonant dipole-dipole and van der Waals interactions. We also give an estimation of experimentally attainable artificial magnetic fields resulting from this mechanism and we discuss their detection through the deflection of the atomic motion.

  9. Inclusion of magnetic dipole–dipole and hydrodynamic interactions in implant-assisted magnetic drug targeting

    Microsoft Academic Search

    P. J. Cregg; Kieran Murphy; Adil Mardinoglu

    2009-01-01

    Mathematical modelling of the implant-assisted magnetic drug targeting system of Avilés, Ebner and Ritter is performed. In order to model the agglomeration of particles known to occur in this system, the magnetic dipole–dipole and hydrodynamic interactions are included. Such interactions were calculated previously by Mikkelsen et al. under low magnetic fields (~0.05T) in microfluidic systems. Here, a higher magnetic field

  10. Giant Skyrmions Stabilized by Dipole-Dipole Interactions in Thin Ferromagnetic Films

    SciTech Connect

    Ezawa, Motohiko [Department of Applied Physics, University of Tokyo, Hongo 7-3-1, 113-8656 (Japan)

    2010-11-05

    Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion radius. The radius is controllable by the external magnetic field. It is intriguing that a Skyrmion may have already been observed as a magnetic domain. A salient feature is that a single Skyrmion can be created or destroyed experimentally. An analysis is made also on Skyrmions in chiral magnets.

  11. Short-cycle pulse sequence for dynamical decoupling of local fields and dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Moiseev, S. A.; Skrebnev, V. A.

    2015-02-01

    We propose an alternate pulse sequence for dynamical averaging of the dipole-dipole interactions and inhomogeneity of the magnetic fields in the nuclear-spin system. The sequence contains a short cycle of the periodic resonant pulse excitation that offers new possibilities for implementing the long-lived multiqubit quantum memory on the condensed spin ensembles that are so important for the construction of a universal quantum computer and long-distance quantum communications.

  12. Short cycle pulse sequence for dynamical decoupling of local fields and dipole-dipole interactions

    E-print Network

    S. A. Moiseev; V. A. Skrebnev

    2014-12-11

    We propose a new pulse sequence for dynamical averaging of the dipole-dipole interactions and inhomogeneities of the magnetic fields in the nuclear spin system. The sequence contains a short cycle of the periodic resonant pulse excitation that offers new possibilities for implementing the long-lived multi-qubit quantum memory on the condensed spin ensembles that are so important for construction of universal quantum computer and long-distance quantum communications.

  13. Measurement-induced disturbance between two atoms in Tavis—Cummings model with dipole—dipole interaction

    NASA Astrophysics Data System (ADS)

    Zhang, Guo-Feng; Wang, Xiao; Lü, Guang-Hong

    2014-10-01

    Quantum correlation, measured by measurement-induced disturbance (MID), between two two-level atoms is investigated in detail in Tavis—Cummings model with dipole—dipole interaction (DDI). We find that MID can be determined only by the dipole—dipole interaction between the two atoms when the cavity and atoms are at resonance. Moreover, DDI will have different effects on MID for two different kinds of initial states.

  14. Soliton stability and collapse in the discrete nonpolynomial Schroedinger equation with dipole-dipole interactions

    SciTech Connect

    Gligoric, Goran; Hadzievski, Ljupco [Vinca Institute of Nuclear Sciences, P.O. Box 522, 11001 Belgrade (Serbia); Maluckov, Aleksandra [Faculty of Sciences and Mathematics, University of Nis, P.O. Box 224, 18001 Nis (Serbia); Malomed, Boris A. [Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978 (Israel)

    2009-05-15

    The stability and collapse of fundamental unstaggered bright solitons in the discrete Schroedinger equation with the nonpolynomial on-site nonlinearity, which models a nearly one-dimensional Bose-Einstein condensate trapped in a deep optical lattice, are studied in the presence of the long-range dipole-dipole (DD) interactions. The cases of both attractive and repulsive contact and DD interaction are considered. The results are summarized in the form of stability-collapse diagrams in the parametric space of the model, which demonstrate that the attractive DD interactions stabilize the solitons and help to prevent the collapse. Mobility of the discrete solitons is briefly considered too.

  15. Magnetic relaxation of a system of superparamagnetic particles weakly coupled by dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Déjardin, Pierre-Michel

    2011-12-01

    Long range dipole-dipole interactions in the thermal fluctuations of the magnetization of an assembly of single-domain ferromagnetic particles are considered, ignoring orientational correlations between the particles, so that the evolution of the magnetization orientations may be described by a nonlinear Fokker-Planck equation (FPE) reducing to the usual linear one in the limit of infinite dilution [W. F. Brown Jr., Phys. Rev. 130, 1677 (1963)]. The thermally activated relaxation time scale of the assembly is estimated, leading to a simple and transparent modification of the axially symmetric asymptotes for the superparamagnetic relaxation time.

  16. Controlling the dipole-dipole interaction using NMR composite rf pulses

    NASA Astrophysics Data System (ADS)

    Baudin, Emmanuel

    2014-08-01

    New composite rf pulses are proposed during which the average dipole-dipole interactions within a spin ensemble are controlled, while a global rotation is achieved. The method used to tailor the pulses is based on the average Hamiltonian theory and relies on the geometrical properties of the spin-spin dipolar interaction. I describe several such composite pulses and analyze quantitatively the improvement brought on the control of the NMR dynamics. Numerical simulations show that the magic sandwich pulse sequence, during which the average dipolar field is effectively reversed, is plagued by defects originating from the finite initial and final ?/2 rf pulses. A numerical test based on a classical description of nuclear magnetic resonance is used to check that, when these pulses are replaced by magic composite pulses, the efficiency of the magic sandwich is improved.

  17. Three-Body Bound States in Dipole-Dipole Interacting Rydberg Atoms

    NASA Astrophysics Data System (ADS)

    Kiffner, Martin; Li, Wenhui; Jaksch, Dieter

    2013-12-01

    We show that the dipole-dipole interaction between three identical Rydberg atoms can give rise to bound trimer states. The microscopic origin of these states is fundamentally different from Efimov physics. Two stable trimer configurations exist where the atoms form the vertices of an equilateral triangle in a plane perpendicular to a static electric field. The triangle edge length typically exceeds R?2?m, and each configuration is twofold degenerate due to Kramers degeneracy. The depth of the potential wells and the triangle edge length can be controlled by external parameters. We establish the Borromean nature of the trimer states, analyze the quantum dynamics in the potential wells, and describe methods for their production and detection.

  18. Dipole-dipole interaction between orthogonal dipole moments in time-dependent geometries

    E-print Network

    S. I. Schmid; J. Evers

    2007-09-13

    In two nearby atoms, the dipole-dipole interaction can couple transitions with orthogonal dipole moments. This orthogonal coupling accounts for a number of interesting effects, but strongly depends on the geometry of the setup. Here, we discuss several setups of interest where the geometry is not fixed, such as particles in a trap or gases, by averaging over different sets of geometries. Two averaging methods are compared. In the first method, it is assumed that the internal electronic evolution is much faster than the change of geometry, whereas in the second, it is vice versa. We find that the orthogonal coupling typically survives even extensive averaging over different geometries, albeit with qualitatively different results for the two averaging methods. Typically, one- and two-dimensional averaging ranges modelling, e.g., low-dimensional gases, turn out to be the most promising model systems.

  19. The Range and Shielding of Dipole-Dipole Interactions in Phospholipid Bilayers

    PubMed Central

    Wohlert, Jakob; Edholm, Olle

    2004-01-01

    In molecular dynamics simulations of lipid bilayers, the structure is sensitive to the precise treatment of electrostatics. The dipole-dipole interactions between headgroup dipoles are not long-ranged, but the area per lipid and, through it, other properties of the bilayer are very sensitive to the detailed balance between the perpendicular and in-plane components of the headgroup dipoles. This is affected by the detailed properties of the cutoff scheme or if long-range interactions are included by Ewald or particle-mesh Ewald techniques. Interaction between the in-plane components of the headgroup dipoles is attractive and decays as the inverse sixth power of distance. The interaction is screened by the square of a dielectric permittivity close to the value for water. Interaction between the components perpendicular to the membrane plane is repulsive and decays as the inverse third power of distance. These interactions are screened by a dielectric permittivity of the order 10. Thus, despite the perpendicular components being much smaller in magnitude than the in-plane components, they will dominate the interaction energies at large distances. PMID:15454441

  20. Anisotropy of dipole-dipole interactions in ferroelectric langmuir films of poly(vinylidene fluoride-trifluoroethylene)

    NASA Astrophysics Data System (ADS)

    Aver'yanov, E. M.

    2014-07-01

    The Lorentz tensor components L j for poly(vinylidene fluoride-trifluoroethylene, 70/30) Langmuir-Blodgett films in the ferroelectric phase are determined experimentally. The results indicate that intralayer dipole-dipole interaction between the segments of the polymer is stronger than interlayer interaction. This conclusion agrees with the absence of the critical film thickness below which ferroelectricity would cease to exist.

  1. Radio-frequency-driven dipole-dipole interactions in spatially separated volumes

    NASA Astrophysics Data System (ADS)

    Tauschinsky, Atreju; van Ditzhuijzen, C. S. E.; Noordam, L. D.; van den Heuvell, H. B. Van Linden

    2008-12-01

    Radio-frequency (rf) fields in the MHz range are used to induce resonant energy transfer between cold Rydberg atoms in spatially separated volumes. After laser preparation of the Rydberg atoms, dipole-dipole coupling excites the 49s atoms in one cylinder to the 49p state while the 41d atoms in the second cylinder are transferred down to the 42p state. The energy exchanged between the atoms in this process is 33GHz . An external rf field brings this energy transfer into resonance. The strength of the interaction has been investigated as a function of amplitude (0-1V/cm) and frequency (1-30MHz) of the rf field and as a function of a static-field offset. Multiphoton transitions up to fifth order as well as selection rules prohibiting the process at certain fields have been observed. The width of the resonances has been reduced compared to earlier results by switching off external magnetic fields of the magneto-optical trap, making sub-MHz spectroscopy possible. All features are well reproduced by theoretical calculations taking the strong ac Stark shift due to the rf field into account.

  2. Few-body bound states of dipole-dipole-interacting Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Kiffner, Martin; Huo, Mingxia; Li, Wenhui; Jaksch, Dieter

    2014-05-01

    We show that the resonant dipole-dipole interaction can give rise to bound states between two and three Rydberg atoms with nonoverlapping electron clouds. The dimer and trimer states arise from avoided level crossings between states converging to different fine-structure manifolds in the limit of separated atoms. We analyze the angular dependence of the potential wells, characterize the quantum dynamics in these potentials, and discuss methods for their production and detection. Typical distances between the atoms are of the order of several micrometers which can be resolved in state-of-the-art experiments. The potential depths and typical oscillation frequencies are about one order of magnitude larger as compared to the dimer and trimer states investigated by M. Kiffner et al. [Phys. Rev. A 86, 031401(R) (2012), 10.1103/PhysRevA.86.031401] and M. Kiffner, W. Li, and D. Jaksch [Phys. Rev. Lett. 111, 233003 (2013), 10.1103/PhysRevLett.111.233003], respectively. We find that the dimer and trimer molecules can be aligned with respect to the axis of a weak electric field.

  3. Radio-frequency driven dipole-dipole interactions in spatially separated volumes

    E-print Network

    Atreju Tauschinsky; C. S. E. van Ditzhuijzen; L. D. Noordam; H. B. van Linden van den Heuvell

    2008-10-14

    Radio-frequency (rf) fields in the MHz range are used to induce resonant energy transfer between cold Rydberg atoms in spatially separated volumes. After laser preparation of the Rydberg atoms, dipole-dipole coupling excites the 49s atoms in one cylinder to the 49p state while the 41d atoms in the second cylinder are transferred down to the 42p state. The energy exchanged between the atoms in this process is 33 GHz. An external rf-field brings this energy transfer into resonance. The strength of the interaction has been investigated as a function of amplitude (0-1 V/cm) and frequency (1-30 MHz) of the rf-field and as a function of a static field offset. Multi-photon transitions up to fifth order as well as selection rules prohibiting the process at certain fields have been observed. The width of the resonances has been reduced compared to earlier results by switching off external magnetic fields of the magneto-optical trap, making sub-MHz spectroscopy possible. All features are well reproduced by theoretical calculations taking the strong ac-Stark shift due to the rf-field into account.

  4. Dipole-dipole interaction and its concentration dependence of magnetic fluid evaluated by alternating current hysteresis measurement

    NASA Astrophysics Data System (ADS)

    Ota, Satoshi; Yamada, Tsutomu; Takemura, Yasushi

    2015-05-01

    Magnetic nanoparticles (MNPs) are used as therapeutic and diagnostic tools, such as for treating hyperthermia and in magnetic particle imaging, respectively. Magnetic relaxation is one of the heating mechanisms of MNPs. Brownian and Néel relaxation times are calculated conventional theories; however, the influence of dipole-dipole interactions has not been considered in conventional models. In this study, water-dispersed MNPs of different concentrations and MNPs fixed with an epoxy bond were prepared. dc and ac hysteresis loops for each sample were measured. With respect to both dc and ac hysteresis loops, magnetization decreased with the increase in MNP concentration because of inhibition of magnetic moment rotation due to dipole-dipole interactions. Moreover, intrinsic loss power (ILP) was estimated from the areas of the ac hysteresis loops. The dependence of ILP on the frequency of the magnetic field was evaluated for each MNP concentration. The peak frequency of ILP increased with the decrease in MNP concentration. These peaks were due to Brownian relaxation, as they were not seen with the fixed sample. This indicates that the Brownian relaxation time became shorter with lower MNP concentration, because the weaker dipole-dipole interactions with lower concentrations suggested that the magnetic moments could rotate more freely.

  5. Ising interaction between two qubits composed of the highest magnetic quantum number states through magnetic dipole–dipole interaction

    NASA Astrophysics Data System (ADS)

    Yun, Sang Jae; Kim, Jaewan; Nam, Chang Hee

    2015-04-01

    In quantum information processing, one of the most useful interactions between qubits is the Ising type interaction. We propose a scheme to implement the exact Ising interaction through magnetic dipole–dipole interaction. Although magnetic dipolar interaction is Heisenberg type in general, this interaction can bring about the exact mathematical form of the Ising interaction if qubit levels are chosen among the highest magnetic quantum number states. Real physical systems to which our scheme can be applied include rotational states of molecules, hyperfine states of atoms, or electronic states of nitrogen-vacancy centers in diamond. We analyze the feasibility of our scheme for these systems. For example, when the hyperfine levels of rubidium 87 atoms are chosen as qubits and the distance of the two atoms is 0.1 micrometer, the controlled-Z gate time will be 8.5 ms. We suggest diverse search and study to achieve optimal implementation of this scheme.

  6. Superradiant decay and dipole-dipole interaction of distant atoms in a two-way cascaded cavity QED system

    NASA Astrophysics Data System (ADS)

    Zeeb, Steffen; Noh, Changsuk; Parkins, A. S.; Carmichael, H. J.

    2015-02-01

    We investigate a two-way cascaded cavity QED system consisting of microtoroidal resonators coupled through an optical fiber. Each microtoroidal cavity supports two counterpropagating whispering-gallery modes coupled to single atoms through their evanescent fields. We focus on a pair of atom-microtoroid systems and compute the spectrum of spontaneous emission into the fiber with one atom initially excited. Explicit results are presented for strong-coupling and bad-cavity regimes, where the latter allows the effective atom-atom interaction to be controlled through the atom-cavity coupling and detuning: the atoms exhibit either collective spontaneous emission with no dipole-dipole interaction or a (coherent) dipole-dipole interaction and independent (single-atom) emission. This capacity for switching the character of the interaction is a feature of bidirectional coupling and connects our two-way cascaded system to work on one-dimensional waveguides. Building upon our bad-cavity results, we generalize to many atom-microtoroid systems coupled through an optical fiber.

  7. Superradiant Decay and Dipole-Dipole Interaction of Distant Atoms in a Two-Way Cascaded Cavity QED System

    E-print Network

    Steffen Zeeb; Changsuk Noh; A. S. Parkins; H. J. Carmichael

    2015-01-12

    We investigate a two-way cascaded cavity QED system consisting of microtoroidal resonators coupled through an optical fiber. Each microtoroidal cavity supports two counter-propagating whispering-gallery modes coupled to single atoms through their evanescent fields. We focus on a pair of atom-microtoroid systems and compute the spectrum of spontaneous emission into the fiber with one atom initially excited. Explicit results are presented for strong-coupling and bad-cavity regimes, where the latter allows the effective atom-atom interaction to be controlled through the atom-cavity coupling and detuning: the atoms exhibit either collective spontaneous emission with no dipole-dipole interaction or a (coherent) dipole-dipole interaction and independent (single-atom) emission. This capacity for switching the character of the interaction is a feature of bi-directional coupling and connects our two-way cascaded system to work on one-dimensional waveguides. Building upon our bad-cavity results, we generalize to many atom-microtoroid systems coupled through an optical fiber.

  8. Zero-quantum frequency-selective recoupling of homonuclear dipole-dipole interactions in solid state nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Hu, Kan-Nian; Tycko, Robert

    2009-07-01

    We describe a method for measuring magnetic dipole-dipole interactions, and hence distances, between pairs of like nuclear spins in a many-spin system under magic-angle spinning (MAS). This method employs a homonuclear dipolar recoupling sequence that creates an average dipole-dipole coupling Hamiltonian under MAS with full zero-quantum symmetry, including both secular and flip-flop terms. Flip-flop terms are then attenuated by inserting rotor-synchronized periods of chemical shift evolution between recoupling blocks, leaving an effective Hamiltonian that contains only secular terms to a good approximation. Couplings between specific pairs of nuclear spins can then be selected with frequency-selective ? pulses. We demonstrate this technique, which we call zero-quantum shift evolution assisted homonuclear recoupling, in a series of one-dimensional and two-dimensional C13 NMR experiments at 17.6 T and 40.00 kHz MAS frequency on uniformly C13-labeled L-threonine powder and on the helix-forming peptide MB(i+4)EK, synthesized with a pair of uniformly C13-labeled L-alanine residues. Experimental demonstrations include measurements of distances between C13 sites that are separated by three bonds, placing quantitative constraints on both sidechain and backbone torsion angles in polypeptides.

  9. Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field K. Afrousheh, P. Bohlouli-Zanjani, J. D. Carter, A. Mugford, and J. D. D. Martin

    E-print Network

    Le Roy, Robert J.

    Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field K electric dipole-dipole interactions between atoms in these two states were probed using the linewidth of the two-photon microwave transition 46d5/2 -47d5/2. The presence of a weak magnetic field 0.5 G reduced

  10. Freezing-Out of Tunneling Motion of OH- in NaCl Crystal Due to Dipole-Dipole Interaction

    NASA Astrophysics Data System (ADS)

    Kayanuma, Yosuke; Tanaka, Satoshi

    1986-06-01

    It is noticed that the dipole-dipole interactions between pairs of off-center impurity ions in alkali halide crystals effectively freeze out the tunneling motions of the individual ions and this can be optically detected. The concentration dependence of the infrared absorption line shape of NaCl: OH observed by Wedding-Klein and Nanba et al. (the O-H stretching band) is explained from this point of view. The so-called B band is assigned as due to the stretching mode excitation of the frozen pairs of dipoles. A fairly good fit to the observed spectra is obtained by the virial expansion theory for the line shape function applied to the six-state hopping model with the tunneling parameter of 1 cm-1 hc and with the magnitude of the dipole moment of 3.3 Debye.

  11. Efficient and robust entanglement generation in a many-particle system with resonant dipole-dipole interactions

    E-print Network

    R. G. Unanyan; M. Fleischhauer

    2001-11-19

    We propose and discuss a scheme for robust and efficient generation of many-particle entanglement in an ensemble of Rydberg atoms with resonant dipole-dipole interactions. It is shown that in the limit of complete dipole blocking, the system is isomorphic to a multimode Jaynes-Cummings model. While dark-state population transfer is not capable of creating entanglement, other adiabatic processes are identified that lead to complex, maximally entangled states, such as the N-particle analog of the GHZ state in a few steps. The process is robust, works for even and odd particle numbers and the characteristic time for entanglement generation scales with N^a, with a being less than unity.

  12. Comparison of double-quantum NMR normalization schemes to measure homonuclear dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Saalwächter, Kay

    2014-08-01

    A recent implementation of a double-quantum (DQ) recoupling solid-state NMR experiment, dubbed DQ-DRENAR, provides a quantitative measure of homonuclear dipole-dipole coupling constants in multispin-1/2 systems. It was claimed to be more robust than another, previously known experiment relying on the recording of point-by-point normalized DQ build-up curves. Focusing on the POST-C7 and BaBa-xy16 DQ pulse sequences, I here present an in-depth comparison of both approaches based upon spin-dynamics simulations, stressing that they are based upon very similar principles and that they are largely equivalent when no imperfections are present. With imperfections, it is found that DQ-DRENAR/POST-C7 does not fully compensate for additional signal dephasing related to chemical shifts (CS) and their anisotropy (CSA), which over-compensates the intrinsic CS(A)-related efficiency loss of the DQ Hamiltonian and leads to an apparent cancellation effect. The simulations further show that the CS(A)-related dephasing in DQ-DRENAR can be removed by another phase cycle step or an improved super-cycled wideband version. Only the latter, or the normalized DQ build-up, are unaffected by CS(A)-related signal loss and yield clean pure dipolar-coupling information subject to unavoidable, pulse sequence specific performance reduction related to higher-order corrections of the dipolar DQ Hamiltonian. The intrinsically super-cycled BaBa-xy16 is shown to exhibit virtually no CS(A) related imperfection terms, but its dipolar performance is somewhat more challenged by CS(A) effects than POST-C7, which can however be compensated when applied at very fast MAS (>50 kHz). Practically, DQ-DRENAR uses a clever phase cycle separation to achieve a significantly shorter experimental time, which can also be beneficially employed in normalized DQ build-up experiments.

  13. Position-dependent property of resonant dipole—dipole interaction mediated by localized surface plasmon of an Ag nanosphere

    NASA Astrophysics Data System (ADS)

    Xu, Dan; Wang, Xiao-Yun; Huang, Yong-Gang; Ouyang, Shi-Liang; He, Hai-Long; He, Hao

    2015-02-01

    We use the photon Green-function method to study the quantum resonant dipole–dipole interaction (RDDI) induced by an Ag nanosphere (ANP). As the distance between the two dipoles increases, the RDDI becomes weaker, which is accompanied by the influence of the higher-order mode of the ANP on RDDI declining more quickly than that of the dipole mode. Across a broad frequency range (above 0.05 eV), the transfer rate of the RDDI is nearly constant since the two dipoles are fixed at the proper position. In addition, this phenomenon still exists for slightly different radius of the ANPs. We find that the frequency corresponding to the maximum transfer rate of RDDI exhibits a monotonic decrease by moving away one dipole as the other dipole and the ANP are kept fixed. In addition, the radius of ANP has little effect on this. When the two dipoles are far from the ANP, the maximum transfer rate of the RDDI takes place at the frequency of the dipole mode. In contrast, when the two dipoles are close to the ANP, the higher-order modes come into effect and they will play a leading role in the RDDI if they match the transition frequency of the dipole. Our results may be used in a biological detector and have a certain guiding significance for further application. Project supported by the National Natural Science Foundation of China (Grant Nos. 11347215, 11464014, and 11104113), the Natural Science Foundation of Hunan Province, China (Grant Nos. 13JJ6059 and 13JJB015), and the Natural Science Foundation of Education Department of Hunan Province, China (Grant Nos. 13C750 and 13B091).

  14. Rabi flopping between ground and Rydberg states with dipole-dipole atomic interactions

    E-print Network

    T. A. Johnson; E. Urban; T. Henage; L. Isenhower; D. D. Yavuz; T. G. Walker; M. Saffman

    2007-11-02

    We demonstrate Rabi flopping of small numbers of $\\rm{^{87}Rb}$ atoms between ground and Rydberg states with $n\\le 43$. Coherent population oscillations are observed for single atom flopping, while the presence of two or more atoms decoheres the oscillations. We show that these observations are consistent with van der Waals interactions of Rydberg atoms.

  15. Spin exchange and magnetic dipole-dipole interactions leading to the magnetic superstructures of MAs2O6 (M = Mn, Co, Ni).

    PubMed

    Koo, Hyun-Joo; Whangbo, Myung-Hwan

    2014-04-01

    The three isostructural magnetic oxides MAs2O6 (M = Mn, Co, Ni) containing high-spin M(2+) ions undergo a long-range antiferromagnetic ordering below 30 K, but their ordered magnetic structures are not identical. While CoAs2O6 and NiAs2O6 adopt the commensurate superstructure of q1 = (0, 0, 1/2), MnAs2O6 has the incommensurate superstructure of q2 = (0.055, 0.389, 0.136). The cause for this difference was examined by calculating their spin exchange and magnetic dipole-dipole interaction energies. In CoAs2O6 and NiAs2O6, the strongest M-O···O-M spin exchange, J1, dominates over other exchanges, hence leading to the q1 superstructure. For MnAs2O6, the spin exchanges are not a deciding factor leading to its magnetic superstructure, being all weak and comparable in strengths, but the magnetic dipole-dipole interactions are. PMID:24601528

  16. Rabi Oscillations between Ground and Rydberg States with Dipole-Dipole Atomic Interactions T. A. Johnson, E. Urban, T. Henage, L. Isenhower, D. D. Yavuz, T. G. Walker, and M. Saffman

    E-print Network

    Yavuz, Deniz

    Rabi Oscillations between Ground and Rydberg States with Dipole-Dipole Atomic Interactions T. A November 2007; published 19 March 2008) We demonstrate Rabi oscillations of small numbers of 87 Rb atoms interaction effects between as few as two atoms and by observation of coherent Rabi oscillations between

  17. Geometric quantum discord and entanglement between two atoms in Tavis-Cummings model with dipole-dipole interaction under intrinsic decoherence

    NASA Astrophysics Data System (ADS)

    Fan, Kai-Ming; Zhang, Guo-Feng

    2014-06-01

    Quantum correlation and entanglement, measured by geometric quantum discord (GQD) and concurrence respectively, between two identical two-level atoms are investigated in detail in Tavis-Cummings model with dipole-dipole interaction (DDI) under intrinsic decoherence. The results show that the phase decoherence rate makes the original harmonic vibration with respective to time decay to a stable value. DDI coupling enhances GQD and corcurrence and even avoids entanglement sudden death (ESD). By the introduction of phase decoherence rate, the atom-light field coupling coefficient makes the decay of periodical curves quicker. Evolution periods are shortened as photon number increases, as well DDI and atomic-light field coupling become stronger. Moreover, both GQD and concurrence have nothing to do with frequency of cavity field and atoms for the resonant case.

  18. Effects of chemical exchange and dipole-dipole interactions on the proton relaxation rates of surface histidyl residues in human hemoglobins

    NASA Astrophysics Data System (ADS)

    Madrid, Marcela; Simplaceanu, Virgil; Ho, Nancy T.; Ho, Chien

    Proton spin-spin and spin-lattice relaxation rates of several C2 protons of the histidyl residues located on the surfaces of human normal adult and sickle cell hemoglobins have been measured as a function of the hemoglobin concentration (10 to 16% (wt/ vol)), temperature ( 17 to 37°C), pH (5.7 to 9.0), and resonance frequency (300 to 600 MHz). The relaxation rates are compared to those calculated from the crystal coordinates of the hemoglobin molecule, assuming dipole-dipole interactions modulated by Brownian tumbling. We have found that the initial recoveries of the longitudinal magnetization of several of the C2 proton resonances of the surface histidyl residues investigated are in good agreement with the spin-lattice relaxation rates predicted by this model. On the other hand, the spin-spin relaxation rates are found to increase with the square of the resonance frequency and appear to be affected by the chemical exchange process between the ionized and unionized forms of the imidazole ring of the histidyl residue. From the experimental results, the lifetime of the exchange process is estimated to be 8 ± 3 ?s for all the resonance lines studied in 10% deoxyhemoglobin at pH 7.0 and at 25°C.

  19. Energy Driven Pattern Formation in Planar Dipole-Dipole Systems in the Presence of Weak Noise

    E-print Network

    Jaron Kent-Dobias; Andrew J. Bernoff

    2015-02-24

    We study pattern formation in planar fluid systems driven by intermolecular cohesion (which manifests as a line tension) and dipole-dipole repulsion which are observed in physical systems including ferrofluids in Hele-Shaw cells and Langmuir layers. When the dipolar repulsion is sufficiently strong, domains undergo forked branching reminiscent of viscous fingering. A known difficulty with these models is that the energy associated with dipole-dipole interactions is singular at small distances. Following previous work, we demonstrate how to ameliorate this singularity and show that in the macroscopic limit, only the relative scale of the microscopic details of a system are relevant, and develop an expression for the system energy that depends only on a generalized line tension, {\\Lambda}, that in turn depends logarithmically on that scale. We conduct numerical studies that use energy minimization to find equilibrium states. Following the subcritical bifurcations from the circle, we find a few highly symmetric stable shapes, but nothing that resembles the observed diversity of experimental and dynamically simulated domains. The application of a weak random background to the energy landscape stabilizes a sm\\"org\\r{a}sbord of domain morphologies recovering the diversity observed experimentally. With this technique, we generate a large sample of qualitatively realistic shapes and use them to create an empirical model for extracting {\\Lambda} using only a shape's perimeter and morphology with high accuracy.

  20. Helping Students Assess the Relative Importance of Different Intermolecular Interactions

    ERIC Educational Resources Information Center

    Jasien, Paul G.

    2008-01-01

    A semi-quantitative model has been developed to estimate the relative effects of dispersion, dipole-dipole interactions, and H-bonding on the normal boiling points ("T[subscript b]") for a subset of simple organic systems. The model is based upon a statistical analysis using multiple linear regression on a series of straight-chain organic…

  1. A basic program to transform continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings

    USGS Publications Warehouse

    Zerilli, A.; Bisdorf, R.J.

    1990-01-01

    An interactive HP 9845B BASIC program transforms continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings. The program features graphic presentation of the field dipole-dipole data as well as the transformed half-Schlumberger data. An example of the transformation and its effectiveness in smoothing "high-frequency" noise is given. ?? 1990.

  2. Intermolecular interactions in solid benzene.

    PubMed

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

    2006-01-28

    The lattice dynamics and molecular vibrations of benzene and deuterated benzene crystals are calculated from force constants derived from density-functional theory (DFT) calculations and compared with measured inelastic neutron-scattering spectra. A very small change (0.5%) in lattice parameter is required to obtain real lattice-mode frequencies across the Brillouin zone. There is a strong coupling between wagging and breathing modes away from the zone center. This coupling and sensitivity to cell size arises from two basic interactions. Firstly, comparatively strong interactions that hold the benzene molecules together in layers. These include an intermolecular interaction in which H atoms of one molecule link to the center of the aromatic ring of a neighboring molecule. The layers are held to each other by weaker interactions, which also have components that hold molecules together within a layer. Small changes in the lattice parameters change this second type of interaction and account for the changes to the lattice dynamics. The calculations also reveal a small auxetic effect in that elongation of the crystal along the b axis leads to an increase in internal pressure in the ac plane, that is, elongation in the b direction induces expansion in the a and c directions. PMID:16460192

  3. Intermolecular interactions in solid benzene

    NASA Astrophysics Data System (ADS)

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

    2006-01-01

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

  4. Intermolecular Attractions

    NSDL National Science Digital Library

    The Concord Consortium

    2011-12-11

    Intermolecular attractions are responsible for everything from the temperatures at which substances boil to the power of your immune system in recognizing pathogens and the climbing ability of geckos! Feel the strength of London dispersion and dipole-dipole attractions, explore how intermolecular attractions affect boiling point and solubility, and investigate the special role of hydrogen bonds in DNA. Finally, design your own antibody based on intermolecular attractions.

  5. Energy-driven pattern formation in planar dipole-dipole systems in the presence of weak noise

    NASA Astrophysics Data System (ADS)

    Kent-Dobias, Jaron; Bernoff, Andrew J.

    2015-03-01

    We study pattern formation in planar fluid systems driven by intermolecular cohesion (which manifests as a line tension) and dipole-dipole repulsion, which are observed in physical systems including ferrofluids in Hele-Shaw cells and Langmuir layers. When the dipolar repulsion is sufficiently strong, domains undergo forked branching reminiscent of viscous fingering. A known difficulty with these models is that the energy associated with dipole-dipole interactions is singular at small distances. Following previous work, we demonstrate how to ameliorate this singularity and show that in the macroscopic limit only the scale of the microscopic details relative to the macroscopic extent of a system is relevant and develop an expression for the system energy that depends only on a generalized line tension ? that in turn depends logarithmically on that scale. We conduct numerical studies that use energy minimization to find equilibrium states. Following the subcritical bifurcations from the circle, we find a few highly symmetric stable shapes, but nothing that resembles the observed diversity of experimental and dynamically simulated domains. The application of a weak random background to the energy landscape stabilizes a wide range of domain morphologies recovering the diversity observed experimentally. With this technique, we generate a large sample of qualitatively realistic shapes and use them to create an empirical model for extracting ? with high accuracy using only a shape's perimeter and morphology.

  6. EPR line shifts and line shape changes due to Heisenberg spin exchange and dipole-dipole interactions of nitroxide free radicals in liquids: 9. An alternative method to separate the effects of the two interactions employing ¹?N and ¹?N.

    PubMed

    Bales, Barney L; Meyer, Michelle; Peric, Miroslav

    2014-08-14

    A method to separate the effects of Heisenberg spin exchange (HSE) and dipole-dipole (DD) interactions on EPR spectra of nitroxide spin probes in solution by employing (15)N and (14)N nitroxide spin probes in parallel experiments is developed theoretically and tested experimentally. Comprehensive EPR measurements are reported of 4-oxo-2,2,6,6-tetramethylpiperidine-d16;1-(15)N-1-oxyl (perdeuterated (15)N Tempone; 15pDT), in 70 wt % aqueous glycerol as functions of concentration and temperature. The method, termed the relative broadening constant method (RBCM), is demonstrated by using the present results together with those in the literature that employed perdeuterated (14)N Tempone (14pDT) under identical conditions. In principle, the separation of DD and HSE is dependent on the model of diffusion and molecular-kinetic parameters; however, within present day experimental uncertainties, the RBCM method turns out to be insensitive to the model. The earlier methods to separate DD and HSE by measuring the dispersion component introduced by the two interactions shows general agreement with the RBCM; however, there are discrepancies larger than estimated uncertainties due to random errors. Thus, further support is found for Salikhov's recent theory of the effects of DD and HSE on EPR spectra (Appl. Magn. Reson. 2010, 38, 237); however, detailed confirmation is still lacking. The RBCM affords a possible approach to separate HSE and DD in spectra complicated by slow motion and/or overlap with other resonance lines, allowing the method to be used in situations more complicated than low-viscosity simple liquids. PMID:25035905

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

    SciTech Connect

    González, M.; Lemus-Santana, A.A. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Rodríguez-Hernández, J. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Instituto de Ciencia y Tecnología de Materiales, Universidad de La Habana, Havana (Cuba); Aguirre-Velez, C.I. [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico); Knobel, M. [Institute of Physics “Gleb Wataghin”, UNICAMP, 13083-970 Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada, Unidad Legaria, Instituto Politécnico Nacional, México, DF (Mexico)

    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 ?–? 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.

  8. EPR Line Shifts and Line Shape Changes Due to Heisenberg Spin Exchange and Dipole-Dipole Interactions of Nitroxide Free Radicals in Liquids: 8. Further Experimental and Theoretical Efforts to Separate the Effects of the Two Interactions

    PubMed Central

    Peric, Mirna; Bales, Barney L; Peric, Miroslav

    2012-01-01

    The work in Part 6 of this series (J. Phys. Chem. A 2009, 113, 4930), addressing the task of separating the effects of Heisenberg spin exchange (HSE) and dipole-dipole (DD) interactions on EPR spectra of nitroxide spin probes in solution, is extended experimentally and theoretically. Comprehensive measurements of perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (pDT) in squalane, a viscous alkane, paying special attention to lower temperatures and lower concentrations were carried out in an attempt to focus on DD, the lesser understood of the two interactions. Theoretically, the analysis has been extended to include the recent comprehensive treatment by Salikhov (Appl. Magn. Reson. 2010, 38, 237). In dilute solutions, both interactions (1) introduce a dispersion component, (2) broaden the lines, and (3) shift the lines. DD introduces a dispersion component proportional to the concentration and of opposite sign to that of HSE. Equations relating the EPR spectral parameters to the rate constants due HSE and DD have been derived. By employing non-linear least-squares fitting of theoretical spectra to a simple analytical function and the proposed equations, the contributions of the two interactions to items (1)–(3) may be quantified and compared with the same parameters obtained by fitting experimental spectra. This comparison supports the theory in its broad predictions, however, at low temperatures, the DD contribution to the experimental dispersion amplitude does not increase linearly with concentration. We are unable to deduce if this discrepancy is due to inadequate analysis of the experimental data or an incomplete theory. A key new aspect of the more comprehensive theory is that there is enough information in the experimental spectra to find items (1)–(3) due to both interactions; however, in principle, appeal must be made to a model of molecular diffusion to separate the two. The permanent diffusion model is used to illustrate the separation in this work. In practice, because the effects of DD are dominated by HSE, negligible error is incurred by using the model-independent extreme DD limit of the spectral density functions which means that DD and HSE may be separated without appealing to a particular model. PMID:22288424

  9. Electron paramagnetic resonance line shifts and line shape changes due to heisenberg spin exchange and dipole-dipole interactions of nitroxide free radicals in liquids 8. Further experimental and theoretical efforts to separate the effects of the two interactions.

    PubMed

    Peric, Mirna; Bales, Barney L; Peric, Miroslav

    2012-03-22

    The work in part 6 of this series (J. Phys. Chem. A 2009, 113, 4930), addressing the task of separating the effects of Heisenberg spin exchange (HSE) and dipole-dipole interactions (DD) on electron paramagnetic resonance (EPR) spectra of nitroxide spin probes in solution, is extended experimentally and theoretically. Comprehensive measurements of perdeuterated 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl (pDT) in squalane, a viscous alkane, paying special attention to lower temperatures and lower concentrations, were carried out in an attempt to focus on DD, the lesser understood of the two interactions. Theoretically, the analysis has been extended to include the recent comprehensive treatment by Salikhov (Appl. Magn. Reson. 2010, 38, 237). In dilute solutions, both interactions (1) introduce a dispersion component, (2) broaden the lines, and (3) shift the lines. DD introduces a dispersion component proportional to the concentration and of opposite sign to that of HSE. Equations relating the EPR spectral parameters to the rate constants due to HSE and DD have been derived. By employing nonlinear least-squares fitting of theoretical spectra to a simple analytical function and the proposed equations, the contributions of the two interactions to items 1-3 may be quantified and compared with the same parameters obtained by fitting experimental spectra. This comparison supports the theory in its broad predictions; however, at low temperatures, the DD contribution to the experimental dispersion amplitude does not increase linearly with concentration. We are unable to deduce whether this discrepancy is due to inadequate analysis of the experimental data or an incomplete theory. A new key aspect of the more comprehensive theory is that there is enough information in the experimental spectra to find items 1-3 due to both interactions; however, in principle, appeal must be made to a model of molecular diffusion to separate the two. The permanent diffusion model is used to illustrate the separation in this work. In practice, because the effects of DD are dominated by HSE, negligible error is incurred by using the model-independent extreme DD limit of the spectral density functions, which means that DD and HSE may be separated without appealing to a particular model. PMID:22288424

  10. Phosphate Stabilization of Intermolecular Interactions

    PubMed Central

    Jackson, Shelley N.; Wang, Hay-Yan J.; Yergey, Alfred; Woods, Amina S.

    2008-01-01

    Receptor heteromerization is an important phenomenon that results from the interaction of epitopes on two receptors. Previous studies have suggested the possibility of Dopamine D2- NMDA receptors’ interaction. We believe that the interaction is through an acidic epitope of the NMDA NR1 subunit (KVNSEEEEEDA) and a basic epitope of the D2 third intracellular loop (VLRRRRRKRVN), which was shown to also interact with the Adenosine A2A receptor. In previous work we highlighted the role of certain amino acid residues, mainly two or more adjacent arginine on one peptide and two or more adjacent glutamate, or aspartate, or a phosphorylated residue on the other in the formation of noncovalent complexes (NCX) between epitopes. In the present work, we use the phosphorylated (KVNSpEEEEEDA), non-phosphorylated (KVNSEEEEEDA) and modified (KVNpSAAAAAAA) forms of the NMDA epitope that possibly interact with the D2 epitope to investigate the gas-phase stability of the NCXs as a function of the nominal energy given to the NCX ion as it enters the collision cell. In addition to theoretical calculations, the experimental data was used to calculate the stability of each electrostatic complex versus that of the dimer of KVNSpEEEEEDA. Our results demonstrate the importance of the phosphate group in stabilizing molecular interactions and that appreciably higher collision energies are required to completely dissociate any of the three different NCX ions that are formed through electrostatic interaction in comparison to the energy required to dissociate the KVNpSEEEEEDA dimer ion, which is mainly kept together by hydrogen bonding. This study emphasizes ionic bonds stability and their importance to protein structure as their potent electrostatic attractions can in the gas phase surpass the strength of covalent bonds. PMID:16396502

  11. Reduced intermolecular interaction in organic ultrathin films

    NASA Astrophysics Data System (ADS)

    Gordan, O. D.; Himcinschi, C.; Zahn, D. R. T.; Cobet, C.; Esser, N.; Braun, W.

    2006-04-01

    Submonolayer sensitivity was achieved using in situ ellipsometry to monitor the evolution of the dielectric function of tris(8-hydroxyquinoline)-aluminum(III) (Alq3) layers from submonolayer coverage to thick bulklike layers. The Alq3 layers were deposited under ultrahigh vacuum conditions onto hydrogen passivated silicon. The characteristic vacuum-ultraviolet (VUV) absorption lines of Alq3 were detected using synchrotron radiation as light source. In such ultrathin films the absorption lines corresponding to molecular transitions of the Alq3 are found to be spectrally blueshifted with respect to bulklike layers. We attribute the shift to the effect of reduced intermolecular interaction in the submonolayer regime.

  12. Coherent dipole-dipole coupling between two single atoms at a Förster resonance

    E-print Network

    Sylvain Ravets; Henning Labuhn; Daniel Barredo; Lucas Béguin; Thierry Lahaye; Antoine Browaeys

    2014-05-30

    Resonant energy transfers, i.e. the non-radiative redistribution of an electronic excitation between two particles coupled by the dipole-dipole interaction, lie at the heart of a variety of chemical and biological phenomena, most notably photosynthesis. In 1948, F\\"orster established the theoretical basis of fluorescence resonant energy transfer (FRET), paving the ground towards the widespread use of FRET as a "spectroscopic ruler" for the determination of nanometer-scale distances in biomolecules. The underlying mechanism is a coherent dipole-dipole coupling between particles, as already recognized in the early days of quantum mechanics, but this coherence was not directly observed so far. Here, we study, both spectroscopically and in the time domain, the coherent, dipolar-induced exchange of electronic excitations between two single Rydberg atoms separated by a controlled distance as large as 15 microns, and brought into resonance by applying a small electric field. The coherent oscillation of the system between two degenerate pair states occurs at a frequency that scales as the inverse third power of the distance, the hallmark of dipole-dipole interactions. Our results not only demonstrate, at the most fundamental level of two atoms, the basic mechanism underlying FRET, but also open exciting prospects for active tuning of strong, coherent interactions in quantum many-body systems.

  13. Sudden transitions of trace distance discord of dipole-dipole coupled two qubits

    E-print Network

    Zheng-Da Hu; Jicheng Wang; Yixin Zhang; Ye-Qi Zhang

    2014-12-01

    We investigate the exact dynamics of trace distance discord by considering two qubits under dephasing whose states belong to a class of $X$ states beyond Bell diagonal form. The necessary condition for the occurrence of freezing trace distance discord is found and compared with that of entropic discord. For an illustration, we consider two interacting qubits coupled to independent reservoirs and demonstrate these dynamical properties of trace distance discord. It is interesting to find that the freezing trace distance discord exists even for $X$ states without maximally mixed marginals and can be tuned by dipole-dipole coupling of two qubits. Moreover, we consider the initial extended Werner-like states and investigate the differences between trace distance discord and entanglement. The influences of initial state and the dipole-dipole coupling of the two qubits on the dynamics of nonclassical correlations are explored.

  14. Intermolecular interactions in a radiation field via the method of induced moments

    SciTech Connect

    Salam, A. [Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486 (United States)

    2006-01-15

    Molecular quantum electrodynamics is employed to calculate a generalized formula for the energy shift between a pair of molecules that have electric polarizability of arbitrary multipole order and are in the presence of an intense electromagnetic field. In contrast to a previous calculation of the dipole-dipole contribution, which required fourth-order time-dependent perturbation theory for its evaluation, the present approach involves calculating the interaction between the multipole moments induced at each center by the incident beam and the resonant multipole-multipole coupling tensor together with the average value of the spatial correlation function of the displacement field for an N-photon state. The theory developed applies to the situation where the molecular pair is held fixed relative to the direction of propagation of the radiation field or is allowed to be completely randomly oriented. Explicit results are obtained for dipole-quadrupole and quadrupole-quadrupole polarizable molecules. For oriented systems the energy shift for linear and circular polarizations is examined for incident radiation propagating in directions parallel and perpendicular to the intermolecular join, and the asymptotic behavior is obtained at the limits of short and large separation distance. After performing a pair orientation average, the energy shift in the near zone is found to exhibit an R{sup -1} power-law behavior with separation distance, while the far zone has a modulated R{sup -2} dependence in all of the cases considered. None of the energy shifts obtained display discriminatory characteristics, with respect to either the handedness of the incident beam or the individual species.

  15. Controlling dipole-dipole frequency shifts in a lattice-based optical atomic clock

    E-print Network

    D. E. Chang; Jun Ye; M. D. Lukin

    2003-08-12

    Motivated by the ideas of using cold alkaline earth atoms trapped in an optical lattice for realization of optical atomic clocks, we investigate theoretically the perturbative effects of atom-atom interactions on a clock transition frequency. These interactions are mediated by the dipole fields associated with the optically excited atoms. We predict resonance-like features in the frequency shifts when constructive interference among atomic dipoles occur. We theoretically demonstrate that by fine-tuning the coherent dipole-dipole couplings in appropriately designed lattice geometries, the undesirable frequency shifts can be greatly suppressed.

  16. 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…

  17. Quantifying cooperative intermolecular interactions for improved carbon dioxide capture materials

    NASA Astrophysics Data System (ADS)

    de Lange, Katrina M.; Lane, Joseph R.

    2011-08-01

    We have optimized the geometry and calculated interaction energies for over 100 different complexes of CO2 with various combinations of electron accepting (Lewis acid) and electron donating (Lewis base) molecules. We have used the recently developed explicitly correlated coupled cluster singles doubles and perturbative triples [CCSD(T)-F12] methods and the associated VXZ-F12 (where X = D,T,Q) basis sets. We observe only modest changes in the geometric parameters of CO2 upon complexation, which suggests that the geometry of CO2 adsorbed in a nanoporous material should be similar to that of CO2 in gas phase. When CO2 forms a complex with two Lewis acids via the two electron rich terminal oxygen atoms, the interaction energy is less than twice what would be expected for the same complex involving a single Lewis acid. We consider a series of complexes that exhibit simultaneous CO2-Lewis acid and CO2-Lewis base intermolecular interactions, with total interaction energies spanning 14.1-105.9 kJ mol-1. For these cooperative complexes, we find that the total interaction energy is greater than the sum of the interaction energies of the constituent complexes. Furthermore, the intermolecular distances of the cooperative complexes are contracted as compared to the constituent complexes. We suggest that metal-organic-framework or similar nanoporous materials could be designed with adsorption sites specifically tailored for CO2 to allow cooperative intermolecular interactions, facilitating enhanced CO2 adsorption.

  18. Studies of pilocarpine:carbomer intermolecular interactions.

    PubMed

    Zoppi, Ariana; Linck, Yamila Garro; Monti, Gustavo A; Genovese, Diego B; Jimenez Kairuz, Alvaro F; Manzo, Rubén H; Longhi, Marcela R

    2012-05-10

    The interactions between pilocarpine (PIL) and the anionic polyelectrolyte carbomer (CBR) were investigated. The effects of the chemical interactions on the chemical stability of the drug also were evaluated. The binary system was characterized by nuclear magnetic resonance techniques, Fourier-transform infrared spectroscopy (FT-IR), X-ray powder diffraction, scanning electron microscopy (SEM) and thermal analysis. The experiments showed that the complex, prepared by freeze-drying, is a solid amorphous form different from its precursors, thereby offering an interesting alternative for the preparation of extended release matrices. The solution stability of PIL was studied at pH 7 and 8, at 70 °C. The PIL solution stability was evaluated alone and in the presence of CBR. Results indicated that the drug in the presence of the polymer is 3.3 and 3.5 times more stable, at pH 7 and pH 8, respectively, than the drug without CBR. The activation energy and the frequency factor, according to Arrhenius plot, were estimated to be 13.9 ± 0.4 and 14.8 ± 0.5 kcalmol(-1), and 6.1 ± 0.3 and 7.6 ± 0.3, with and without the polymer, respectively. PMID:22349054

  19. Intermolecular interactions and the thermodynamic properties of supercritical fluids.

    PubMed

    Yigzawe, Tesfaye M; Sadus, Richard J

    2013-05-21

    The role of different contributions to intermolecular interactions on the thermodynamic properties of supercritical fluids is investigated. Molecular dynamics simulation results are reported for the energy, pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, Joule-Thomson coefficient, and speed of sound of fluids interacting via both the Lennard-Jones and Weeks-Chandler-Andersen potentials. These properties were obtained for a wide range of temperatures, pressures, and densities. For each thermodynamic property, an excess value is determined to distinguish between attraction and repulsion. It is found that the contributions of intermolecular interactions have varying effects depending on the thermodynamic property. The maxima exhibited by the isochoric and isobaric heat capacities, isothermal compressibilities, and thermal expansion coefficient are attributed to interactions in the Lennard-Jones well. Repulsion is required to obtain physically realistic speeds of sound and both repulsion and attraction are necessary to observe a Joule-Thomson inversion curve. Significantly, both maxima and minima are observed for the isobaric and isochoric heat capacities of the supercritical Lennard-Jones fluid. It is postulated that the loci of these maxima and minima converge to a common point via the same power law relationship as the phase coexistence curve with an exponent of ? = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids. PMID:23697423

  20. Constraints on exotic dipole-dipole couplings between electrons at the micrometer scale

    E-print Network

    Kotler, Shlomi; Kimball, Derek F Jackson

    2015-01-01

    New constraints on exotic dipole-dipole interactions between electrons at the micrometer scale are established, based on a recent measurement of the magnetic interaction between two trapped $^{88}$Sr$^+$ ions. For light bosons (mass $\\le$ 0.1 eV) we obtain $90\\%$ confidence intervals on pseudo-scalar and axial-vector mediated interaction strengths of $\\left|g_P^eg_P^e/4\\pi\\hbar c\\right|\\le 1.5\\times 10^{-3}$ and $\\left|g_A^eg_A^e/4\\pi\\hbar c\\right|\\le 1.2\\times 10^{-17}$, respectively. These bounds significantly improve on previous work for this mass range. Assuming CPT invariance, these constraints are compared to those on anomalous electron-positron interactions, derived from positronium hyperfine spectroscopy. For axial-vector mediated interaction the electron-electron constraints are six orders of magnitude more stringent than the electron-positron constraints. Bounds on torsion gravity are also derived and compared with previous work performed at different length scales.

  1. Coherent dipole-dipole coupling between two single Rydberg atoms at an electrically-tuned Förster resonance

    NASA Astrophysics Data System (ADS)

    Ravets, Sylvain; Labuhn, Henning; Barredo, Daniel; Béguin, Lucas; Lahaye, Thierry; Browaeys, Antoine

    2014-12-01

    Resonant energy transfers, the non-radiative redistribution of an electronic excitation between two particles coupled by the dipole-dipole interaction, lie at the heart of a variety of phenomena, notably photosynthesis. In 1948, Förster established the theory of fluorescence resonant energy transfer (FRET) between broadband, nearly-resonant donors and acceptors. The 1/R6 scaling of the energy transfer rate, where R is the distance between particles, enabled widespread use of FRET as a `spectroscopic ruler’ for determining nanometric distances in biomolecules. The underlying mechanism is a coherent dipolar coupling between particles, as recognized in the early days of quantum mechanics, but this coherence has not been directly observed so far. Here we study, spectroscopically and in the time domain, the coherent, dipolar-induced exchange of excitations between two Rydberg atoms separated by up to 15 ?m, and brought into resonance by applying an electric field. Coherent oscillation of the system between two degenerate pair states then occurs at a frequency scaling as 1/R3, the hallmark of resonant dipole-dipole interactions. Our results not only demonstrate, at the fundamental level of two atoms, the basic mechanism underlying FRET, but also open exciting prospects for active tuning of strong, coherent interactions in quantum many-body systems.

  2. Effective dipole-dipole interactions in multilayered dipolar Bose ...

    E-print Network

    2013-07-10

    Jul 10, 2013 ... such as a superfluid-to-crystal quantum phase transition [13], supersolids [14], or even .... We assume that an external field polarizes the ... means of a rotating magnetic field [55]. ... from shape resonances, the wave function ? = ?(r,t) of the dipolar BEC ..... Consequently, the matrix of the system of. Eqs. (17) ...

  3. Energy decomposition analysis of covalent bonds and intermolecular interactions.

    PubMed

    Su, Peifeng; Li, Hui

    2009-07-01

    An energy decomposition analysis method is implemented for the analysis of both covalent bonds and intermolecular interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their density functional theory analogs. For HF methods, the total interaction energy from a supermolecule calculation is decomposed into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Møller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham density functional interaction energy is decomposed into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. Insights are provided by the energy decomposition analysis into H(2), methane C-H, and ethane C-C covalent bond formation, CH(3)CH(3) internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, BH(3)NH(3) and BH(3)CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions. PMID:19586091

  4. Energy decomposition analysis of covalent bonds and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Su, Peifeng; Li, Hui

    2009-07-01

    An energy decomposition analysis method is implemented for the analysis of both covalent bonds and intermolecular interactions on the basis of single-determinant Hartree-Fock (HF) (restricted closed shell HF, restricted open shell HF, and unrestricted open shell HF) wavefunctions and their density functional theory analogs. For HF methods, the total interaction energy from a supermolecule calculation is decomposed into electrostatic, exchange, repulsion, and polarization terms. Dispersion energy is obtained from second-order Møller-Plesset perturbation theory and coupled-cluster methods such as CCSD and CCSD(T). Similar to the HF methods, Kohn-Sham density functional interaction energy is decomposed into electrostatic, exchange, repulsion, polarization, and dispersion terms. Tests on various systems show that this algorithm is simple and robust. Insights are provided by the energy decomposition analysis into H2, methane C-H, and ethane C-C covalent bond formation, CH3CH3 internal rotation barrier, water, ammonia, ammonium, and hydrogen fluoride hydrogen bonding, van der Waals interaction, DNA base pair formation, BH3NH3 and BH3CO coordinate bond formation, Cu-ligand interactions, as well as LiF, LiCl, NaF, and NaCl ionic interactions.

  5. Role of Intermolecular Interactions of Vesicular Stomatitis Virus Nucleoprotein in RNA Encapsidation

    Microsoft Academic Search

    Xin Zhang; Todd J. Green; Jun Tsao; Shihong Qiu; Ming Luo

    2008-01-01

    The crystal structure of the vesicular stomatitis virus nucleoprotein (N) in complex with RNA reveals extensive and specific intermolecular interactions among the N molecules in the 10-member oligomer. What roles these interactions play in encapsidating RNA was studied by mutagenesis of the N protein. Three N mutants intended for disruption of the intermolecular interactions were designed and coexpressed with the

  6. 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

  7. 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…

  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 ?M 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. Characterization of intermolecular interaction between two substances when one substance does not possess any characteristic peak

    NASA Astrophysics Data System (ADS)

    Li, Xiaopei; Fan, Xiaokun; Huang, Kun; Liu, Huizhou; Zhao, Ying; Wei, Yongju; Liu, Cuige; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2014-07-01

    We explore whether it is possible to use 2D correlation spectrum to characterize intermolecular interactions between two solutes dissolved in the same solution when one substance does not possesses any characteristic peak. We demonstrate that the interaction can be manifested by characteristic cross peaks in 2D asynchronous correlated spectrum. The above cross peaks reflect the subtle spectral variations on the characteristic peak of another solute under intermolecular interaction. On the other hand, 2D synchronous spectrum is not suitable to characterize intermolecular interaction since the cross peaks contain irremovable interfering parts. The terbium-chloride/benzamide/methanol system is used to demonstrate that this approach is applicable in the real chemical system.

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

    E-print Network

    Mukamel, Shaul

    and dispersive interactions of polarizable molecules are expressed in terms of generalized (nonretarded) charge originating from correlated charge density fluctuations [1­6] control many important chemical and biological on accurate predictions of intermolecular forces. The most widely studied and best un- derstood interactions

  11. Matter-wave solitons supported by field-induced dipole-dipole repulsion with spatially modulated strength

    NASA Astrophysics Data System (ADS)

    Li, Yongyao; Liu, Jingfeng; Pang, Wei; Malomed, Boris A.

    2013-11-01

    We demonstrate the existence of one- and two-dimensional (1D and 2D, respectively) bright solitons in the Bose-Einstein condensate with repulsive dipole-dipole interactions induced by a combination of dc and ac polarizing fields, oriented perpendicular to the plane in which the BEC is trapped, assuming that the strength of the fields grows in the radial (r) direction faster than r3. Stable tightly confined 1D and 2D fundamental solitons, twisted solitons in 1D, and solitary vortices in 2D are found in a numerical form. The fundamental solitons remain robust under the action of an expulsive potential, which is induced by the interaction of the dipoles with the polarizing field. The confinement and scaling properties of the soliton families are explained analytically. The Thomas-Fermi approximation is elaborated for fundamental solitons. The mobility of the fundamental solitons is limited to the central area. Stable 1D even and odd solitons are also found in the setting with a double-well modulation function, along with a regime of Josephson oscillations.

  12. INFRARED SPECTROSCOPY METHOD REVEALS HYDROGEN BONDING AND INTERMOLECULAR INTERACTION BETWEEN COMPONENTS IN POLYMER BLENDS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An infrared spectroscopy method was devised to uncover evidence of hydrogen bonding and intermolecular interaction between components in solid poly(lactic acid) (PHA) and poly(hydroxyester ether) (PHEE) blends. The methods compares Gaussian/Lorentzian deconvoluted infrared spectra of the polymer bl...

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

  14. Ab initio investigation of intermolecular interactions in solid benzene

    E-print Network

    O. Bludsky; M. Rubes; P. Soldan

    2008-01-04

    A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and non-additive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the solid benzene are reproduced, and the value of 480 meV/molecule is calculated for its cohesive energy.

  15. Ab initio investigation of intermolecular interactions in solid benzene

    E-print Network

    Bludsky, O; Soldan, P; 10.1103/PhysRevB.77.092103

    2009-01-01

    A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and non-additive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the solid benzene are reproduced, and the value of 480 meV/molecule is calculated for its cohesive energy.

  16. Distinguishability and chiral stability in solution: Effects of decoherence and intermolecular interactions

    SciTech Connect

    Han, Heekyung [Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario M5T 3M7 (Canada); Wardlaw, David M., E-mail: dwardlaw@mun.ca [Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador A1C 5S7 (Canada); Frolov, Alexei M., E-mail: afrolov@uwo.ca [Department of Applied Mathematics, University of Western Ontario, London, Ontario N6H 5B7 (Canada)

    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.

  17. Intermolecular interactions in the bilirubin-cholate-silica system

    NASA Astrophysics Data System (ADS)

    Vlasova, N. N.; Golovkova, L. P.; Severinovskaya, O. V.

    2007-06-01

    Bilirubin-cholate interactions in aqueous solutions were studied. The constants of binding of bilirubin with taurocholate dimers and taurodeoxycholate trimers were calculated. The adsorption of bilirubin and cholates on the surface of highly dispersed silica was studied. It was shown that taurine-conjugated cholates are poorly adsorbed from micellar solutions on the silica surface, the specific amount of bilirubin adsorbed decreases with increasing concentration of cholates in the solution, the affinity of free bilirubin for the silica surface is independent of the nature of the cholic acid, and that the affinity of cholate-bilirubin complexes for the silica surface is lower than the affinity of free bilirubin.

  18. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    SciTech Connect

    Alocci, Davide, E-mail: alodavide@gmail.com [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy)] [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Bernini, Andrea, E-mail: andrea.bernini@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy)] [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); Niccolai, Neri, E-mail: neri.niccolai@unisi.it [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy) [Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via A. Fiorentina 1, 53100 Siena (Italy); SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena (Italy)

    2013-07-12

    Highlights: •3D atom depth analysis is proposed to identify different layers in protein structures. •Amino acid contents for each layers have been analyzed for a large protein dataset. •Charged amino acids in the most external layer are present at very different extents. •Atom depth indexes of K residues reflect their side chains flexibility. •Mobile surface charges can be responsible for long range protein–protein recognition. -- Abstract: The systematic analysis of amino acid distribution, performed inside a large set of resolved protein structures, sheds light on possible mechanisms driving non random protein–protein approaches. Protein Data Bank entries have been selected using as filters a series of restrictions ensuring that the shape of protein surface is not modified by interactions with large or small ligands. 3D atom depth has been evaluated for all the atoms of the 2,410 selected structures. The amino acid relative population in each of the structural layers formed by grouping atoms on the basis of their calculated depths, has been evaluated. We have identified seven structural layers, the inner ones reproducing the core of proteins and the outer one incorporating their most protruding moieties. Quantitative analysis of amino acid contents of structural layers identified, as expected, different behaviors. Atoms of Q, R, K, N, D residues are increasingly more abundant in going from core to surfaces. An opposite trend is observed for V, I, L, A, C, and G. An intermediate behavior is exhibited by P, S, T, M, W, H, F and Y. The outer structural layer hosts predominantly E and K residues whose charged moieties, protruding from outer regions of the protein surface, reorient free from steric hindrances, determining specific electrodynamics maps. This feature may represent a protein signature for long distance effects, driving the formation of encounter complexes and the eventual short distance approaches that are required for protein–protein functional interactions.

  19. Amyloid nanospheres from polyglutamine rich peptides: assemblage through an intermolecular salt bridge interaction.

    PubMed

    Mishra, Rahul; Thakur, Ashwani K

    2015-04-14

    We have shown the conversion of an amyloid fiber forming nucleation pathway of polyglutamine (polyGln) to a non-nucleated pathway, generating nanospherical amyloid particles. This is achieved by engineering an intermolecular salt bridge interaction between the positively charged lysine and the negatively charged glutamate residues, in two polyGln rich peptides. The mechanism of their formation is characterized by chromatography, infrared, fluorescence and imaging methods. PMID:25692827

  20. 1H NMR study on the intermolecular interactions of macrocyclic and single ?-amino acids

    NASA Astrophysics Data System (ADS)

    Quevedo, Rodolfo; Pabón, Laura; Quevedo-Acosta, Yovanny

    2013-06-01

    Through analysis of 1H NMR spectra, evidence was found for intermolecular interactions between macrocyclic amino acid derivatives from L-tyrosine and their importance in the formation of aggregates in solution. It was also shown that both macrocyclic and simple amino acids are capable of retaining alcohol molecules through hydrogen bonding, where the alcohol molecule acts as a proton donor and the amino group acts as an acceptor.

  1. Long range intermolecular interactions between the alkali diatomics Na2, K2, and NaK

    NASA Astrophysics Data System (ADS)

    Zemke, Warren T.; Byrd, Jason N.; Michels, H. Harvey; Montgomery, John A.; Stwalley, William C.

    2010-06-01

    Long range interactions between the ground state alkali diatomics Na2-Na2, K2-K2, Na2-K2, and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential ELR=Eelec+Edisp+Eind is shown to accurately represent the intermolecular interactions for these systems at long range.

  2. Long range intermolecular interactions between the alkali diatomics Na(2), K(2), and NaK.

    PubMed

    Zemke, Warren T; Byrd, Jason N; Michels, H Harvey; Montgomery, John A; Stwalley, William C

    2010-06-28

    Long range interactions between the ground state alkali diatomics Na(2)-Na(2), K(2)-K(2), Na(2)-K(2), and NaK-NaK are examined. Interaction energies are first determined from ab initio calculations at the coupled-cluster with singles, doubles, and perturbative triples [CCSD(T)] level of theory, including counterpoise corrections. Long range energies calculated from diatomic molecular properties (polarizabilities and dipole and quadrupole moments) are then compared with the ab initio energies. A simple asymptotic model potential E(LR)=E(elec)+E(disp)+E(ind) is shown to accurately represent the intermolecular interactions for these systems at long range. PMID:20590191

  3. Intermolecular interactions in dioxane-water solutions of substituted coumarins according to ultrasonic data

    NASA Astrophysics Data System (ADS)

    Mandakmare, A. U.; Narwade, M. L.; Tayade, D. T.; Naik, A. B.

    2014-12-01

    Density, ultrasonic velocity of pure dioxane (Dx) and ligands, 4,6-dimethyl-7-hydroxycoumarin (L1), 6-ethyl-7-hydroxy-4-methylcoumarin (L2), and 3-chloro-7-hydroxy-4-methylcoumarin (L3) in different percent of Dx-water mixture have been investigated at 303.15 K. Acoustical parameters such as adiabatic compressibility (?), intermolecular free length ( L f), acoustical impedance ( Z), relative association ( R A), apparent molar compressibility (??), and apparent molar volume (?V) have also been evaluated from the experimental data of density and ultrasonic velocity. An excellent correlation between a given parameters is observed at all percent of dioxane-water and the result suggests nature of intermolecular interactions between the components.

  4. 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.

  5. 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

  6. 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

  7. Electric field effects on the intermolecular interactions in water whiskers: insight from structures, energetics, and properties.

    PubMed

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

    2015-03-12

    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 paper, 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. Overall, these results help shed new insight on the effects of electric fields on water whisker formation. PMID:25695357

  8. Kinetics of Intermolecular Interaction during Protein Folding of Reduced Cytochrome c

    PubMed Central

    Nishida, Shinpei; Nada, Tomokazu; Terazima, Masahide

    2004-01-01

    Kinetics of intermolecular interaction between reduced cytochrome c (Cyt c) protein and solvent during the protein-refolding process is studied by monitoring the time dependence of apparent diffusion coefficient (D) using the pulsed-laser-induced transient grating technique. The refolding was triggered by photoinduced reduction of unfolded Fe(III) Cyt c in 3.5 M guanidine hydrochloride (GdnHCl) solution and the change in the diffusion coefficient was monitored in time domain. The relationship between D and the protein conformations under equilibrium condition were investigated at various GdnHCl concentrations using a photolabeling reagent. The time dependence of the observed transient grating signal was analyzed using these data and two models: a continuous change model of the intermolecular interaction and a two-state model. It was found that the TG signals in various time ranges can be consistently reproduced well by the two-state model. The dynamics of D is expressed well by a single exponential function with a rate constant of 22 ± 7 s?1 in a whole time range. The folding process of Cyt c is discussed based on these observations. PMID:15454461

  9. 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 sheets which suggests a switch from very small corrugation to stick-slip behavior at interlayer distances smaller than 6 Å. Our results for gas phase clusters agree reasonably with methods using more demanding quantum chemical methods to treat the van der Waals interactions, thus providing support for the relatively fast density functional theory methods used here for studying water-graphene interactions in nanoscale systems. PMID:25356833

  10. About intermolecular interactions in binary and ternary solutions of some azo-benzene derivatives

    NASA Astrophysics Data System (ADS)

    Ivan, Liliana Mihaela; Closca, Valentina; Burlea, Marin; Rusu, Elena; Airinei, Anton; Dorohoi, Dana Ortansa

    2015-02-01

    The nature and strength of the intermolecular interactions in the solutions of three azo-benzene derivatives (ADi, i = 1, 2, 3) were established by solvatochromic effects in solvents with different electric permittivities, refractive indices and Kamlet-Taft constants. A quantum mechanical analysis corroborated with spectral data offered information about the excited state dipole moments and polarizabilities of the studied compounds. The separation of the supply of universal and specific interactions to the total spectral shift was made based on the regression coefficients from the equations describing the solvatochromic effect. Supplementary information about the composition of the first solvation shell and the energy in the solute-solvent molecular pairs were obtained analyzing the ternary solutions of ADi, i = 1, 2, 3 compounds in solvent mixture Methanol (M) + n-Hexane (H).

  11. About intermolecular interactions in binary and ternary solutions of some azo-benzene derivatives.

    PubMed

    Ivan, Liliana Mihaela; Closca, Valentina; Burlea, Marin; Rusu, Elena; Airinei, Anton; Dorohoi, Dana Ortansa

    2015-02-01

    The nature and strength of the intermolecular interactions in the solutions of three azo-benzene derivatives (ADi, i=1, 2, 3) were established by solvatochromic effects in solvents with different electric permittivities, refractive indices and Kamlet-Taft constants. A quantum mechanical analysis corroborated with spectral data offered information about the excited state dipole moments and polarizabilities of the studied compounds. The separation of the supply of universal and specific interactions to the total spectral shift was made based on the regression coefficients from the equations describing the solvatochromic effect. Supplementary information about the composition of the first solvation shell and the energy in the solute-solvent molecular pairs were obtained analyzing the ternary solutions of ADi, i=1, 2, 3 compounds in solvent mixture Methanol (M)+n-Hexane (H). PMID:25168003

  12. 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.

  13. Unrestricted absolutely localized molecular orbitals for energy decomposition analysis: theory and applications to intermolecular interactions involving radicals.

    PubMed

    Horn, Paul R; Sundstrom, Eric Jon; Baker, Thomas A; Head-Gordon, Martin

    2013-04-01

    Radical-closed shell and radical-radical intermolecular interactions are less well-understood than those between closed shell species. With the objective of gaining additional insight, this work reports a generalization of the absolutely localized molecular orbital (ALMO) energy decomposition analysis (EDA) to open shell fragments, described by self-consistent field methods, such as standard density functional theory. The ALMO-EDA variationally partitions an intermolecular interaction energy into three separate contributions; frozen orbital interactions, polarization, and charge transfer. The first examples involve comparison of the interactions of alkanes and alkyl radicals (methyl radical, methane, tertiary butyl radical, and isobutane) with sodium, potassium, hydronium, and ammonium cations. A second series of examples involve benzene cation interacting with a series of nucleophiles in both on-top and side-on geometries. The ALMO-EDA yields a variety of interesting insights into the relative roles of its component contributions as the interacting partners and their geometries are changed. PMID:23574220

  14. The same number of optimized parameters scheme for determining intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul; Jensen, Frank; Jørgensen, Poul

    2015-03-01

    We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave function parameters for the noninteracting system is the same as for the interacting system. This ensures a delicate balance between the quality of the monomer and dimer finite basis set calculations. We compare the SNOOP scheme to the uncorrected and counterpoise schemes theoretically as well as numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP interaction energies calculated using a given basis set are of similar quality as those determined by basis set extrapolation of counterpoise-corrected results obtained at a similar computational cost.

  15. 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 (?H0 = -149.6 kJ mol-1 and ?S0 = -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.

  16. The same number of optimized parameters scheme for determining intermolecular interaction energies.

    PubMed

    Kristensen, Kasper; Ettenhuber, Patrick; Eriksen, Janus Juul; Jensen, Frank; Jørgensen, Poul

    2015-03-21

    We propose the Same Number Of Optimized Parameters (SNOOP) scheme as an alternative to the counterpoise method for treating basis set superposition errors in calculations of intermolecular interaction energies. The key point of the SNOOP scheme is to enforce that the number of optimized wave function parameters for the noninteracting system is the same as for the interacting system. This ensures a delicate balance between the quality of the monomer and dimer finite basis set calculations. We compare the SNOOP scheme to the uncorrected and counterpoise schemes theoretically as well as numerically. Numerical results for second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster with single, double, and approximate triple excitations (CCSD(T)) show that the SNOOP scheme in general outperforms the uncorrected and counterpoise approaches. Furthermore, we show that SNOOP interaction energies calculated using a given basis set are of similar quality as those determined by basis set extrapolation of counterpoise-corrected results obtained at a similar computational cost. PMID:25796240

  17. Dynamical theory for modeling dipole-dipole interactions in a microcavity: The Green dyadic approach

    E-print Network

    Leung, Pui-Tak "Peter"

    silver nanoparticles,9 that of the enhanced energy-transfer process between donors and acceptors,10 medium of infinite extent on each side of the microcavity,13,14 and iii the modeling of a single pair. Though our following theory is based on

  18. Spectroscopic Observation of Resonant Electric Dipole-Dipole Interactions between Cold Rydberg Atoms

    E-print Network

    Le Roy, Robert J.

    Atoms K. Afrousheh, P. Bohlouli-Zanjani, D. Vagale, A. Mugford, M. Fedorov, and J. D. D. Martin between cold Rydberg atoms were observed using microwave spectroscopy. Laser-cooled 85Rb atoms pulse transferred a fraction of these Rydberg atoms to the 46p3=2 state. A second microwave pulse

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

    PubMed

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

    2014-08-14

    Intermolecular potential models for water and alkanes describe pure component properties fairly well, but fail to reproduce properties of water-alkane mixtures. Understanding interactions between water and non-polar molecules like alkanes is important not only for the hydrocarbon industry but has implications to biological processes as well. Although non-polar solutes in water have been widely studied, much less work has focused on water in non-polar solvents. In this study we calculate the solubility of water in different alkanes (methane to dodecane) at ambient conditions where the water content in alkanes is very low so that the non-polar water-alkane interactions determine solubility. Only the alkane-rich phase is simulated since the fugacity of water in the water rich phase is calculated from an accurate equation of state. Using the SPC/E model for water and TraPPE model for alkanes along with Lorentz-Berthelot mixing rules for the cross parameters produces a water solubility that is an order of magnitude lower than the experimental value. It is found that an effective water Lennard-Jones energy ?(W)/k = 220?K is required to match the experimental water solubility in TraPPE alkanes. This number is much higher than used in most simulation water models (SPC/E-?(W)/k = 78.2?K). It is surprising that the interaction energy obtained here is also higher than the water-alkane interaction energy predicted by studies on solubility of alkanes in water. The reason for this high water-alkane interaction energy is not completely understood. Some factors that might contribute to the large interaction energy, such as polarizability of alkanes, octupole moment of methane, and clustering of water at low concentrations in alkanes, are examined. It is found that, though important, these factors do not completely explain the anomalously strong attraction between alkanes and water observed experimentally. PMID:25134597

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  1. Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin

    SciTech Connect

    Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T. (Globel Phasing); (Scripps)

    2012-03-13

    The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic {alpha}-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 {angstrom} resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 {alpha}-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle.

  2. Dimensionality of intermolecular interactions in layered crystals by electronic-structure theory and geometric analysis.

    PubMed

    George, Janine; Deringer, Volker L; Dronskowski, Richard

    2015-02-01

    Two-dimensional (2D) and layered structures gained a lot of attention in the recent years ("post-graphene era"). The chalcogen cyanides S(CN)(2) and Se(CN)(2) offer themselves as interesting model systems to study layered inorganic crystal structures; both are built up from cyanide molecules connected by chalcogen bonds (ChBs). Here, we investigate ChBs and their cooperativity directly within the layers of the S(CN)(2) and Se(CN)(2) crystal structures and, furthermore, in putative O(CN)(2) and Te(CN)(2) crystal structures derived therefrom. Moreover, we determine the energetic contributions of ChBs within the layers to the overall stabilization energy. To compare these structures not only energetically but also geometrically, we derive a direction-dependent root mean square of the Cartesian displacement, a possible tool for further computational investigations of layered compounds. The molecular chains connected by ChBs are highly cooperative but do not influence each other when combined to layers: the ChBs are nearly orthogonal in terms of energy when connected to the same chalcogen acceptor atom. Layers built up from ChBs account for 41% to 79% of the overall interaction energy in the crystal. This provides new, fundamental insight into the meaning of ChBs, and therefore directed intermolecular interactions, for the stability of crystal structures. PMID:25363246

  3. Anti-plasticizing effect of amorphous indomethacin induced by specific intermolecular interactions with PVA copolymer.

    PubMed

    Ueda, Hiroshi; Aikawa, Shohei; Kashima, Yousuke; Kikuchi, Junko; Ida, Yasuo; Tanino, Tadatsugu; Kadota, Kazunori; Tozuka, Yuichi

    2014-09-01

    The mechanism of how poly(vinyl alcohol-co-acrylic acid-co-methyl methacrylate) (PVA copolymer) stabilizes an amorphous drug was investigated. Solid dispersions of PVA copolymer, poly(vinyl pyrrolidone) (PVP), and poly(vinyl pyrrolidone-co-vinyl acetate) (PVPVA) with indomethacin (IMC) were prepared. The glass transition temperature (Tg)-proportion profiles were evaluated by differential scanning calorimetry (DSC). General Tg profiles decreasing with the IMC ratio were observed for IMC-PVP and IMC-PVPVA samples. An interesting antiplasticizing effect of IMC on PVA copolymer was observed; Tg increased up to 20% IMC ratio. Further addition of IMC caused moderate reduction with positive deviation from theoretical values. Specific hydrophilic and hydrophobic interactions between IMC and PVA copolymer were revealed by infrared spectra. The indole amide of IMC played an important role in hydrogen bonding with PVA copolymer, but not with PVP and PVPVA. X-ray diffraction findings and the endotherm on DSC profiles suggested that PVA copolymer could form a semicrystalline structure and a possibility of correlation of the crystallographic nature with its low hygroscopicity was suggested. PVA copolymer was able to prevent crystallization of amorphous IMC through both low hygroscopicity and the formation of a specific intermolecular interaction compared with that with PVP and PVPVA. PMID:24890320

  4. Intermolecular vs molecule–substrate interactions: A combined STM and theoretical study of supramolecular phases on graphene/Ru(0001)

    PubMed Central

    Roos, Michael; Uhl, Benedikt; Künzel, Daniela; Hoster, Harry E; Groß, Axel

    2011-01-01

    Summary The competition between intermolecular interactions and long-range lateral variations in the substrate–adsorbate interaction was studied by scanning tunnelling microscopy (STM) and force field based calculations, by comparing the phase formation of (sub-) monolayers of the organic molecules (i) 2-phenyl-4,6-bis(6-(pyridin-3-yl)-4-(pyridin-3-yl)pyridin-2-yl)pyrimidine (3,3'-BTP) and (ii) 3,4,9,10-perylene tetracarboxylic-dianhydride (PTCDA) on graphene/Ru(0001). For PTCDA adsorption, a 2D adlayer phase was formed, which extended over large areas, while for 3,3'-BTP adsorption linear or ring like structures were formed, which exclusively populated the areas between the maxima of the moiré structure of the buckled graphene layer. The consequences for the competing intermolecular interactions and corrugation in the adsorption potential are discussed and compared with the theoretical results. PMID:22003444

  5. Oligopeptide repeats in the yeast protein Sup35p stabilize intermolecular prion interactions

    PubMed Central

    Parham, Steven N.; Resende, Catarina G.; Tuite, Mick F.

    2001-01-01

    The nuclear-encoded Sup35p protein is responsible for the prion-like [PSI+] determinant of yeast, with Sup35p existing largely as a high molecular weight aggregate in [PSI+] strains. Here we show that the five oligopeptide repeats present at the N-terminus of Sup35p are responsible for stabilizing aggregation of Sup35p in vivo. Sequential deletion of the oligopeptide repeats prevented the maintenance of [PSI+] by the truncated Sup35p, although deletants containing only two repeats could be incorporated into pre-existing aggregates of wild-type Sup35p. The mammalian prion protein PrP also contains similar oligopeptide repeats and we show here that a human PrP repeat (PHGGGWGQ) is able functionally to replace a Sup35p oligopeptide repeat to allow stable [PSI+] propagation in vivo. Our data suggest a model in which the oligopeptide repeats in Sup35p stabilize intermolecular interactions between Sup35p proteins that initiate establishment of the aggregated state. Modulating repeat number therefore alters the rate of yeast prion conversion in vivo. Furthermore, there appears to be evolutionary conservation of function of the N-terminally located oligopeptide repeats in prion propagation. PMID:11331577

  6. 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. (Aarhus); (UWA); (UC)

    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.

  7. Hyperpolarizabilities for the one-dimensional infinite single-electron periodic systems: I. Analytical solutions under dipole-dipole correlations

    E-print Network

    Shidong Jiang; Minzhong Xu

    2005-05-14

    The analytical solutions for the general-four-wave-mixing hyperpolarizabilities $\\chi^{(3)}(-(w_1+w_2+w_3);w_1,w_2,w_3)$ on infinite chains under both Su-Shrieffer-Heeger and Takayama-Lin-Liu-Maki models of trans-polyacetylene are obtained through the scheme of dipole-dipole correlation. Analytical expressions of DC Kerr effect $\\chi^{(3)}(-w;0,0,w)$, DC-induced second harmonic generation $\\chi^{(3)}(-2w;0,w,w)$, optical Kerr effect $\\chi^{(3)}(-w;w,-w,w)$ and DC-electric-field-induced optical rectification $\\chi^{(3)}(0;w,-w,0)$ are derived. By including or excluding ${\\bf \

  8. Mapping Protein Family Interactions: Intramolecular and Intermolecular Protein Family Interaction Repertoires in the PDB and Yeast

    Microsoft Academic Search

    Jong Park; Michael Lappe; Sarah A. Teichmann

    In the postgenomic era, one of the most interesting and important chal- lenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist indepen- dently. To study the large-scale patterns and

  9. Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

    NASA Astrophysics Data System (ADS)

    Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D.

    2014-10-01

    We perform an ab initio computational study of molecular complexes with the general formula CF3X—B that involve one trifluorohalomethane CF3X (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 (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single ?-pair (C2H4) and two ?-pairs (C2H2). 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 ?-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 ?-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.

  10. Photo-induced spin transition of Iron(III) compounds with pi-pi intermolecular interactions.

    PubMed

    Hayami, Shinya; Hiki, Kenji; Kawahara, Takayoshi; Maeda, Yonezo; Urakami, Daisuke; Inoue, Katsuya; Ohama, Mitsuo; Kawata, Satoshi; Sato, Osamu

    2009-01-01

    Iron(III) spin-crossover compounds [Fe(pap)(2)]ClO(4) (1), [Fe(pap)(2)]BF(4) (2), [Fe(pap)(2)]PF(6) (3), [Fe(qsal)(2)]NCS (4), and [Fe(qsal)(2)]NCSe (5) (Hpap=2-(2-pyridylmethyleneamino)phenol and Hqsal=2-[(8-quinolinylimino)methyl]phenol) were prepared and their spin-transition properties investigated by magnetic susceptibility and Mössbauer spectroscopy measurements. The iron(III) compounds exhibited spin transition with thermal hysteresis. Single crystals of the iron(III) compounds were obtained as suitable solvent adducts for X-ray analysis, and structures in high-spin (HS) and low-spin (LS) states were revealed. Light-induced excited-spin-state trapping (LIESST) effects of the iron(III) compounds were induced by light irradiation at 532 nm for 1-3 and at 800 nm for 4 and 5. The activation energy E(a) and the low-temperature tunneling rate k(HL)(T-->0) of iron(III) LIESST compound 1 were estimated to be 1079 cm(-1) and 2.4x10(-8) s(-1), respectively, by HS-->LS relaxation experiments. The Huang-Rhys factor S of 1 was also estimated to be 50, which was similar to that expected for iron(II) complexes. It is thought that the slow relaxation in iron(III) systems is achieved by the large structural distortion between HS and LS states. Introduction of strong intermolecular interactions, such as pi-pi stacking, can also play an important role in the relaxation behavior, because it can enhance the structural distortion of the LIESST complex. PMID:19191246

  11. Studies on the stability and intermolecular interactions of cellulose and polylactide systems using molecular modeling

    NASA Astrophysics Data System (ADS)

    Karst, David T.

    The stability and intermolecular interactions of cellulose and polylactide (PLA) systems were studied using molecular modeling. This work explains how grafting various groups onto cellulose increases hydrolysis of the glycosidic linkages of cellulose. A substituent increases hydrolysis of cellulose by serving as an anchor to the end of the cleaved cellulose to which it is bonded, making it less mobile, and allowing it to have stronger interactions than those in pure hydrolyzed cellulose. Hydrolysis increases with the size of the substituent. Molecules sorbed but not grafted to cellulose do not increase hydrolysis. Hydrolysis mainly occurs at glucoses bonded to the substituent. A substituent on the sixth carbon position of cellulose increases hydrolysis to a greater extent than does one on the second or third carbon position. The effect of blending poly(L-lactide) (PLLA) and poly(D-lactide) (PDLA) and the effect of various arrangements of L-lactide and D-lactide in poly(L-lactide-co-D-lactide) on the resistance of polylactide (PLA) to hydrolysis has been explained. Among the homopolymer blends, the 50/50 PLLA/PDLA blend has the greatest resistance to hydrolysis due to its having stronger hydrogen-bonding and van der Waals forces than pure PLLA or PDLA. The change in potential energy for hydrolysis decreases linearly with increasing % PLLA or % PDLA from 0 to 50%. Among the copolymers containing a given percentage of L-lactide and D-lactide, those containing longer blocks of L-lactide and D-lactide have greater resistance to hydrolysis compared to those with shorter blocks or random copolymers because copolymers with longer blocks are more stable before hydrolysis compared to the other copolymers. Among the copolymers with long blocks of L- and D-lactide, those containing 50% L-lactide have a greater resistance to hydrolysis compared to the copolymers with 26% or 74% L-lactide. Blends or copolymers that are mirror images of each other have the same resistance to hydrolysis. The effect of the structure of a molecule on its ability to adsorb onto PLA has been explained. The adsorbate-PLA interaction energies calculated for various disperse dyes and drugs agree with experimental data for their percent sorption onto PLA.

  12. 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...

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

    Microsoft Academic Search

    M. Plato; K. Moebius; M. E. Michel-Beyerle; M. Bixon; Joshua. Jortner

    1988-01-01

    In this paper the intermolecular overlap approximation is used to calculate the relative magnitudes of the electronic transfer integrals between the excited singlet state (¹P*) of the bacteriochlorophyll dimer (P) and the accessory bacteriochlorophyll (B) and between B⁻ and bacteriopheopytin (H), along the L and M subunits of the reaction center (RC) of Rps. viridis. The ratio of the electron-transfer

  14. Iodine Bonding Stabilizes Iodomethane in MIDAS Pesticide. Theoretical Study of Intermolecular Interactions between

    E-print Network

    Glaser, Rainer

    Iodine Bonding Stabilizes Iodomethane in MIDAS Pesticide. Theoretical Study of Intermolecular resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5

  15. Variation of intermolecular interaction and local lattice distortion of parahydrogen crystals upon vibrational excitation

    Microsoft Academic Search

    Robert M. Dickson; Takeshi Oka

    1998-01-01

    When a hydrogen molecule in a parahydrogen crystal is excited to a high vibrational overtone state, its electronic properties vary significantly since the energy of excitation is a sizable fraction of the energies of the excited electronic states. Thus the vibrational excitation leads to a significant variation of the intermolecular potential and resultant local distortion of the crystal lattice. Such

  16. Universal scaling of potential energy functions describing intermolecular interactions. II. The halide-water and alkali metal-water interactions

    SciTech Connect

    Werhahn, Jasper C.; Akase, Dai; Xantheas, Sotiris S.

    2014-08-14

    The scaled forms of the newly introduced generalized potential energy functions (PEFs) describing intermolecular interactions [J. Chem. Phys. xx, yyyyy (2011)] have been used to fit the ab-initio minimum energy paths (MEPs) for the halide- and alkali metal-water systems X-(H2O), X=F, Cl, Br, I, and M+(H2O), M=Li, Na, K, Rb, Cs. These generalized forms produce fits to the ab-initio data that are between one and two orders of magnitude better in the ?2 than the original forms of the PEFs. They were found to describe both the long-range, minimum and repulsive wall of the potential energy surface quite well. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gB-e6) potentials were found to best fit the ab-initio data. Furthermore, a single set of parameters of the reduced form was found to describe all candidates within each class of interactions. The fact that in reduced coordinates a whole class of interactions can be represented by a single PEF, yields the simple relationship between the molecular parameters associated with energy (well depth, ?), structure (equilibrium distance, rm) and spectroscopy (anharmonic frequency, ?):€? = A? (? /?)1/ 2 /rm + B?? /rm 3 , where A and B are constants depending on the underlying PEF. This more general case of Badger’s rule has been validated using the experimentally measured frequencies of the hydrogen bonded OH stretching vibrations in the halide-water series.

  17. Quantum phase transitions for two coupled cavities with dipole-interaction atoms

    NASA Astrophysics Data System (ADS)

    Tan, Lei; Zhang, Yu-Qing; Liu, Wu-Ming

    2011-12-01

    We investigate the quantum phase transitions for two weakly coupled atom-cavity sites. The interatomic dipole-dipole interaction is considered. Our numerical results show that the dipole-dipole interaction is a crucial parameter for the quantum phase transition. For small atom-cavity detuning, the “superfluid” becomes more and more obvious with the increase of the dipole-dipole interaction. In addition, the strong dipole-dipole interaction can lead the atomic excitation to be suppressed completely, and only the photonic excitation exists for the ground states. When the atom-cavity detuning is comparable with the dipole-dipole interaction, the dipole-dipole interaction enlarges the positive detunings, which is in favor of exhibiting superfluid photonic states. While for the negative detuning, the dipole-dipole interaction will reduce it, and contribute to the formation of the polaritonic insulator states. The cases for extended models have also been briefly analyzed. We also discuss how to find these novel phenomena in future experiments.

  18. Influence of intermolecular interactions on solid state luminescence of imidazopyridines: theoretical interpretations using FMO-TDDFT and ONIOM approaches.

    PubMed

    Shigemitsu, Yasuhiro; Mutai, Toshiki; Houjou, Hirohiko; Araki, Koji

    2014-07-28

    6-Cyano-2-(2'-hydroxyphenyl)imidazo[1,2-a]-pyridine (6CN-HPIP) shows polymorph-dependent luminescence with the three different crystal forms exhibiting the packing-controlled tuning of bright colors, orange, yellow, and red. The distinctive emission in aggregated states was treated with finite cluster models and analyzed by means of quantum chemistry calculations. The influence of structural displacements and intermolecular interactions in the crystalline state on solid state luminescence was examined in detail using the Fragment Molecular Orbital (FMO) scheme, suitable for studies of aggregated molecular systems. The FMO pair interaction analysis of the S1-S0 emission maxima indicated that the intermolecular side-to-side interactions cause hypsochromic shifts; facial interactions induce bathochromic shifts; and crystal packing effects in total induce hypsochromic shifts. The FMO predictions of the emission maxima offered qualitatively satisfactory agreements with the experiments. However, the small cluster models including up to 17 molecules did not reach quantitative convergence, i.e., the emission colour order among them was not well reproduced. PMID:24598819

  19. Cooperativity of anion⋯? and ?⋯? interactions regulates the self-assembly of a series of carbene proligands: Towards quantitative analysis of intermolecular interactions with Hirshfeld surface

    NASA Astrophysics Data System (ADS)

    Samanta, Tapastaru; Dey, Lingaraj; Dinda, Joydev; Chattopadhyay, Shyamal Kumar; Seth, Saikat Kumar

    2014-06-01

    The cooperative effect of weak non-covalent forces between anions and electron deficient aromatics by ?⋯? stacking of a series of carbene proligands (1-3) have been thoroughly explored by crystallographic studies. Structural analysis revealed that the anion⋯? and ?⋯? interactions along with intermolecular hydrogen bonding mutually cooperate to facilitate the assembling of the supramolecular framework. The ?⋯? and corresponding anion⋯? interactions have been investigated in the title carbene proligands despite their association with counter ions. The presence of the anion in the vicinity of the ?-system leads to the formation of anion⋯?/?⋯?/?⋯anion network for an inductive stabilization of the assemblies. To assess the dimensionality of the supramolecular framework consolidated by cooperative anion⋯?/?⋯? interactions and hydrogen bonding, different substituent effects in the carbene backbone have been considered to tune these interactions. These facts show that the supramolecular framework based on these cooperative weak forces may be robust enough for application in molecular recognition. The investigation of close intermolecular interactions between the molecules via Hirshfeld surface analyses is presented in order to reveal subtle differences and similarities in the crystal structures. The decomposition of the fingerprint plot area provides a percentage of each intermolecular interaction, allowing for a quantified analysis of close contacts within each crystal.

  20. Structural aspects of intermolecular interactions in the solid state of 1,4-dibenzylpiperazines bearing nitrile or amidine groups

    PubMed Central

    Rezler, Mateusz; ?o?ek, Teresa; Wolska, Irena; Maciejewska, Dorota

    2014-01-01

    The crystal structures of the title 1,4-bis(4-cyanobenzyl)piperazine (1) and 1,4-bis(4-amidinobenzyl)piperazine tetrahydrochloride tetrahydrate (2) are reported. Compound (1) crystallizes in the triclinic space group and compound (2) in the monoclinic space group P21 /n. In both (1) and (2) the asymmetric unit contains one half of the molecule because the central piperazine rings were located across a symmetry center. The packing of both molecules was dominated by hydrogen bonds. The crystal lattice of (1) was formed by weak C—H?N and C—H?? interactions. The crystal structure of (2) was completely different, with cations as well as chloride anions and water molecules taking part in intermolecular interactions. Single-crystal X-ray diffraction studies combined with density functional theory (DFT) calculations allowed the characterization of the intermolecular interactions in those two systems having different types of very strong electrophilic groups: non-ionic nitrile and ionic amidine. Chemical shift data from 13C CP/MAS (Cross Polarization Magic Angle Spinning) NMR spectra were analyzed using the different procedures for the theoretical computation of shielding constants. PMID:25274515

  1. A method based on the DAOSD approach to estimate the variation of the peak position and bandwidth caused by intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Bi, Quan; Chen, Jing; Li, Xiaopei; Shi, Jia-Jia; Guo, Ran; Zhai, Yanjun; Xu, Yizhuang; Noda, Isao; Wu, Jinguang

    2014-07-01

    Subtle spectral variations caused by intermolecular interactions, which are hardly observed in the original one-dimensional spectra or the second derivative spectra, can be distinctly visualized via spectral patterns in two-dimensional spectra generated by using double asynchronous orthogonal sample designed scheme (DAOSD). If intermolecular interaction only brings about band-shift on a characteristic peak, a pair of cross peaks appears in the corresponding near diagonal region. If intermolecular interaction induces variation of bandwidth only, a cluster of cross peaks forms a diamond pattern in the near diagonal region. In both cases, the variation of peak position or bandwidth can be deduced quantitatively from the pattern of cross peaks. If intermolecular interaction causes variations on both peak position and bandwidth, four cross peaks form a butterfly pattern. In this case, however, it is not straightforward to estimate the variation of peak position and bandwidth directly from the patterns of the cross peaks. In this paper, we propose an algorithm to estimate the variations of peak position and bandwidth of a characteristic peak caused by intermolecular interactions. The validity of this approach was confirmed by computer simulation on several model systems.

  2. Identification of molecular crystals capable of undergoing an acyl-transfer reaction based on intermolecular interactions in the crystal lattice.

    PubMed

    Tamboli, Majid I; Krishnaswamy, Shobhana; Gonnade, Rajesh G; Shashidhar, Mysore S

    2013-09-16

    Investigation of the intermolecular acyl-transfer reactivity in molecular crystals of myo-inositol orthoester derivatives and its correlation with crystal structures enabled us to identify the essential parameters to support efficient acyl-transfer reactions in crystals: 1)?the favorable geometry of the nucleophile (-OH) and the electrophile (C-O) and 2)?the molecular assembly, reinforced by C-H???? interactions, which supports a domino-type reaction in crystals. These parameters were used to identify another reactive crystal through a data-mining study of the Cambridge Structural Database. A 2:1 co-crystal of 2,3-naphthalene diol and its di-p-methylbenzoate was selected as a potentially reactive crystal and its reactivity was tested by heating the co-crystals in the presence of solid sodium carbonate. A facile intermolecular p-toluoyl group transfer was observed as predicted. The successful identification of reactive crystals opens up a new method for the detection of molecular crystals capable of exhibiting acyl-transfer reactivity. PMID:23934729

  3. Hyperspherical representation of potential energy surfaces: intermolecular interactions in tetra-atomic and penta-atomic systems

    NASA Astrophysics Data System (ADS)

    Barreto, Patricia R. P.; Albernaz, Alessandra F.; Palazzetti, Federico; Lombardi, Andrea; Grossi, Gaia; Aquilanti, Vincenzo

    2011-08-01

    In this paper, we discuss the applications of spherical and hyperspherical harmonics expansions for potential energy surfaces for intermolecular interactions, focusing on four- and five-body problems. Case studies include diatomic-molecule-diatomic-molecule systems, floppy-molecule-rare-gas-atom cases, atom-triatomic, and nonlinear-molecule-linear-molecule systems. Among these systems, the important ones regarding water interaction with atoms and diatomic molecules are presented here to illustrate the use of spherical and hyperspherical coordinates and harmonics for weakly interacting systems. The interaction potential representation involves the distance between the centers of mass of the two molecules and a set of angles that defines the mutual orientation of the molecules, whose geometries are assumed to be either 'frozen' in their equilibrium configurations or to vary according to specific large-amplitude modes. The potential energy surfaces in the given examples of water-hydrogen, nitrogen and oxygen interactions are generated at the CCSD(T)/aug-cc-pVTZ level. Comparisons to the theoretical and experimental results of recent works for these and similar systems are presented.

  4. Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobic versus electrostatic inter-molecular interactions.

    PubMed

    Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R; Sek, David; Allen, Martin J

    2015-01-01

    High viscosity of monoclonal antibody formulations at concentrations ?100 mg/mL can impede their development as products suitable for subcutaneous delivery. The effects of hydrophobic and electrostatic intermolecular interactions on the solution behavior of MAB 1, which becomes unacceptably viscous at high concentrations, was studied by testing 5 single point mutants. The mutations were designed to reduce viscosity by disrupting either an aggregation prone region (APR), which also participates in 2 hydrophobic surface patches, or a negatively charged surface patch in the variable region. The disruption of an APR that lies at the interface of light and heavy chain variable domains, VH and VL, via L45K mutation destabilized MAB 1 and abolished antigen binding. However, mutation at the preceding residue (V44K), which also lies in the same APR, increased apparent solubility and reduced viscosity of MAB 1 without sacrificing antigen binding or thermal stability. Neutralizing the negatively charged surface patch (E59Y) also increased apparent solubility and reduced viscosity of MAB 1, but charge reversal at the same position (E59K/R) caused destabilization, decreased solubility and led to difficulties in sample manipulation that precluded their viscosity measurements at high concentrations. Both V44K and E59Y mutations showed similar increase in apparent solubility. However, the viscosity profile of E59Y was considerably better than that of the V44K, providing evidence that inter-molecular interactions in MAB 1 are electrostatically driven. In conclusion, neutralizing negatively charged surface patches may be more beneficial toward reducing viscosity of highly concentrated antibody solutions than charge reversal or aggregation prone motif disruption. PMID:25559441

  5. Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: Comparison with propane dimer

    Microsoft Academic Search

    Seiji Tsuzuki; Tadafumi Uchimaru; Masuhiro Mikami; Shingo Urata

    2004-01-01

    Intermolecular interaction energies of 12 orientations of C3F8 dimers were calculated with electron correlation correction by the second-order Møller-Plesset perturbation method. The antiparallel C2h dimer has the largest interaction energy (-1.45 kcal\\/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C3F8

  6. Regulatory R region of the CFTR chloride channel is a dynamic integrator of phospho-dependent intra- and intermolecular interactions

    PubMed Central

    Bozoky, Zoltan; Krzeminski, Mickael; Muhandiram, Ranjith; Birtley, James R.; Al-Zahrani, Ateeq; Thomas, Philip J.; Frizzell, Raymond A.; Ford, Robert C.; Forman-Kay, Julie D.

    2013-01-01

    Intrinsically disordered proteins play crucial roles in regulatory processes and often function as protein interaction hubs. Here, we present a detailed characterization of a full-length disordered hub protein region involved in multiple dynamic complexes. We performed NMR, CD, and fluorescence binding studies on the nonphosphorylated and highly PKA-phosphorylated human cystic fibrosis transmembrane conductance regulator (CFTR) regulatory region, a ?200-residue disordered segment involved in phosphorylation-dependent regulation of channel trafficking and gating. Our data provide evidence for dynamic, phosphorylation-dependent, multisite interactions of various segments of the regulatory region for its intra- and intermolecular partners, including the CFTR nucleotide binding domains 1 and 2, a 42-residue peptide from the C terminus of CFTR, the SLC26A3 sulphate transporter and antisigma factor antagonist (STAS) domain, and 14-3-3?. Because of its large number of binding partners, multivalent binding of individually weak sites facilitates rapid exchange between free and bound states to allow the regulatory region to engage with different partners and generate a graded or rheostat-like response to phosphorylation. Our results enrich the understanding of how disordered binding segments interact with multiple targets. We present structural models consistent with our data that illustrate this dynamic aspect of phospho-regulation of CFTR by the disordered regulatory region. PMID:24191035

  7. plasma desorption mass spectrometry of quinolinium salts and method of estimation of their intermolecular interactions with phospholipids

    NASA Astrophysics Data System (ADS)

    Andrievsky, Grigory V.; Lisnyak, Yury V.; Klochkov, Vladimir K.; Volyansky, Yury L.; Malaya, Lubov T.

    1997-06-01

    Using plasma desorption mass spectrometry, the fragmentation of 1-phenyl-2(p-aminostyryl)quinolinium and 1-phenyl-2(p-aminostyryl)benzo(f)quinolinium derivatives, with various substituents at the amino nitrogen, was studied. With plasma desorption ionization, the fragmentation features of the compounds studied are mainly determined by the nature of the N',N'' substituents. The behaviour of some quinolinium derivatives in the presence of lecithin, a basic component of the phospholipid fraction of cell membranes, was investigated. For the benzo(f)quinolinium derivative, the analysis of changes in the mass spectra indicates a strong interaction between these substances, leading to the formation of a molecular complex stabilized by the interactions of the negatively charged phosphate group of lecithin with the quinolinium quaternary nitrogen and the lecithin quaternary nitrogen with the benzene part of the aminophenyl fragment. The effect of the third aromatic ring of the benzoquinolinium system on complex stabilization is discussed. For the benzoquinolinium derivative with lecithin, the changes in the mass spectrometric fragmentation pattern of the molecule can be used as a sensitive and informative method for the characterization of intermolecular interactions which may result in molecular complex formation.

  8. 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.

  9. 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. (Freie Universitaet Berlin (West Germany))

    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.

  10. Intermolecular interactions in binary and ternary solutions of two cycloimmonium-carboethoxy-anilido-methylids.

    PubMed

    Closca, Valentina; Ivan, Liliana Mihaela; Dorohoi, Dana Ortansa

    2014-03-25

    Two cycloimmonium ylids with pyridinium and iso-quinolinium as heterocycle and having common carbanion were studied from the point of view of the solvent influence on electronic absorption spectra in binary and ternary solutions. The supplies of the universal and specific interactions to the spectral shifts in the electronic absorption spectra of hydroxyl solutions were separated. The strength of the specific interactions of the ylid molecules with octanol was estimated by using ternary solutions in binary solvent Octanol+Dichloroethane, in which the universal interactions have similar strengths. Quantum mechanical calculations and also the solvatochromic effect allowed us estimating the values of the molecular dipole moments in the excited state of the studied ylids. The conclusions showed that by excitation the molecular dipole moment of the studied ylids decreases or changes its sense, due to the electronic charge transport from the carbanion towards the heterocycle. PMID:24342294

  11. Magnitude and orientation dependence of intermolecular interaction of perfluoropropane dimer studied by high-level ab initio calculations: Comparison with propane dimer

    NASA Astrophysics Data System (ADS)

    Tsuzuki, Seiji; Uchimaru, Tadafumi; Mikami, Masuhiro; Urata, Shingo

    2004-11-01

    Intermolecular interaction energies of 12 orientations of C3F8 dimers were calculated with electron correlation correction by the second-order Møller-Plesset perturbation method. The antiparallel C2h dimer has the largest interaction energy (-1.45 kcal/mol). Electron correlation correction increases the attraction considerably. Electrostatic energy is not large. Dispersion is mainly responsible for the attraction. Orientation dependence of the interaction energy of the C3F8 dimer is substantially smaller than that of the C3H8 dimer. The calculated interaction energy of the C3F8 dimer at the potential minimum is 78% of that of the C3H8 dimer (-1.85 kcal/mol), whereas the interaction energies of the CF4 and C2F6 dimers are larger than those of the CH4 and C2H6 dimers. The intermolecular separation in the C3F8 dimer at the potential minimum is substantially larger than that in the C3H8 dimer. The larger intermolecular separation due to the steric repulsion between fluorine atoms is the cause of the smaller interaction energy of the C3F8 dimer at the potential minimum. The calculated intermolecular interaction energy potentials of the C3F8 dimers using an all atom model OPLS-AA (OPLS all atom model) force field and a united atom model force field were compared with the ab initio calculations. Although the two force fields well reproduces the experimental vapor and liquid properties of perfluoroalkenes, the comparison shows that the united atom model underestimates the potential depth and orientation dependence of the interaction energy. The potentials obtained by the OPLS-AA force field are close to those obtained by the ab initio calculations.

  12. Computational investigation of intermolecular interactions in polymer mixtures: Polycarbonate and poly(methyl methacrylate)

    SciTech Connect

    Fitzwater, S. [Rohm and Haas Co., Spring House, PA (United States)

    1993-12-31

    Molecular modeling and semiempirical quantum mechanical calculations on model compounds can give us detailed information about specific interactions in polymer mixtures. This study examines interactions between a poly(methyl methacrylate) (PMMA) tetramer and the polycarbonate (PC) repeat unit. The results suggested that PC-PMMA mixtures are stabilizing by hydrogen bonds between a carbonyl oxygen on one polymer and a proton or protons on the other. Multiple hydrogen bonds occur; stabilized generally increases with the number of hydrogen bonds. Several configurations had a PMMA carbonyl O H-bonded to a PC ring H, and the adjacent PC carbyonyl O H-bonded to PMMA methyl and methylene H`s. This suggests that the reduced PC mobility observed in PC-PMMA mixtures arises from suppression of both ring flips and carbonate group motion.

  13. Intradimer/Intermolecular Interactions Suggest Autoinhibition Mechanism in Endophilin A1

    PubMed Central

    2015-01-01

    Endophilin A1 is a homodimeric membrane-binding endocytic accessory protein with a high dimerization affinity. Its function has been hypothesized to involve autoinhibition. However, the autoinhibition mechanism, as well as the physicochemical basis for the high dimerization affinity of endophilin in solution, have remained unclear. In this contribution, we use a Förster resonance energy transfer (FRET) method to investigate the homodimerization mechanism and intradimer molecular interactions in endophilin. For the endophilin N-BAR domain (which lacks the SH3 domain including a linker region of the full length protein), we observe a large temperature dependence of the dimerization affinity and dimer dissociation kinetics, implying large dimerization enthalpy and dissociation activation enthalpy, respectively. Our evaluation of the protein concentration dependence of dimer dissociation kinetics implies that endophilin reversibly forms monomers via a dissociation/reassociation mechanism. Furthermore, we use a kinetic method that allows us to compare the dissociation kinetics of full-length endophilin to that of truncated mutants. We find that mutants that lack either H0 helix or SH3 domain show significantly faster dissociation kinetics relative to full-length endophilin. This observation supports the presence of an intradimer, intermonomer cross-interaction between H0 helix and SH3 domain from different subunits within a homodimer. Because the H0 helix is known to play a significant role in endophilin’s membrane interactions, our measurements support a syngergistic model where these interactions are inhibited in the absence of SH3 domain binding ligands such as dynamin’s prolin rich domains, and where the binding of these ligands may be suppressed for non-membrane-bound endophilin. PMID:24568626

  14. Synovial Fluid Response to Extensional Flow: Effects of Dilution and Intermolecular Interactions

    PubMed Central

    Haward, Simon J.

    2014-01-01

    In this study, a microfluidic cross-slot device is used to examine the extensional flow response of diluted porcine synovial fluid (PSF) samples using flow-induced birefringence (FIB) measurements. The PSF sample is diluted to 10× 20× and 30× its original mass in a phosphate-buffered saline and its FIB response measured as a function of the strain rate at the stagnation point of the cross-slots. Equivalent experiments are also carried out using trypsin-treated PSF (t-PSF) in which the protein content is digested away using an enzyme. The results show that, at the synovial fluid concentrations tested, the protein content plays a negligible role in either the fluid's bulk shear or extensional flow behaviour. This helps support the validity of the analysis of synovial fluid HA content, either by microfluidic or by other techniques where the synovial fluid is first diluted, and suggests that the HA and protein content in synovial fluid must be higher than a certain minimum threshold concentration before HA-protein or protein-protein interactions become significant. However a systematic shift in the FIB response as the PSF and t-PSF samples are progressively diluted indicates that HA-HA interactions remain significant at the concentrations tested. These interactions influence FIB-derived macromolecular parameters such as the relaxation time and the molecular weight distribution and therefore must be minimized for the best validity of this method as an analytical technique, in which non-interaction between molecules is assumed. PMID:24651529

  15. Intermolecular interactions in highly concentrated protein solutions upon compression and the role of the solvent

    NASA Astrophysics Data System (ADS)

    Grobelny, S.; Erlkamp, M.; Möller, J.; Tolan, M.; Winter, R.

    2014-12-01

    The influence of high hydrostatic pressure on the structure and protein-protein interaction potential of highly concentrated lysozyme solutions up to about 370 mg ml-1 was studied and analyzed using small-angle X-ray scattering in combination with a liquid-state theoretical approach. In the concentration region below 200 mg ml-1, the interaction parameters of lysozyme solutions are affected by pressure in a nonlinear way, which is probably due to significant changes in the structural properties of bulk water, i.e., due to a solvent-mediated effect. Conversely, for higher concentrated protein solutions, where hydration layers below ˜4 water molecules are reached, the interaction potential turns rather insensitive to compression. The onset of transient (dynamic) clustering is envisaged in this concentration range. Our results also show that pressure suppresses protein nucleation, aggregation and finally crystallization in supersaturated condensed protein solutions. These findings are of importance for controlling and fine-tuning protein crystallization. Moreover, these results are also important for understanding the high stability of highly concentrated protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the kbar-level are reached.

  16. Intermolecular interactions in highly concentrated protein solutions upon compression and the role of the solvent.

    PubMed

    Grobelny, S; Erlkamp, M; Möller, J; Tolan, M; Winter, R

    2014-12-14

    The influence of high hydrostatic pressure on the structure and protein-protein interaction potential of highly concentrated lysozyme solutions up to about 370 mg ml(-1) was studied and analyzed using small-angle X-ray scattering in combination with a liquid-state theoretical approach. In the concentration region below 200 mg ml(-1), the interaction parameters of lysozyme solutions are affected by pressure in a nonlinear way, which is probably due to significant changes in the structural properties of bulk water, i.e., due to a solvent-mediated effect. Conversely, for higher concentrated protein solutions, where hydration layers below ?4 water molecules are reached, the interaction potential turns rather insensitive to compression. The onset of transient (dynamic) clustering is envisaged in this concentration range. Our results also show that pressure suppresses protein nucleation, aggregation and finally crystallization in supersaturated condensed protein solutions. These findings are of importance for controlling and fine-tuning protein crystallization. Moreover, these results are also important for understanding the high stability of highly concentrated protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the kbar-level are reached. PMID:25494777

  17. Intermolecular Interaction and the Extended Wormlike Chain Conformation of Chitin in NaOH/Urea Aqueous Solution.

    PubMed

    Fang, Yan; Duan, Bo; Lu, Ang; Liu, Maili; Liu, Huili; Xu, Xiaojuan; Zhang, Lina

    2015-04-13

    The intra- and intermolecular interactions of chitin in NaOH/urea aqueous system were studied by a combination of NMR measurements (including (13)C NMR, (23)Na NMR, and (15)N NMR) and differential scanning calorimetry. The results revealed that the NaOH and chitin formed a hydrogen-bonded complex that was surrounded by the urea hydrates to form a sheath-like structure, leading to the good dissolution. The optimal concentration range, in which chitin was molecularly dispersed in NaOH/urea aqueous, was found to investigate the chain conformation in the dilute solution with a combination of static and dynamic light scattering. The weight-average molecular weight (Mw), radii of gyration (?Rg?z), and hydrodynamic radii (?Rh?z) values of chitin were determined, and the structure-sensitive parameter (?) and persistent length (Lp) were calculated to be >2.0 and ?30 nm, respectively, suggesting an extended wormlike chain conformation. The visualized images from TEM, cryo-TEM, and AFM indicated that, chitin nanofibers were fabricated from the parallel aggregation of chitin chains in NaOH/urea system. This work would provide a theoretical guidance for constructing novel chitin-based nanomaterials via "bottom-up" method at the molecular level. PMID:25712045

  18. Solar cell efficiency, self-assembly, and dipole-dipole interactions of isomorphic narrow-band-gap molecules.

    PubMed

    Takacs, Christopher J; Sun, Yanming; Welch, Gregory C; Perez, Louis A; Liu, Xiaofeng; Wen, Wen; Bazan, Guillermo C; Heeger, Alan J

    2012-10-10

    We examine the correlations of the dipole moment and conformational stability to the self-assembly and solar cell performance within a series of isomorphic, solution-processable molecules. These charge-transfer chromophores are described by a D(1)-A-D-A-D(1) structure comprising electron-rich 2-hexylbithiophene and 3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene moieties as the donor units D(1) and D, respectively. The building blocks 2,1,3-benzothiadiazole (BT) and [1,2,5]thiadiazolo[3,4-c]pyridine (PT) were used as the electron-deficient acceptor units A. Using a combination of UV-visible spectroscopy, field-effect transistors, solar cell devices, grazing incident wide-angle X-ray scattering, and transmission electron microscopy, three PT-containing compounds (1-3) with varying regiochemistry and symmetry, together with the BT-based compound 5,5'-bis{(4-(7-hexylthiophen-2-yl)thiophen-2-yl)-[1,2,5]thiadiazolobenzene}-3,3'-di-2-ethylhexylsilylene-2,2'-bithiophene (4), are compared and contrasted in solution, in thin films, and as blends with the electron acceptor [6,6]-phenyl-C(70)-butyric acid methyl ester. The molecules with symmetric orientations of the PT acceptor, 1 and 2, yield highly ordered blended thin films. The best films, processed with the solvent additive 1,8-diiodooctane, show donor "crystallite" length scales on the order of 15-35 nm and photovoltaic power conversion efficiencies (PCEs) of 7.0 and 5.6%, respectively. Compound 3, with an unsymmetrical orientation of PT heterocycles, shows subtle differences in the crystallization behavior and a best PCE of 3.2%. In contrast, blends of the BT-containing donor 4 are highly disordered and give PCEs below 0.2%. We speculate that the differences in self-assembly arise from the strong influence of the BT acceptor and its orientation on the net dipole moment and geometric description of the chromophore. PMID:22950622

  19. Exploring contribution of intermolecular interactions in supramolecular layered assembly of naphthyridine co-crystals: Insights from Hirshfeld surface analysis of their crystalline states

    NASA Astrophysics Data System (ADS)

    Seth, Saikat Kumar; Das, Nirmal Kumar; Aich, Krishnendu; Sen, Debabrata; Fun, Hoong-Kun; Goswami, Shyamaprasad

    2013-09-01

    Co-crystals of 1a and 1b have been prepared by slow evaporation of the solutions of mixtures of 2,7-dimethyl-1,8-naphthyridine (1), urea (a) and thiourea (b). The structures of the complexes are determined by the single crystal X-ray diffraction and a detailed investigation of the crystal packing and classification of intermolecular interactions is presented by means of Hirshfeld surface analysis which is of considerable current interest in crystal engineering. The X-ray study reveals that the co-crystal formers are envisioned to produce N-H⋯N hydrogen bond as well as N-H⋯O/N-H⋯S pair-wise hydrogen bonds and also the weaker aromatic ?⋯? interactions which cooperatively take part in the crystal packing. The recurring feature of the self-assembly in the compounds is the appearance of the molecular ribbon through multiple hydrogen bonding which are further stacked into molecular layers by ?⋯? stacking interactions. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D Fingerprint plots have been used to examine molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

  20. The effect of intermolecular interactions on the electric dipole polarizabilities of nucleic acid base complexes

    NASA Astrophysics Data System (ADS)

    Czy?nikowska, ?aneta; Góra, Robert W.; Zale?ny, Robert; Bartkowiak, Wojciech; Baranowska-??czkowska, Angelika; Leszczynski, Jerzy

    2013-01-01

    In this Letter, we report on the interaction-induced electric dipole polarizabilities of 70 Watson-Crick B-DNA pairs (27 adenine-thymine and 43 guanine-cytosine complexes) and 38 structures of cytosine dimer in stacked alignment. In the case of hydrogen-bonded Watson-Crick base pairs the electrostatic as well as the induction and exchange-induction interactions, increase the average polarizability of the studied complexes, whereas the exchange-repulsion effects have the opposite effect and consistently diminish this property. On the other hand, in the case of the studied cytosine dimers in stacked alignment the dominant electrostatic contribution has generally much larger magnitude and the opposite sign, resulting in a significant reduction of the average polarizability of these complexes. As a part of this model study, we also assess the performance of recently developed LPol-ds reduced-size polarized basis set. Although being much smaller than the aug-cc-pVTZ set, the LPol-ds performs equally well as far as the excess polarizabilities of the studied hydrogen-bonded complexes are concerned.

  1. Co-amorphous simvastatin and glipizide combinations show improved physical stability without evidence of intermolecular interactions.

    PubMed

    Löbmann, Korbinian; Strachan, Clare; Grohganz, Holger; Rades, Thomas; Korhonen, Ossi; Laitinen, Riikka

    2012-05-01

    The objective of this study was to prepare a co-amorphous drug/drug combination between two BCS class II drugs, simvastatin (SVS) and glipizide (GPZ). This pharmacologically relevant combination of two drugs could produce a promising candidate for formulations intended for combination therapy of metabolic disorders. The co-amorphous SVS-GPZ mixtures (molar ratios 2:1, 1:1 and 1:2) were prepared by mechanical activation (ball milling or cryomilling) and characterized with respect to their thermal properties, possible molecular interactions, dissolution properties and physical stability, and compared to the behaviour of pure amorphous forms and their physical mixtures. It was found that even though a molecular mixture was achieved with all SVS-GPZ mixture ratios, no molecular interactions between the drugs could be detected. By formation of co-amorphous single-phase mixtures, only the dissolution rate of GPZ could be improved. The co-amorphous mixtures showed improved stability compared to the pure amorphous forms and the amorphous physical mixtures. It was concluded that this was attributable to the molecular level mixing of SVS with GPZ upon milling, and GPZ is acting as an anti-plasticizer in these mixtures. PMID:22353489

  2. Theoretical Studies on the Intermolecular Interactions of Potentially Primordial Base-Pair Analogues

    SciTech Connect

    Leszczynski, Jerzy [Computational Center for Molecular Structure and Interactions, Jackson, MS; Sponer, Judit [Academy of Sciences of the Czech Republic; Sponer, Jiri [Academy of Sciences of the Czech Republic; Sumpter, Bobby G [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL

    2010-01-01

    Recent experimental studies on the Watson Crick type base pairing of triazine and aminopyrimidine derivatives suggest that acid/base properties of the constituent bases might be related to the duplex stabilities measured in solution. Herein we use high-level quantum chemical calculations and molecular dynamics simulations to evaluate the base pairing and stacking interactions of seven selected base pairs, which are common in that they are stabilized by two NH O hydrogen bonds separated by one NH N hydrogen bond. We show that neither the base pairing nor the base stacking interaction energies correlate with the reported pKa data of the bases and the melting points of the duplexes. This suggests that the experimentally observed correlation between the melting point data of the duplexes and the pKa values of the constituent bases is not rooted in the intrinsic base pairing and stacking properties. The physical chemistry origin of the observed experimental correlation thus remains unexplained and requires further investigations. In addition, since our calculations are carried out with extrapolation to the complete basis set of atomic orbitals and with inclusion of higher electron correlation effects, they provide reference data for stacking and base pairing energies of non-natural bases.

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

    We explore different variants of the random phase approximation to the correlation energy derived from closed-shell ring-diagram approximations to coupled cluster doubles theory. We implement these variants in range-separated density-functional theory, i.e., by combining the long-range random phase approximations with short-range density-functional approximations. We perform tests on the rare-gas dimers He2, Ne2, and Ar2, and on the weakly interacting molecular complexes of the S22 set of Jure?ka et al. [P. Jure?ka, J. Šponer, J. ?erný, and P. Hobza, Phys. Chem. Chem. Phys. 8, 1985 (2006), 10.1039/b600027d]. The two best variants correspond to the ones originally proposed by Szabo and Ostlund [A. Szabo and N. S. Ostlund, J. Chem. Phys. 67, 4351 (1977), 10.1063/1.434580]. With range separation, they reach mean absolute errors on the equilibrium interaction energies of the S22 set of about 0.4 kcal/mol, corresponding to mean absolute percentage errors of about 4%, with the aug-cc-pVDZ basis set.

  4. Interaction of red blood cells with a polarized electrode: evidence of long-range intermolecular forces.

    PubMed Central

    Gingell, D; Fornes, J A

    1976-01-01

    We have investigated the electrostatic interaction of glutaraldehyde-fixed human red cells with a polarizable electrode carrying a defined surface charge density which can be varied continuously through a wide range. Cells in a dilute salt solution are unable to adhere to the electrode at high negative charge, but at lower negative charge densities they are reversibly adherent and can be forced off by increasing the negative polarization. Near zero electrode charge they become irreversibly stuck to the electrode and cannot be evicted even at maximum electrode polarization. Calculation of the electrostatic repulsive force using measured charge densities indicates the existence of an attractive force which may be acting over several hundred angstroms. PMID:822894

  5. Intermolecular interactions as actors in energy-transfer processes in lanthanide complexes with 2,2'-bipyridine.

    PubMed

    Puntus, Lada N; Lyssenko, Konstantin A; Pekareva, Irina S; Bünzli, Jean-Claude G

    2009-07-01

    A series of lanthanide complexes [LnCl(x)(bpy)(y)(H(2)O)(z)]Cl(3-x)(H(2)O)(n)(EtOH)(m) (Ln = Eu, Gd, Tb; x = 1, 2; y = 1, 2; z = 2-4) with different numbers of 2,2'-bipyridine (bpy), chloride ions, and water molecules in the inner coordination sphere were synthesized and investigated with the aim of relating their molecular geometry and crystal packing to the efficiency of ligand-to-metal energy transfer. In conjunction to the rotation of the pyridine rings upon coordination to the Ln ion, the high flexibility displayed by bpy ligands leads to rather unexpected bending of these rings with respect to the central bond, owing to intermolecular interactions such as Cl...pi and pi-stacking ones. Deciphering the luminescence properties of the Eu and Tb complexes needs to take into account both the composition of the inner coordination sphere and the peculiarities of the crystal packing. For instance, in addition to the classical ligand --> Eu charge-transfer state (LMCT), another charge-transfer state induced by pi-stacking interactions (SICT) could be identified. These two states, located between the singlet and triplet states of the bpy ligand(s), provide relays facilitating the energy migration from the singlet to the triplet states and eventually to the excited Eu states, improving the overall ligand-to-Eu energy transfer. Another point is the involvement of the inner-sphere water molecules in H-bonding with chloride ions, which considerably lowers their luminescence quenching ability, so that the adducts remain highly luminescent. For instance, the terbium chloride with two bpy ligands is an efficient near-UV to green light converter, with an overall quantum yield equal to 37% despite the coordinated water molecules. The interpretations given are substantiated by DFT and TD-DFT theoretical calculations of the complexes and ligand assemblies. PMID:19522489

  6. Fine structures in vibrational circular dichroism spectra of chiral molecules with rotatable hydroxyl groups and their application in the analysis of local intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Konno, Kohzo; Shiina, Isamu; Yui, Hiroharu

    2013-03-01

    The effect of hydroxyl group on vibrational circular dichroism is addressed. (-)-Menthol is investigated as a representative chiral molecule which has been widely used as a chiral starting material. Free rotation of the hydroxyl group in (-)-menthol allows it to exist in various conformations in solution. The variety of conformations inevitably affects local intermolecular interactions and the resultant efficiency of asymmetric syntheses. However, the precise relationship between the conformations and intermolecular interactions arising from rotation of the hydroxyl group has remained an unsolved issue despite the molecule's importance. Here, the conformations and interactions are investigated using vibrational circular dichroism (VCD). VCD is quite sensitive to slight differences in the conformation of chiral molecules and their local environment. We examined various conformers in (-)-menthol and compared the VCD spectrum with that of (-)-menthone. It revealed the rotation of the polar hydroxyl group sensitively affects the VCD activity, resulting in the emergence of various patterns in the corresponding VCD spectra, especially in the wavenumber regions at around 1064 cm-1 and 1254 cm-1. Among these regions, the latter one is further investigated to examine the feasibility of applying the sensitive response to the analysis on the local intermolecular environment. It includes solute-solvent interactions via hydroxyl groups, which is important for biomacromolecule structural stability and efficient stereoselective syntheses. As a consequence, distinctive fine structures in the VCD spectra, including an unpredicted band, are observed when varying temperature and concentration. Their possible assignment is also discussed.

  7. Fabrication and Intermolecular Interactions of Silk Fibroin/Hydroxybutyl Chitosan Blended Nanofibers

    PubMed Central

    Zhang, Kui-Hua; Yu, Qiao-Zhen; Mo, Xiu-Mei

    2011-01-01

    The native extracellular matrix (ECM) is composed of a cross-linked porous network of multifibril collagens and glycosaminoglycans. Nanofibrous scaffolds of silk fibroin (SF) and hydroxybutyl chitosan (HBC) blends were fabricated using 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) and trifluoroacetic acid (TFA) as solvents to biomimic the native ECM via electrospinning. Scanning electronic microscope (SEM) showed that relatively uniform nanofibers could be obtained when 12% SF was blended with 6% HBC at the weight ratio of 50:50. Meanwhile, the average nanofibrous diameter increased when the content of HBC in SF/HBC blends was raised from 20% to 100%. Fourier transform infrared spectra (FTIR) and 13C nuclear magnetic resonance (NMR) showed SF and HBC molecules existed in hydrogen bonding interactions but HBC did not induce conformation of SF transforming from random coil form to ?-sheet structure. X-ray diffraction (XRD) confirmed the different structure of SF/HBC blended nanofibers from both SF and HBC. Thermogravimetry-Differential thermogravimetry (TG-DTG) results demonstrated that the thermal stability of SF/HBC blend nanofibrous scaffolds was improved. The results indicated that the rearrangement of HBC and SF molecular chain formed a new structure due to stronger hydrogen bonding between SF and HBC. These electrospun SF/HBC blended nanofibers may provide an ideal tissue engineering scaffold and wound dressing. PMID:21731435

  8. Radiative recombination of trapped excitons in Alq3 films: Importance of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Ajward, A. M.; Wang, X.; Wickremasinghe, N.; DeSilva, L. A. A.; Wagner, H. P.

    2013-07-01

    We investigate the light emission of optically excited tris(8-hydroxyquinolinato) aluminum (Alq3) films by temperature-dependent, time-integrated, as well as time-resolved photoluminescence (PL) at various photon densities. The Alq3 films are deposited on Si (001) substrate using organic molecular beam deposition. At high excitation densities, the PL efficiency decreases when the temperature is reduced from 170 to 15 K. At low laser intensities, the PL efficiency is nearly temperature independent. The observed PL quenching at high-excitation densities is assigned to singlet-singlet annihilation revealing a low-temperature bimolecular quenching coefficient that is more than two orders of magnitude higher than previously reported at room temperature. The observed strong bimolecular interaction at low temperature is attributed to an enhanced local (microscopic) density of captured excitons in extended traps. The reduction of the exciton annihilation with increasing temperature is assigned to a thermally activated occupation of nonquenchable localized exciton states. Above 190 K, the PL efficiency starts to decrease independently from the excitation level which is ascribed to a thermally activated detrapping of excitons and subsequent migration to nonradiative centers outside the traps. A coupled-rate equation model, including bimolecular quenching, thermally activated occupation of nonquenchable states, and detrapping of excitons at higher temperatures, supports these interpretations.

  9. Theory of elastic interaction between colloidal particles in the nematic cell in the presence of the external electric or magnetic field

    Microsoft Academic Search

    S. B. Chernyshuk; O. M. Tovkach; B. I. Lev

    2011-01-01

    The Green function method developed in Ref.[S. B. Chernyshuk and B. I. Lev, Phys. Rev. E \\\\textbf{81}, 041707 (2010)] is used to describe elastic interactions between axially symmetric colloidal particles in the nematic cell in the presence of the external electric or magnetic field. General formulas for dipole-dipole, dipole-quadrupole and quadrupole-quadrupole interactions in the homeotropic and planar nematic cells with

  10. Clarification of isomeric structures and the effect of intermolecular interactions in blue-emitting aluminum complex Alq3 using first-principles 27Al NMR calculations

    NASA Astrophysics Data System (ADS)

    Suzuki, Furitsu; Nishiyama, Yusuke; Kaji, Hironori

    2014-06-01

    We have performed structure analysis of the blue-emitting aluminum complex Alq3 using 27Al NMR and gauge-including projector-augmented wave calculations. The results clearly show that 27Al NMR spectra are insensitive to intermolecular interactions, thus providing a means of carrying out precise intramolecular structure determination. The key determinant of the blue-shifted emission of Alq3 is the facial isomerization.

  11. Molecular-beam study of the ammonia-noble gas systems: Characterization of the isotropic interaction and insights into the nature of the intermolecular potential

    NASA Astrophysics Data System (ADS)

    Pirani, Fernando; Roncaratti, Luiz F.; Belpassi, Leonardo; Tarantelli, Francesco; Cappelletti, D.

    2011-11-01

    We report new high resolution molecular beam experiments aimed at characterizing the intermolecular interaction in the NH3-Ng (Ng = He, Ne, Ar, Kr, Xe) weakly bound complexes. Integral cross section data are obtained over a sufficiently wide velocity range and with rotationally hot NH3 molecules to produce (except for the NH3-He case) a well resolved "glory" quantum interference pattern. Data analysis, carried out by employing a recently proposed potential model, allows unique information on the absolute scale of the intermolecular interaction to be obtained both at long range and at the equilibrium distance. An extensive and internally consistent comparison with the behavior of the corresponding Kr-Ng systems is exploited in order to identify those cases where an interaction component due to charge transfer effects provides an appreciable intermolecular bond stabilization that is clearly distinct from and must be added to the standard van der Waals plus induction picture. The results of the present investigation extend the phenomenology of perturbative charge transfer effects in gas phase complexes involving hydrogenated molecules.

  12. 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 (?k+, ?k-) 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 (?0).

  13. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast1

    Microsoft Academic Search

    Jong Park; Michael Lappe; Sarah A Teichmann

    2001-01-01

    In the postgenomic era, one of the most interesting and important chal- lenges is to understand protein interactions on a large scale. The physical interactions between protein domains are fundamental to the workings of a cell: in multi-domain polypeptide chains, in multi-subunit proteins and in transient complexes between proteins that also exist indepen- dently. To study the large-scale patterns and

  14. Design, synthesis, and optoelectronic properties of dendrimeric Pt(II) complexes and their ability to inhibit intermolecular interaction.

    PubMed

    Li, Hui; Li, Jing; Ding, Junqiao; Yuan, Wei; Zhang, Zilong; Zou, Luyi; Wang, Xingdong; Zhan, Hongmei; Xie, Zhiyuan; Cheng, Yanxiang; Wang, Lixiang

    2014-01-21

    Dendrimeric Pt(II) complexes [(C(?)N)Pt(dpm)] and [Pt(C(?)N)2] (Hdpm = dipivaloylmethane, HC(?)N = 1,2-diphenylbenzoimidazole and its derivatives containing the carbazole dendrons) have been synthesized and characterized systematically. All of the complexes display green emission in the range of 495-535 nm that originated from the 360-440 nm absorption bands, which are assigned to d?(Pt)??*(L) metal-to-ligand charge transfer (MLCT) mixed with intraligand ?(L)??*(L) transition. Solution photoluminescence quantum yield (?p 0.26-0.31) of the heteroleptic complexes [(C(?)N)Pt(dpm)] obviously increases when compared with that of complex [(C(?)N)Pt(acac)]. Organic light-emitting diode devices based on these Pt(II) complexes with a multilayer configuration were fabricated and gave desirable electroluminescent (EL) performances, such as non- or less red-shifted EL spectra, in comparison with the photoluminescence spectra and slow efficiency roll-off with increasing brightness or current density. Complex [(t-BuCzCzPBI)Pt(dpm)] (where t-BuCzCzPBI = 1-(4-(3,6-di-(3,6-di-t-butyl-carbazol-9-yl))carbazol-9-yl)phenyl-2-phenylbenzoimidazole) showed the best performance, with a maximum current efficiency of 29.31 cd/A and a maximum external quantum efficiency (EQE) of 9.04% among the fabricated devices. Likewise, for homoleptic [Pt(t-BuCzCzPBI)2] dendrimer, the powder ?p (0.14) and maximum EQE (0.74%) improve by 7 and 7.4 times, respectively, as high as they do for nondendrimeric [Pt(1,2-diphenylbenzoimidazole)2] (0.02, 0.10%), although its efficiency is still lower than that of the heteroleptic counterpart due to the severely distorted square-planar geometry of the emitting core. These results reveal that large steric hindrance from ancillary ligand (dpm) or the homoleptic conformation can effectively inhibit intermolecular interaction for these dendrimeric Pt(II) complexes. PMID:24393007

  15. Effect of alkylamino group fixation on the spectral-luminescence properties of coumarines and their ability to participate in intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Sokolova, I. V.; Vasil'Eva, N. Yu.; Loboda, L. I.; Sidorenko, E. A.; Kochkina, O. I.; Il'Chenko, A. Ya.; Kropachev, A. V.

    1986-11-01

    The spectral-luminescence properties of substituted 7-alkylaminocoumarines with nonfixed and fixed amino groups and AC3F are studied theoretically and experimentally. The calculation is carried out by the method of partial neglect of differential overlapping. It is shown that fixation of alkylamino groups in coumarines increases the quantum yield of fluorescence in polar solutions with virtually no effect on the position of the absorption and fluorescence spectra. Data from molecular electrostatic potential calculations show that the coumarines with a fixed aikylamino group have a high probability for participating in intermolecular interactions in the proton acceptor centers.

  16. Influence of inter-molecular interactions on the elasto-damage mechanics of collagen fibrils: A bottom-up approach towards macroscopic tissue modeling

    NASA Astrophysics Data System (ADS)

    Marino, Michele; Vairo, Giuseppe

    2014-12-01

    In this paper, a novel modeling approach for describing the elasto-damage mechanical response of collagen fibrils is proposed. The model is developed by adopting a multiscale rationale that allows to consistently account for nanoscale mechanisms and to introduce model parameters with a clear biophysical/biochemical meaning. A detailed description of nanoscale inter-molecular interactions is considered, highlighting their great influence on fibril mechanical response. The model is successfully validated by comparisons with available data based on molecular dynamics simulations. Proposed results prove model capability to reproduce many well-established features of fibril mechanics, fully in agreement with available experimental evidence.

  17. Orthogonal Interactions of CO Molecules on a One-Dimensional Substrate

    SciTech Connect

    Feng, Min; Cabrera-Sanfelix, Pepa; Lin, Chungwei; Arnau, Andres; Sanchez-Portal, Daniel; Zhao, Jin; Echenique, P. M.; Petek, Hrvoje

    2011-11-22

    We investigate the chemisorption structure of CO molecules on the quasi-one-dimensional Cu(110)-(2×1)-O surface by low-temperature scanning tunneling microscopy and density functional theory. Contrary to flat metal surfaces, where CO molecules adsorb in an upright geometry and interact through repulsive intermolecular interactions, we find the most stable adsorption structure of single CO molecules to be at Cu atoms of substrate Cu—O— chains with the Cu—CO unit bent by?±45° in two equivalent structures at low coverages. At higher coverages, CO molecules combine in the same structure into highly ordered single-molecule-wide rows perpendicular to the substrate chains in an approximately 8 ×1 full monolayer structure. Firstprinciples calculations attribute the unprecedented chemisorption behavior of CO molecules to lifting of the host Cu atoms by 1 Å from the surface Cu—O— chains, in order to optimize the bonding and reduce the repulsive interactions with the substrate. This structural distortion enables short-range intermolecular dipole—dipole attraction and creates orthogonal long-range surface-mediated repulsion leading to unusual self-assembly of CO molecules into coherent nanometer scale molecular grating structures.

  18. Attenuated T2 Relaxation by Mutual Cancellation of Dipole-Dipole Coupling and Chemical Shift Anisotropy Indicates an Avenue to NMR Structures of Very Large Biological Macromolecules in Solution

    Microsoft Academic Search

    Konstantin Pervushin; Roland Riek; Gerhard Wider; Kurt Wuthrich

    1997-01-01

    Fast transverse relaxation of 1H, 15N, and 13C by dipole-dipole coupling (DD) and chemical shift anisotropy (CSA) modulated by rotational molecular motions has a dominant impact on the size limit for biomacromolecular structures that can be studied by NMR spectroscopy in solution. Transverse relaxation-optimized spectroscopy (TROSY) is an approach for suppression of transverse relaxation in multidimensional NMR experiments, which is

  19. Investigations on stabilities and intermolecular interactions of different naphthalene derivatives dimers by using B3LYP and M06-2X density functional calculations

    NASA Astrophysics Data System (ADS)

    Karakaya, M.; Çiçek, A.; Ucun, F.; Yildiz, M.

    2014-12-01

    In this paper, the stabilities and hydrogen bond interactions of 4-chloro-1-naphthol, 1-hydrox-ynaphthalene and 1,4-dihydroxynaphthalene dimers have been theoretically investigated by means of study on binding energies with nonlocal hybrid three-parameter Lee-Yang-Parr, B3LYP, and M06-class functional calculations. Calculations on dimers aim to provide as a test of the efficacy of M06 calculations for intermolecular interaction calculations and more strongly bound systems. For hydroxyl- and halo-substituted derivatives of naphthalene, total electronic energies, their correction for the zero point vibrational energies with some calculated thermodynamic properties and their relative differences are together in order to discuss the rotamer structures. Static (hyper) polarizabilities and the electric dipole moments, frontier molecular orbital energy gaps and the relationships between them have been interpreted. Generally, they are seen that the calculated geometric parameters and spectral results were in a good agreement with the corresponding experimental data.

  20. Protein-RNA affinity of ribosomal protein L1 mutants does not correlate with the number of intermolecular interactions.

    PubMed

    Tishchenko, Svetlana; Kostareva, Olga; Gabdulkhakov, Azat; Mikhaylina, Alisa; Nikonova, Ekaterina; Nevskaya, Natalia; Sarskikh, Alena; Piendl, Wolfgang; Garber, Maria; Nikonov, Stanislav

    2015-02-01

    Ribosomal protein L1, as part of the L1 stalk of the 50S ribosomal subunit, is implicated in directing tRNA movement through the ribosome during translocation. High-resolution crystal structures of four mutants (T217V, T217A, M218L and G219V) of the ribosomal protein L1 from Thermus thermophilus (TthL1) in complex with a specific 80?nt fragment of 23S rRNA and the structures of two of these mutants (T217V and G219V) in the RNA-unbound form are reported in this work. All mutations are located in the highly conserved triad Thr-Met-Gly, which is responsible for about 17% of all protein-RNA hydrogen bonds and 50% of solvent-inaccessible intermolecular hydrogen bonds. In the mutated proteins without bound RNA the RNA-binding regions show substantial conformational changes. On the other hand, in the complexes with RNA the structures of the RNA-binding surfaces in all studied mutants are very similar to the structure of the wild-type protein in complex with RNA. This shows that formation of the RNA complexes restores the distorted surfaces of the mutant proteins to a conformation characteristic of the wild-type protein complex. Domain I of the mutated TthL1 and helix 77 of 23S rRNA form a rigid body identical to that found in the complex of wild-type TthL1 with RNA, suggesting that the observed relative orientation is conserved and is probably important for ribosome function. Analysis of the complex structures and the kinetic data show that the number of intermolecular contacts and hydrogen bonds in the RNA-protein contact area does not correlate with the affinity of the protein for RNA and cannot be used as a measure of affinity. PMID:25664749

  1. Impact of Protein-Protein Interactions on Global Intermolecular Translocation Rates of the Transcription Factors Sox2 and Oct1 Between DNA Cognate Sites Analyzed by z-Exchange

    E-print Network

    Clore, G. Marius

    of the Transcription Factors Sox2 and Oct1 Between DNA Cognate Sites Analyzed by z-Exchange NMR Spectroscopy Yuki of Sox2/Oct1 interaction on intermolecular translocation 1 Address correspondence to: G. Marius Clore and intersegment transfer / z-exchange spectroscopy Background: Sox2 and Oct1 interact on a variety of promoters

  2. A Structural Basis for the Regulation of the LIM-Homeodomain Protein Islet 1 (Isl1) by Intra- and Intermolecular Interactions*

    PubMed Central

    Gadd, Morgan S.; Jacques, David A.; Nisevic, Ivan; Craig, Vanessa J.; Kwan, Ann H.; Guss, J. Mitchell; Matthews, Jacqueline M.

    2013-01-01

    Islet 1 (Isl1) is a transcription factor of the LIM-homeodomain (LIM-HD) protein family and is essential for many developmental processes. LIM-HD proteins all contain two protein-interacting LIM domains, a DNA-binding homeodomain (HD), and a C-terminal region. In Isl1, the C-terminal region also contains the LIM homeobox 3 (Lhx3)-binding domain (LBD), which interacts with the LIM domains of Lhx3. The LIM domains of Isl1 have been implicated in inhibition of DNA binding potentially through an intramolecular interaction with or close to the HD. Here we investigate the LBD as a candidate intramolecular interaction domain. Competitive yeast-two hybrid experiments indicate that the LIM domains and LBD from Isl1 can interact with apparently low affinity, consistent with no detection of an intermolecular interaction in the same system. Nuclear magnetic resonance studies show that the interaction is specific, whereas substitution of the LBD with peptides of the same amino acid composition but different sequence is not specific. We solved the crystal structure of a similar but higher affinity complex between the LIM domains of Isl1 and the LIM interaction domain from the LIM-HD cofactor protein LIM domain-binding protein 1 (Ldb1) and used these coordinates to generate a homology model of the intramolecular interaction that indicates poorer complementarity for the weak intramolecular interaction. The intramolecular interaction in Isl1 may provide protection against aggregation, minimize unproductive DNA binding, and facilitate cofactor exchange within the cell. PMID:23750000

  3. Solid solution of triptycenequinone and triptycenehydroquinone as a non-stoichiometric quinhydrone. Bathochromic changes in color caused by local intermolecular interaction between p-benzoquinone and hydroquinone moieties

    NASA Astrophysics Data System (ADS)

    Yamamura, Kimiaki; Kawashima, Taiga; Eda, Kazuo; Tajima, Fukue; Hashimoto, Masao

    2005-02-01

    Binary crystal formed by 9,10-dihydro-9,10-[ o]benzenoanthracene-1,4-dione (triptycenequinone, TPQ, yellow) and 9,10-dihydro-9,10-[ o]benzenoanthracene-1,4-diol (triptycenehydroquinone, TPHQ, colorless) was found to be a substitutional solid solution of TPQ doped by TPHQ with concentration of TPHQintermolecular CT interaction between the p-benzoquinone and hydroquinone moieties of TPQ and TPHQ, respectively, enabled by a disorder in the binary crystal. It seemed appropriate to regard the solid solution as non-stoichiometric quinhydrone. Crystal structure of pure TPHQ is also reported. A common molecular arrangement in the crystals of pure TPQ and pure TPHQ, as well as the resemblance in the molecular structure, seems to be favorable for the formation of the solid solution.

  4. Universal scaling of potential energy functions describing intermolecular interactions. I. Foundations and scalable forms of new generalized Mie, Lennard-Jones, Morse, and Buckingham exponential-6 potentials

    SciTech Connect

    Xantheas, Sotiris S.; Werhahn, Jasper C.

    2014-08-14

    Based on the formulation of the analytical expression of the potential V(r) describing intermolecular interactions in terms of the dimensionless variables r*=r/rm and !*=V/!, where rm is the separation at the minimum and ! the well depth, we propose more generalized scalable forms for the commonly used Lennard-Jones, Mie, Morse and Buckingham exponential-6 potential energy functions (PEFs). These new generalized forms have an additional parameter from and revert to the original ones for some choice of that parameter. In this respect, the original forms can be considered as special cases of the more general forms that are introduced. We also propose a scalable, but nonrevertible to the original one, 4-parameter extended Morse potential.

  5. A surface plasmon resonance study of the intermolecular interaction between Escherichia coli topoisomerase I and pBAD/Thio supercoiled plasmid DNA

    PubMed Central

    Tiwari, Purushottam Babu; Annamalai, Thirunavukkarasu; Cheng, Bokun; Narula, Gagandeep; Wang, Xuewen; Tse-Dinh, Yuk-Ching; He, Jin; Darici, Yesim

    2014-01-01

    To date, the bacterial DNA topoisomerases are one of the major target biomolecules for the discovery of new antibacterial drugs. DNA topoisomerase regulates the topological state of DNA, which is very important for replication, transcription and recombination. The relaxation of negatively supercoiled DNA is catalyzed by bacterial DNA topoisomerase I (topoI) and this reaction requires Mg2+. In this report, we first quantitatively studied the intermolecular interactions between Escherichia coli topoisomerase I (EctopoI) and pBAD/Thio supercoiled plasmid DNA using surface plasmon resonance (SPR) technique. The equilibrium dissociation constant (Kd) for EctopoI-pBAD/Thio interactions is determined to be about 8 nM. We then studied the effect of Mg2+ on the catalysis of EctopoI-pBAD/Thio reaction. A slightly higher equilibrium dissociation constant (~15 nM) was obtained for Mg2+ coordinated EctopoI (Mg2+EctopoI)-pBAD/Thio interactions. In addition, we observed a larger dissociation rate constant (kd) for Mg2+EctopoI-pBAD/Thio interactions (~0.043 s?1), compared to EctopoI-pBAD/Thio interactions (~0.017 s?1). These results suggest that enzyme turnover during plasmid DNA relaxation is enhanced due to the presence of Mg2+ and furthers the understanding of importance of the Mg2+ ion for bacterial topoisomerase I catalytic activity. PMID:24530905

  6. Bose condensates with strong anisotropic interaction

    NASA Astrophysics Data System (ADS)

    Avdeenkov, Alexander; Bohn, John L.; Bortolotti, Daniele C. E.

    2004-05-01

    We theoretically investigate trapped Bose condensates with strong dipolar interactions, in the presence of an external electrostatic field. As a prototype we consider polar OH molecules. Previously such systems have been studied in the case of a very strong external field that aligns all the dipoles along the field axis[1,2]. Here we relax this assumption and investigate the influence of finite external field, also taking into account the internal fine structure of the molecules. As a first approximation we treat the intermolecular coordinates as adiabatic and construct an effective potential by diagonalizing Stark and dipole-dipole hamiltonians. The anisotropy of these adiabatic surfaces is a function of an external field, and does not always resemble the interaction between polarized dipoles. We discuss the implications of finite electric field on the stability and geometry of the condensate. [1] K.Goral, K.Rzazewski, and T.Pfau, Phys.Rev.A 61, 051601/1(2000) [2] L.Santos, G.V.Shlyapnikov, P.Zoller and M.Lewenstein, Phys.Rev.Lett.85,1791(2000)

  7. Structural Analysis of Intermolecular Interactions in the Kinesin Adaptor Complex Fasciculation and Elongation Protein Zeta 1/ Short Coiled-Coil Protein (FEZ1/SCOCO)

    PubMed Central

    da Silva, Júlio César; Sforça, Maurício Luís; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jörg

    2013-01-01

    Cytoskeleton and protein trafficking processes, including vesicle transport to synapses, are key processes in neuronal differentiation and axon outgrowth. The human protein FEZ1 (fasciculation and elongation protein zeta 1 / UNC-76, in C. elegans), SCOCO (short coiled-coil protein / UNC-69) and kinesins (e.g. kinesin heavy chain / UNC116) are involved in these processes. Exploiting the feature of FEZ1 protein as a bivalent adapter of transport mediated by kinesins and FEZ1 protein interaction with SCOCO (proteins involved in the same path of axonal growth), we investigated the structural aspects of intermolecular interactions involved in this complex formation by NMR (Nuclear Magnetic Resonance), cross-linking coupled with mass spectrometry (MS), SAXS (Small Angle X-ray Scattering) and molecular modelling. The topology of homodimerization was accessed through NMR (Nuclear Magnetic Resonance) studies of the region involved in this process, corresponding to FEZ1 (92-194). Through studies involving the protein in its monomeric configuration (reduced) and dimeric state, we propose that homodimerization occurs with FEZ1 chains oriented in an anti-parallel topology. We demonstrate that the interaction interface of FEZ1 and SCOCO defined by MS and computational modelling is in accordance with that previously demonstrated for UNC-76 and UNC-69. SAXS and literature data support a heterotetrameric complex model. These data provide details about the interaction interfaces probably involved in the transport machinery assembly and open perspectives to understand and interfere in this assembly and its involvement in neuronal differentiation and axon outgrowth. PMID:24116125

  8. Directional Fe–C?O?S intermolecular interaction leading to chain-like crystal packing in binuclear Fe(0)–M(II) (M=Hg, Cd) complexes with 2-(diphenylphosphino)thiazole

    Microsoft Academic Search

    Shan-Ming Kuang; Zheng-Zhi Zhang; Feng Xue; Thomas C. W. Mak

    1999-01-01

    A new thiazole-based phosphine ligand was designed to construct heterobinuclear complexes (CO)3Fe(?-Ph2PNS)2MX2 (M=Hg, X=SCN; M=Cd, X=I; Ph2PNS=2-(diphenylphosphino)thiazole), in which weak Fe–C?O?S intermolecular interaction led to chain-like molecular packing in the solid state.

  9. Trading polymeric microspheres: Exchanging DNA molecules via microsphere interaction.

    PubMed

    Morimoto, Nobuyuki; Muramatsu, Kanna; Nomura, Shin-Ichiro M; Suzuki, Makoto

    2015-04-01

    A new class of artificial molecular transport system is constructed by polymeric microspheres. The microspheres are prepared by self-assembly of poly(ethylene glycol)-block-poly(3-dimethyl(methacryloyloxyethyl)ammonium propane sulfonate), PEG-b-PDMAPS, by intermolecular dipole-dipole interaction of sulfobetaine side chains in water. Below the upper critical solution temperature (UCST) of PEG-b-PDMAPS, the microspheres (?1?m) interact with other microspheres by partial and transit fusion. In order to apply the interaction between microspheres, a 3'-TAMRA-labeled single-stranded DNA oligomer (ssDNA) is encapsulated into a PEG-b-PDMAPS microsphere by thermal treatment. The exchange of ssDNA between microspheres is confirmed by fluorescence resonance energy transfer (FRET) quenching derived from double-stranded formation with complementary 5'-BHQ-2-labeled ssDNA encapsulated in PEG-b-PDMAPS microspheres. The exchange rate of ssDNA is controllable by tuning the composition of the polymer. The contact-dependent transport of molecules can be applied in the areas of microreactors, sensor devices, etc. PMID:25731098

  10. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

    PubMed

    Pley, H W; Flaherty, K M; McKay, D B

    1994-11-01

    In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs. PMID:7526219

  11. A programmable optimization environment using the GAMESS-US and MERLIN/MCL packages. Applications on intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Kalatzis, Fanis G.; Papageorgiou, Dimitrios G.; Demetropoulos, Ioannis N.

    2006-09-01

    The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of

  12. Isotherm-based thermodynamic model for electrolyte and nonelectrolyte solutions incorporating long- and short-range electrostatic interactions.

    PubMed

    Ohm, Peter B; Asato, Caitlin; Wexler, Anthony S; Dutcher, Cari S

    2015-04-01

    The activities of solutes and solvents in solutions govern numerous physical phenomena in a wide range of practical applications. In prior work, we used statistical mechanics and multilayer adsorption isotherms to develop a transformative model for capturing thermodynamic properties of multicomponent aqueous solutions over the entire concentration range (Dutcher et al. J. Phys. Chem. 2011, 2012, 2013). That model needed only a few adsorption energy values to represent the solution thermodynamics of each solute. In the current work, we posit that the adsorption energies are due to dipole-dipole electrostatic forces in solute-solvent and solvent-solvent interactions. This hypothesis was tested in aqueous solutions on (a) 37 1:1 electrolytes, over a range of cation sizes, from H(+) to tetrabutylammonium, for common anions including Cl(-), Br(-), I(-), NO3(-), OH(-), ClO4(-), and (b) 20 water-soluble organic molecules including alcohols and polyols. For both electrolytes and organic solutions, the energies of adsorption can be calculated with the dipole moments of the solvent, molecular size of the solvent and solute, and the solvent-solvent and solvent-solute intermolecular bond lengths. Many of these physical properties are available in the literature, with the exception of the solute-solvent intermolecular bond lengths. For those, predictive correlations developed here enable estimation of solute and solvent solution activities for which there are little or no activity data. PMID:25685901

  13. Surface activity at the planar interface in relation to the thermodynamics of intermolecular interactions in the ternary system: maltodextrin-small-molecule surfactant-legumin.

    PubMed

    Myasoedova, M S.; Semenova, M G.; Belyakova, L E.; Antipova, A S.

    2001-07-01

    We report on the effect of potato maltodextrins with variable dextrose equivalent (Paselli SA-2, SA-6 and SA-10) on the surface behavior at the air-water interface of the mixture: legumin+small-molecule surfactant. Distinct in nature small-molecule surfactants (model: sodium salt of capric acid, Na-caprate; and commercially important: a citric acid ester of monoglyceride, CITREM) have been under our consideration. The role of the structure of both of the maltodextrins and the small-molecule surfactants in the effect studied has been elucidated by measurements in a bulk aqueous medium of the enthalpy of their interaction from mixing calorimetry, value of weight average molecular weight of the maltodextrins and the thermodynamics of the pair maltodextrin-solvent and maltodextrin-protein interactions from laser static light scattering. The combined data of mixing calorimetry and light scattering suggest some complex formation between the small-molecule surfactants and the maltodextrins. Predominantly hydrophobic interactions along with hydrogen bonding form the basis of the complexes. The effect of the maltodextrins on the thermodynamics of the protein heat denaturation and thereby on the protein conformational stability in the presence of the small-molecule surfactants has been studied by differential scanning calorimetry. The interrelation between the thermodynamics of intermolecular interactions in a bulk and the surface behavior at the planar air-water interface of the ternary systems (maltodextrin+legumin+small-molecule surfactant) has been elucidated by tensiometry. The effect of the maltodextrins on the surface activity of mixtures of legumin with the small-molecule surfactants is governed by the competitive in relation to the protein interactions with the small-molecule surfactants and a subsequent change in the thermodynamic properties of the both biopolymers, which are favorable to the ternary complex formation. PMID:11377947

  14. Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS

    Microsoft Academic Search

    Gajjela Raju; Ragampeta Srinivas; Vangala Santhosh Reddy; Mohammed M. Idris; Ahmed Kamal; Narayana Nagesh

    2012-01-01

    Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine

  15. Solvent interactions with the Trp-cage peptide in 35% ethanol-water.

    PubMed

    Neuman, Robert C; Gerig, John T

    2008-10-01

    Intermolecular NOE experiments have been used to explore interactions of water and ethanol molecules in 35% ethanol/65% water (v/v) with the peptide Trp-cage at temperatures from 5 to 25 degrees C. Magnetic dipole-dipole cross-relaxation terms sigma(HH) (NOE) and sigma(HH) (ROE) for interaction of solvent components with spins of the peptide suggest that ethanol molecules associate with backbone atoms for times of the order of nanoseconds at 5 degrees C. Formation of peptide-ethanol complexes can also account for the larger-than-expected values of cross-relaxation terms at higher temperatures. Hydrocarbon side chains of the peptide do not appear to experience such interactions with ethanol. Cross relaxation resulting from water-peptide interactions are consistent with long-lived water interactions with the backbone atoms. Water cross relaxation with nonpolar side chains of the peptide (Leu2, Ile4, Leu7, and proline residues) are only those expected for bulk solvent. However, long-lived association of both water and ethanol with the polar side chains of Tyr3 and Trp6 is indicated by the data. PMID:18506810

  16. Basis sets for the evaluation of van der Waals complex interaction energies: Ne-N2 intermolecular potential and microwave spectrum.

    PubMed

    Baranowska-??czkowska, Angelika; Fernández, Berta

    2014-01-30

    In order to obtain efficient basis sets for the evaluation of van der Waals complex intermolecular potentials, we carry out systematic basis set studies. For this, interaction energies at representative geometries on the potential energy surfaces are evaluated using the CCSD(T) correlation method and large polarized LPol-n and augmented polarization-consistent aug-pc-2 basis sets extended with different sets of midbond functions. On the basis of the root mean square errors calculated with respect to the values for the most accurate potentials available, basis sets are selected for fitting the corresponding interaction energies and getting analytical potentials. In this work, we study the Ne-N2 van der Waals complex and after the above procedure, the aug-pc-2-3321 and the LPol-ds-33221 basis set results are fitted. The obtained potentials are characterized by T-shaped global minima at distances between the Ne atom and the N2 center of mass of 3.39 Å, with interaction energies of -49.36 cm(-1) for the aug-pc-2-3321 surface and -50.28 cm(-1) for the LPol-ds-33221 surface. Both sets of results are in excellent agreement with the reference surface. To check the potentials further microwave transition frequencies are calculated that agree well with the experimental and the aV5Z-33221 values. The success of this study suggests that it is feasible to carry out similar accurate calculations of interaction energies and ro-vibrational spectra at reduced cost for larger complexes than has been possible hitherto. PMID:24375320

  17. Dipole interactions in electrofusion. Contributions of membrane potential and effective dipole interaction pressures.

    PubMed Central

    Stenger, D A; Kaler, K V; Hui, S W

    1991-01-01

    The contributions of pulse-induced dipole-dipole interaction to the total pressure acting normal to the membranes of closely positioned pronase treated human erythrocytes during electrofusion was calculated. The total pressure was modeled as the sum of pressures arising from membrane potential and dipole-dipole attraction opposed by interbilayer repulsion. The dipole-dipole interaction was derived from the experimentally obtained cell polarizability. The threshold electric field amplitude necessary for fusion of pronase-treated human erythrocytes was experimentally obtained at various combinations of pulse duration, frequency, and the conductivity of the external medium. The theoretical values of the critical electric field amplitude compared favorably to the experimentally obtained threshold field amplitudes. Fusion by dc pulses may be primarily attributed to attainment of sufficiently high membrane potentials. However, with decreasing external conductivity and increasing sinusoidal pulse frequency (100 kHz-2.5 MHz), the induced dipole-dipole interactions provide the principal driving force for membrane failure leading to fusion. Images FIGURE 5 PMID:1868154

  18. Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction

    SciTech Connect

    Yang, Li; Tunega, Daniel; Xu, Lai; Govind, Niranjan; Sun, Rui; Taylor, Ramona; Lischka, Hans; De Jong, Wibe A.; Hase, William L.

    2013-08-29

    In a previous study (J. Phys. Chem. C 2011, 115, 12403) cluster models for the TiO2 rutile (110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared with DFT "slab" calculations for DMMP interacting with the TiO2 (110) surface and with DFT cluster models for the TiO2 (110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/ TiO2 (110) potential energy curves in excellent agreement with those obtained from the slab calculations. The cluster models for the TiO2 (110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functional. These DFT calculations do not give DMMP/TiO2 (110) interaction energies which agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster models show that they do not accurately represent the HOMO and LUMO for the surface, which should be 2p and 3d orbitals, respectively, and the models also do not give an accurate band gap. The MP2 cluster models do not accurately represent the LUMO and that they give accurate DMMP/TiO2 (110) interaction energies is apparently fortuitous, arising from their highly inaccurate band gaps. Accurate cluster models, consisting of 7, 10, and 15 Ti-atoms and which have the correct HOMO and LUMO properties, are proposed. The work presented here illustrates the care that must be taken in "constructing" cluster models which accurately model surfaces.

  19. Problem-Based Learning in 9th Grade Chemistry Class: `Intermolecular Forces'

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

    This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students’ understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student’s alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified by cognitive levels and then randomly assigned to experimental (PBL, 40 students) and control (lecture-style teaching, 38 students) groups. Following a preparatory lesson where activation and remediation of existing knowledge occur, a pre-test was given, and no significant difference was found between the two groups of students ( p > .05). After the instruction was completed, a post-test and also a questionnaire related to the quality of the problem, the teacher’s role and group functioning were administered. Results from the post-test of both groups ( p < .05) and questionnaire showed that PBL is affective on students’ achievement, remedying formation of alternate conceptions and also social skills.

  20. Vibrational absorption, vibrational circular dichroism, and theoretical studies of methyl lactate self-aggregation and methyl lactate-methanol intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Yang, Guochun; Losada, Martin; Xu, Yunjie

    2010-06-01

    The infrared vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of methyl lactate in carbon tetrachloride and methanol have been measured in the 1000-1800 cm-1 region. Noticeable changes due to the solute self-aggregation and solvent-solute intermolecular hydrogen-bonding interactions have been detected in the reported spectra of the 2M methyl lactate solution in CCl4 and in methanol, respectively. Molecular dynamics simulations and a series of density functional theory (DFT) B3LYP/6-311++G??) and single point MP2/6-311++G?? energy calculations have been performed to identify and to model the explicit hydrogen-bonding interactions between the methanol solvent and the methyl lactate solute and among the methyl lactate molecules. Geometry search and optimization have been performed for the most stable conformers of the methyl lactate dimer and the methyl lactate-(methanol)N clusters, with N =1, 2, and 3. The relative single point MP2 energies among conformers are noticeably different from those obtained with DFT for the larger methyl lactate-methanol complexes. The VA and VCD spectra of these complexes have been simulated and compared to the corresponding experimental spectra. From the combined experimental and theoretical VA and VCD studies, it has been identified that both the methyl lactate monomer and dimer are the main species in the 2M CCl4 solution with 65% and 35% relative abundances, respectively, while the binary (55%) and quaternary (30%) methyl lactate-methanol clusters dominate in the 2M methanol solution, together with a smaller amount (15%) of the methyl lactate monomer. The effects of solute self-aggregation and solute-solvent interactions have been investigated in detail.

  1. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf{sup 3+}

    SciTech Connect

    Galbis, Elsa; Pappalardo, Rafael R.; Marcos, Enrique Sánchez, E-mail: sanchez@us.es [Departmento de Química Física, Universidad de Sevilla, 41012 Seville (Spain); Hernández-Cobos, Jorge [Instituto de Ciencias Físicas, UNAM, Apartado Postal 48-3, 62251 Cuernavaca (Mexico)

    2014-06-07

    This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H{sub 2}O){sub n}]{sup m+}(H{sub 2}O){sub ?} clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H{sub 2}O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R{sub Cf??O} in the range 2.43–2.48 Å, whereas the fourth one is closer to 9 with R{sub Cf??O} = 2.54 Å. Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

  2. Ligand field and intermolecular interactions tuning the magnetic properties of spin-crossover Fe(II) polymer with 4,4?-bipyridine

    NASA Astrophysics Data System (ADS)

    Luo, Yang-Hui; Liu, Qing-Ling; Yang, Li-Jing; Ling, Yang; Wang, Wei; Sun, Bai-Wang

    2015-02-01

    A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4?-bipyridine (4,4?-bipy) family: {Fe(4,4?-bipy)2(H2O)2}·(4,4?-bipy)· 8(H2O)·2(ClO4) (3), which displays half spin transitions between 100 and 300 K, has been synthesized and structurally characterized. Compound 3 featured with two-dimensional (2-D) grids connected by hydrogen bonds and ?…? packing between one-dimensional (1-D) chains, the 2-D grids expand to three-dimensional (3-D) architecture supported by a 'S-shaped holder' involving lattice 4-4?-bipy, water molecules and perchlorate anion. We compared 3 with the other two analogous complexes: ({Fe(4,4?-bipy) (H2O)2 (NCS)2}·4,4?-bipy, 1 and {Fe(4,4?-bipy)2(NCS)2}·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS-) and lone-pair…H contacts contribute to the stabilization of HS (high-spin) state of the Fe(II) ion, while the high ligand field strength (4,4?-bipy) and strong intermolecular contacts (hydrogen bonds and ?…? packing interactions) make for the LS (low-spin) state.

  3. The analysis of intermolecular interactions in concentrated hyaluronan solutions suggest no evidence for chain-chain association.

    PubMed Central

    Gribbon, P; Heng, B C; Hardingham, T E

    2000-01-01

    Confocal fluorescence recovery after photobleaching (confocal-FRAP) was used to examine the influence of electrolytes (NaCl, KCl, MgCl(2), MnCl(2) and CaCl(2)) on the network and hydrodynamic properties of fluoresceinamine-labelled hyaluronan (FA-HA) at concentrations up to 10 mg/ml. Self and tracer lateral diffusion coefficients showed that in Ca(2+) and Mn(2+), FA-HA (830 kDa) was more compact than in Mg(2+), Na(+) or K(+). These results were correlated with changes in the hydrodynamic radius of HA, determined by multi-angle laser-light-scattering analysis in dilute solution, which was smaller in CaCl(2) (36 nm) than in NaCl (43 nm). The permeability of more concentrated solutions of HA (<10 mg/ml) to FITC-dextran tracers (2000 kDa) was higher in CaCl(2). The properties of HA in urea (up to 6 M) were investigated to test for hydrophobic interactions and also in ethanol/water (up to 62%, v/v). In both, there was reduced hydrodynamic size and increased permeability to FITC-dextran, suggesting increased chain flexibility, but it did not show the changes predicted if chain-chain association was disrupted by urea, or enhanced by ethanol. Oligosaccharides of HA (HA(20-26)) also had no effect on the self diffusion of high-molecular-mass FA-HA (830 kDa) solutions, or on dextran tracer diffusion, showing that there were no chain-chain interactions open to competition by short-chain segments. The results suggest that the effects of electrolytes and solvent are determined primarily by their effect on HA chain flexibility, with no evidence for association between chain segments contributing significantly to the major properties. PMID:10926861

  4. Intermolecular interactions between the A and B subunits of heat-labile enterotoxin from Escherichia coli promote holotoxin assembly and stability in vivo.

    PubMed

    Streatfield, S J; Sandkvist, M; Sixma, T K; Bagdasarian, M; Hol, W G; Hirst, T R

    1992-12-15

    Cholera toxin and the related heat-labile enterotoxin (LT) produced by Escherichia coli consist of a holotoxin of one A subunit and five B subunits (AB5). Here we investigate the domains of the A subunit (EtxA) of E. coli LT which influence the events of B-subunit (EtxB) oligomerization and the formation of a stable AB5 holotoxin complex. We show that the C-terminal 14 amino acids of the A subunit comprise two functional domains that differentially affect oligomerization and holotoxin stability. Deletion of the last 14 amino acids (-14) from the A subunit resulted in a molecule that was significantly impaired in its capacity to promote the assembly of a mutant B subunit, EtxB191.5. In contrast, deletion of the last four amino acids (-4) from the A subunit gave a molecule that retained such a capacity. This suggests that C-terminal residues within the -14 to -4 region of the A subunit are important for promoting the oligomerization of EtxB. In addition, we demonstrate that the truncated A subunit lacking the last 4 amino acids was unable to form a stable AB5 holotoxin complex even though it promoted B-subunit oligomerization. This suggests that the last 4 residues of the A subunit function as an "anchoring" sequence responsible for maintaining the stability of A/B subunit interaction during holotoxin assembly. These data represent an important example of how intermolecular interactions between polypeptides in vivo can modulate the folding and assembly of a macromolecular complex. PMID:1465452

  5. Observation of Stckelberg oscillations in dipole-dipole interactions C. S. E. van Ditzhuijzen, Atreju Tauschinsky, and H. B. van Linden van den Heuvell

    E-print Network

    Amsterdam, Universiteit van

    , Atreju Tauschinsky, and H. B. van Linden van den Heuvell Van der Waals-Zeeman Institute, University states we use show a quadratic Stark shift, which leads to a fundamentally different behavior than in the linearly shifting case and by the generalized Bessel function in the quadratically shifting case

  6. PHYSICAL REVIEW B 87, 035440 (2013) Role of charge transfer, dipole-dipole interactions, and electrostatics in Fermi-level pinning

    E-print Network

    Peters, Achim

    2013-01-01

    , such as light emitting diodes, solar cells, or field effect transistors. The efficiency of these devices depends alignment (ELA) at organic-organic (O-O) heterojunctions grown on electrodes. In this paper, we aim relevant heterojunctions, e.g. in organic opto-electronic devices. DOI: 10.1103/PhysRevB.87.035440 PACS

  7. FT-IR study on interactions between medroxyprogesterone acetate and solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems

    NASA Astrophysics Data System (ADS)

    Shi, Jie-hua; Fan, Chun-hui

    2012-09-01

    The intermolecular interactions between medroxyprogesterone acetate (MPA) and CHCl3 and CCl4 solvent in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems have been studied by Fourier transform infrared spectroscopy (FT-IR). The experimental results showed that there are hydrogen bonding interactions between oxygen atoms of all carbonyl groups in MPA and hydrogen atom of CHCl3 so as to form 1:3 complex of MPA with CHCl3 and produce three new absorption bands at 1728.9-1736.1, 1712.7-1717.4 and 1661.9-1673.8 cm-1, respectively. And, 1:1 complex of MPA with CCl4 is formed in CCl4/cyclo-C6H12 binary solvent as a result of hydrogen bonding interaction between C3 carbonyl group and empty d-orbital in chlorine atom of CCl4 leading to producing new absorption band at 1673.2-1674.2 cm-1. However, all free carbonyl and associated carbonyl stretching vibrations of MPA in CHCl3/cyclo-C6H12 and CCl4/cyclo-C6H12 binary solvent systems shift to lower wavenumbers with the increasing of volume fraction of CHCl3 and CCl4 in binary solvent systems owing to the dipole-dipole interaction and the dipole-induced dipole interaction between MPA and solvents.

  8. ?,?-Bis(3,6-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)alkanes and products of their cyclization, pyrimidinophanes: intra- and intermolecular interaction in crystals and in solutions

    Microsoft Academic Search

    V. E. Semenov; O. A. Lodochnikova; A. T. Gubaidullin; O. N. Kataeva; A. V. Chernova; Y. Ya. Efremov; S. V. Kharlamov; Sh. K. Latypov; V. S. Reznik

    2008-01-01

    Reaction of ?,?-bis(3,6-dimethyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)alkanes with paraformaldehyde leads to pyrimidinophanes,\\u000a which contain four 3,6-dimethyluracil fragments, connected to each other by the methylene chains. A comparative study of intra-\\u000a and intermolecular interactions of “open” and macrocyclic uracil derivatives in the crystal state and in solution was performed.\\u000a According to the NMR spectroscopy data, there is no self-association of “open” and macrocyclic compounds in

  9. Desensitization of metastable intermolecular composites

    DOEpatents

    Busse, James R. (South Fork, CO); Dye, Robert C. (Los Alamos, NM); Foley, Timothy J. (Los Alamos, NM); Higa, Kelvin T. (Ridgecrest, CA); Jorgensen, Betty S. (Jemez Springs, NM); Sanders, Victor E. (White Rock, NM); Son, Steven F. (Los Alamos, NM)

    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.

  10. How resonance assists hydrogen bonding interactions: an energy decomposition analysis.

    PubMed

    Beck, John Frederick; Mo, Yirong

    2007-01-15

    Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs. PMID:17143867

  11. Interactions between ions with orbital angular momentum in insulators

    Microsoft Academic Search

    J M Baker

    1971-01-01

    Until recently most interest in interactions between paramagnetic ions has centred upon ions with quenched orbital angular momentum, for which exchange has the isotropic Heisenberg form JS1.S2 and the major anisotropic terms are due to magnetic dipole-dipole interaction. The interactions for ions with unquenched orbital angular momentum are quite different; exchange is anisotropic, and in addition to exchange and magnetic

  12. Effect of the strong magnetic field on the magnetic interaction between two non-magnetic particles migrating in a conductive fluid

    Microsoft Academic Search

    Z. Sun; T. Kokalj; M. Guo; F. Verhaeghe; O. Van der Biest; B. Blanpain; K. Van Reusel

    2009-01-01

    This paper presents a theoretical analysis of the interaction between two non-magnetic particles migrating in a conductive fluid due to an imposed strong magnetic field. A repulsive force induced by the conductive fluid flow around the particles is first derived and calculated for a concrete example. From the numerical results, a counteracting behavior with the interparticle magnetic dipole-dipole attractive force

  13. Impact of Protein/Protein Interactions on Global Intermolecular Translocation Rates of the Transcription Factors Sox2 and Oct1 between DNA Cognate Sites Analyzed by z-Exchange NMR Spectroscopy*

    PubMed Central

    Takayama, Yuki; Clore, G. Marius

    2012-01-01

    Oct1 and Sox2 synergistically regulate developmental genes by binding to adjacent sites within promoters. We have investigated the kinetics of global intermolecular translocation of Sox2 and Oct1 between cognate sites located on different DNA molecules by z-exchange NMR spectroscopy. In the Hoxb1 promoter, the Sox2 and Oct1 sites are immediately adjacent to one another, and the intermolecular translocation rates are too slow to be measured by z-exchange spectroscopy. By introducing a 3-bp insertion between the Sox2 and Oct1 sites to mimic the spacing in the FGF4 enhancer, the interprotein contact surface is reduced, and the translocation rates are increased. Interaction between Sox2 and the POU-specific domain (POUS) of Oct1 does not affect the translocation mechanism but modulates the rates. Translocation involves only jumping (dissociation and reassociation) for Sox2, but both jumping and direct intersegment transfer (no dissociation into free solution) for Oct1. The dissociation (koff ?1.5 s?1) and association (kon ?5.1 × 109 m?1s?1) rate constants for Sox2 are reduced 4-fold and increased 5-fold, respectively, in the presence of Oct1. koff (?3.5 s?1) for Oct1 is unaffected by Sox2, whereas kon (?1.3 × 109 m?1s?1) is increased ?13-fold. The direct intermolecular translocation rate (kinter ?1.8 × 104 m?1s?1) for the POUS domain of Oct1 is reduced 2-fold by Sox2, whereas that for the POU homeodomain (POUHD) of Oct1 (kinter ? 1.7 × 104 m?1s?1) remains unaltered, consistent with the absence of contacts between Sox2 and POUHD. The data suggest a model for the sequence of binding events involved in synergistic gene regulation by Sox2 and Oct1. PMID:22718759

  14. Two body and multibody interaction in a cold Rydberg gas

    NASA Astrophysics Data System (ADS)

    Han, Jianing; Gallagher, Tom

    2009-05-01

    Cold Rydberg atoms trapped in a Magneto Optical Trap (MOT) are not isolated and they tend to bond through dipole-dipole and multiple-multiple interactions between Rydberg atoms. The dipole-dipole interaction and van der Waals interaction between two atoms have been intensively studied. However, the fact that the dipole-dipole interaction and van der Waals interaction show the same size of broadening, studied by Raithel's group, and there is transition between two molecular states, studied by Farooqi and Overstreet, can not be explained by the two atom picture. The purpose of this paper is to show the multibody nature of a dense cold Rydberg gas by studying the molecular state microwave spectrum. Specifically, single body, two body and three body interaction regions are separated. Moreover, the multibody energy levels for selected geometries are calculated. In addition, multibody blockade will be discussed. [3pt] [1] A. Reinhard, K. C. Younge, T. Cubel Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett. 100, 233201 (2008).[0pt] [2] S.M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic,Y.P. Zhang, J.R. Ensher, A.S. Estrin, C. Boisseau, R. Cote, E.E. Eyler, and P.L. Gould, Phys. Rev. Lett. 91, 183002 (2003).[0pt] [3] K. Richard Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 76, 011403 (2007).

  15. Platelet activating factor antagonist design. 3. X-ray crystal structure and intermolecular crystal lattice interactions of methyl trans-4-acetoxymethyl-4,5-dihydro-2,5-bis(3,4-methylenedioxyphenyl)- 3-furancarboxylate.

    PubMed

    Peterson, J R; Horsley, D B; Brozik, J A; Rogers, R D

    1989-08-15

    C23H20O9, Mr = 440.41, monoclinic, P21/c, a = 11.433 (1), b = 7.808 (2), c = 23.313 (3) A, beta = 99.67 (1) degree, V = 2052 A3, Z = 4, Dx = 1.43 g cm-3, lambda(MoK alpha) = 0.71073 A, mu = 0.69 cm-1, F(000) = 920, T = 293 K, final R = 0.048 for 1645 observed [Fo greater than or equal to 5 sigma(Fo)] reflections. The observed structure reveals a trans relationship for the 4-acetoxymethyl and 5-aryl substituents. The 4,5-dihydrofuran ring system adopts an envelope conformation. There is no crystallographically imposed symmetry. Several intermolecular van der Waals interactions occur in the cell lattice of this compound. PMID:2604943

  16. Long-range and frustrated spin-spin interactions in crystals of cold polar molecules

    NASA Astrophysics Data System (ADS)

    Zhou, Y. L.; Ortner, M.; Rabl, P.

    2011-11-01

    We describe a simple scheme for the implementation and control of effective spin-spin interactions in self-assembled crystals of cold polar molecules. In our scheme, spin states are encoded in two long-lived rotational states of the molecules and coupled via state-dependent dipole-dipole forces to the lattice vibrations. We show that, by choosing an appropriate time-dependent modulation of the induced dipole moments, the resulting phonon-mediated interactions compete with the direct dipole-dipole coupling and lead to long-range and tunable spin-spin interaction patterns. We illustrate how this technique can be used for the generation of multiparticle entangled spin states and the implementation of spin models with long-range and frustrated interactions, which exhibit nontrivial phases of magnetic ordering.

  17. Intermolecular Forces: Solids and Liquids

    NSDL National Science Digital Library

    General chemistry WebCT exam/quiz questions. The Intermolecular Forces: Solids and Liquids topic covers the forces that exist between atoms and molecules in solids and liquids, and how these affect properties such as boiling point, conductivity, and lattice energy.

  18. Evidence for Intermolecular Interactions between the Intracellular Domains of the Arabidopsis Receptor-Like Kinase ACR4, Its Homologs and the Wox5 Transcription Factor

    PubMed Central

    Meyer, Matthew R.; Shah, Shweta; Zhang, J.; Rohrs, Henry; Rao, A. Gururaj

    2015-01-01

    Arabidopsis CRINKLY4 (ACR4) is a receptor-like kinase (RLK) involved in the global development of the plant. The Arabidopsis genome encodes four homologs of ACR4 that contain sequence similarity and analogous architectural elements to ACR4, termed Arabidopsis CRINKLY4 Related (AtCRRs) proteins. Additionally, a signaling module has been previously proposed including a postulated peptide ligand, CLE40, the ACR4 RLK, and the WOX5 transcription factor that engage in a possible feedback mechanism controlling stem cell differentiation. However, little biochemical evidence is available to ascertain the molecular aspects of receptor heterodimerization and the role of phosphorylation in these interactions. Therefore, we have undertaken an investigation of the in vitro interactions between the intracellular domains (ICD) of ACR4, the CRRs and WOX5. We demonstrate that interaction can occur between ACR4 and all four CRRs in the unphosphorylated state. However, phosphorylation dependency is observed for the interaction between ACR4 and CRR3. Furthermore, sequence analysis of the ACR4 gene family has revealed a conserved ‘KDSAF’ motif that may be involved in protein-protein interactions among the receptor family. We demonstrate that peptides harboring this conserved motif in CRR3 and CRK1are able to bind to the ACR4 kinase domain. Our investigations also indicate that the ACR4 ICD can interact with and phosphorylate the transcription factor WOX5. PMID:25756623

  19. Roles of Intramolecular and Intermolecular Interactions in Functional Regulation of the Hsp70 J-protein Co-Chaperone Sis1.

    PubMed

    Yu, Hyun Young; Ziegelhoffer, Thomas; Osipiuk, Jerzy; Ciesielski, Szymon J; Baranowski, Maciej; Zhou, Min; Joachimiak, Andrzej; Craig, Elizabeth A

    2015-04-10

    Unlike other Hsp70 molecular chaperones, those of the eukaryotic cytosol have four residues, EEVD, at their C-termini. EEVD(Hsp70) binds adaptor proteins of the Hsp90 chaperone system and mitochondrial membrane preprotein receptors, thereby facilitating processing of Hsp70-bound clients through protein folding and translocation pathways. Among J-protein co-chaperones functioning in these pathways, Sis1 is unique, as it also binds the EEVD(Hsp70) motif. However, little is known about the role of the Sis1:EEVD(Hsp70) interaction. We found that deletion of EEVD(Hsp70) abolished the ability of Sis1, but not the ubiquitous J-protein Ydj1, to partner with Hsp70 in in vitro protein refolding. Sis1 co-chaperone activity with Hsp70?EEVD was restored upon substitution of a glutamic acid of the J-domain. Structural analysis revealed that this key glutamic acid, which is not present in Ydj1, forms a salt bridge with an arginine of the immediately adjacent glycine-rich region. Thus, restoration of Sis1 in vitro activity suggests that intramolecular interactions between the J-domain and glycine-rich region control co-chaperone activity, which is optimal only when Sis1 interacts with the EEVD(Hsp70) motif. However, we found that disruption of the Sis1:EEVD(Hsp70) interaction enhances the ability of Sis1 to substitute for Ydj1 in vivo. Our results are consistent with the idea that interaction of Sis1 with EEVD(Hsp70) minimizes transfer of Sis1-bound clients to Hsp70s that are primed for client transfer to folding and translocation pathways by their preassociation with EEVD binding adaptor proteins. These interactions may be one means by which cells triage Ydj1- and Sis1-bound clients to productive and quality control pathways, respectively. PMID:25687964

  20. An alternative multipolar expansion for intermolecular potential functions

    Microsoft Academic Search

    Sheng Der Chao; Joel D. Kress; Antonio Redondo

    2004-01-01

    We have derived a new multipolar expansion for intermolecular potential-energy functions with applications in molecular physics, theoretical chemistry, and mathematical physics. The new formulation employs a separation of radial and angular terms with a simple index structure that leads to computational efficiency and ease of physical interpretation. For the case of the Coulomb interaction, we compare the present formulation with

  1. Metallic ferroelectricity induced by anisotropic unscreened Coulomb interaction in LiOsO3

    NASA Astrophysics Data System (ADS)

    Liu, H. M.; Du, Y. P.; Xie, Y. L.; Liu, J.-M.; Duan, Chun-Gang; Wan, Xiangang

    2015-02-01

    As the first experimentally confirmed ferroelectric metal, LiOsO3 has received extensive research attention recently. Using density-functional calculations, we perform a systematic study on the origin of the metallic ferroelectricity in LiOsO3. We confirm that the ferroelectric transition in this compound is order-disorder-like. By doing electron screening analysis, we unambiguously demonstrate that the long-range ferroelectric order in LiOsO3 results from the incomplete screening of the dipole-dipole interaction along the nearest-neighboring Li-Li chain direction. We conclude that highly anisotropic screening and local dipole-dipole interactions are the two most important keys to form LiOsO3-type metallic ferroelectricity.

  2. Adsorption geometry of tetracene on SiO 2/Si (1 1 1) substrate with the balance of molecule-substrate and intermolecular interaction

    NASA Astrophysics Data System (ADS)

    Mao, Hongying; Guan, Dandan; Chen, Meiliang; Dou, Weidong; Song, Fei; Zhang, Hanjie; Li, Haiyang; He, Pimo; Bao, Shining

    2010-02-01

    The growth of tetracene on SiO 2/Si(1 1 1) substrate has been studied by ultraviolet photoemission spectroscopy measurements. Seven emission features of the organic material are located at 2.26, 3.56, 4.77, 5.88, 6.98, 8.18 and 9.90 eV, respectively, below the Fermi level. The changes in binding energy and work function during the deposition of tetracene molecules on SiO 2 substrate indicate an interaction between tetracene molecule and substrate. The interaction between tetracene molecule and substrate is weaker than that between the organic and silicon substrate. The reduction in work function is due to the formation of interface dipole. Based on the density functional theory (DFT) calculation, tetracene molecules are arranged in an upright standing manner with the optimal growth of a small cluster consisting four molecules.

  3. Redetermined structure of diphenyl­phospho­nimidotriphenyl­phospho­rane: location of the hydrogen atoms and analysis of the inter­molecular inter­actions

    PubMed Central

    Betz, Richard; Gerber, Thomas; Hosten, Eric; Schalekamp, Henk

    2011-01-01

    The title compound, C30H25NOP2, is a bulky phosphazene derivative. Its previous crystal structure [Cameron et al. (1979 ?). Acta Cryst. B35, 1373–1377] is confirmed and its H atoms have been located in the present study. The formal P=N double bond is about 0.05?Å shorter than the P—N single bond and the large P=N—P bond angle reflects the steric strain in the mol­ecule. An intra­molecular C—H?O inter­action occurs. In the crystal, short C—H?O contacts connect the mol­ecules into chains propagating in [011], which are cross-linked via C—H?? inter­actions, generating a three-dimensional network. Aromatic ?–? stacking also occurs [shortest centroid–centroid separation = 3.6012?(11)?Å]. PMID:21754359

  4. Redetermined structure of diphenyl-phospho-nimidotriphenyl-phospho-rane: location of the hydrogen atoms and analysis of the inter-molecular inter-actions.

    PubMed

    Betz, Richard; Gerber, Thomas; Hosten, Eric; Schalekamp, Henk

    2011-05-01

    The title compound, C(30)H(25)NOP(2), is a bulky phosphazene derivative. Its previous crystal structure [Cameron et al. (1979 ?). Acta Cryst. B35, 1373-1377] is confirmed and its H atoms have been located in the present study. The formal P=N double bond is about 0.05?Å shorter than the P-N single bond and the large P=N-P bond angle reflects the steric strain in the mol-ecule. An intra-molecular C-H?O inter-action occurs. In the crystal, short C-H?O contacts connect the mol-ecules into chains propagating in [011], which are cross-linked via C-H?? inter-actions, generating a three-dimensional network. Aromatic ?-? stacking also occurs [shortest centroid-centroid separation = 3.6012?(11)?Å]. PMID:21754359

  5. Iodine⋯X(O, N, S) intermolecular contacts: models of thyroid hormone?protein binding interactions using information from the cambridge crystallographic data files

    NASA Astrophysics Data System (ADS)

    Cody, Vivian; Murray-Rust, Peter

    1984-02-01

    Automated methods were used to search the Cambridge Crystallographic Data Files for all compounds containing C?I bonds that had C?I⋯X(O, N, S) contact distances less than 3.55 Å for O and for N, and less than 4.0 Å for S. Analysis of these data from 86 crystal structures showed that the distribution of nucleophile (O, N, S) contacts to iodine is non-spherical with the highest density and the shortest contacts (e.g., I⋯O = 2.96 Å) and C?I ⋯ X angle, ? = 180°. These data suggest that, where possible, that donor group is arranged so that one of its lone pairs is directed toward the iodine atom. Because the thyroid hormones are the only active iodine-containing compounds, C?I⋯X interactions were considered as possible contributros to enhanced protein binding affinity. In the crystal structure of the thyroxine—prealbumin complex there is a close contact between the proximal outer-ring iodine of thyroxine and the carbonyl oxygen of Ala-109A in the prealbumin backbone. The geometry of this interaction (I⋯O, 2.96 Å, C?I⋯O, 161°) is within the distribution of the iodine—oxygen interactions observed in this analysis, and suggests that this model can explain (in part) the unique role of iodine in the binding of the thyroid hormones to their specific binding proteins.

  6. Nature and strength of C-H···O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes.

    PubMed

    Thakur, Tejender S; Kirchner, Michael T; Bläser, Dieter; Boese, Roland; Desiraju, Gautam R

    2011-08-21

    Structural and electronic properties of C-H···O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of ?-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H···O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H···O interactions in the crystal packing of formyl compounds. PMID:21475764

  7. Important role of molecular packing and intermolecular interactions in two polymorphs of (Z)-2-phenyl-3-(4-(pyridin-2-yl)phenyl)acrylonitrile. Preparation, structures, and optical properties

    NASA Astrophysics Data System (ADS)

    Percino, M. Judith; Cerón, Margarita; Ceballos, Paulina; Soriano-Moro, Guillermo; Castro, M. Eugenia; Chapela, Víctor M.; Bonilla-Cruz, José; Reyes-Reyes, Marisol; López-Sandoval, Román; Siegler, Maxime A.

    2014-12-01

    The novel compound Z-2-phenyl-3-(4-(pyridin-2-yl)phenyl)acrylonitrile (PPyPAN) was synthesized from the condensation reaction between phenylacetonitrile and 4-(pyridin-2-yl)benzaldehyde. This compound crystallizes in two forms: polymorph I (triclinic, P - 1, Z? = 2) and polymorph II (orthorhombic, Pbc21, Z? = 2). The molecular structures and optical properties of the two polymorphs have been characterized via1H NMR, EI, FTIR, UV-Vis spectroscopy, DSC, single-crystal and XRPD. The molecular structure, packing properties, and intermolecular interactions were examined for both polymorphs of PPyPAN in order to interpret the emission properties. A subtle change in the molecular conformation (e.g., a rotation around single Csbnd C bonds) found for both polymorph plays an important role in their solid-state properties. The structure and optical properties of the new structures were well characterized and showed unique features for both polymorphic phases. For phase I, we observed an excitation spectrum with an ?ex at 325-346 nm, which is the maximum excitation or absorption wavelength for the lowest So ? S1 transition, which is characteristic to the ?-?* transition, and an emission spectrum with an ?emmax at 454 nm. For phase II, the excitation spectrum showed an ?exmax at 325 nm, whereas the ?emmax showed a red-shift to 492 nm.

  8. Adsorption geometry of tetracene on SiO 2\\/Si (1 1 1) substrate with the balance of molecule–substrate and intermolecular interaction

    Microsoft Academic Search

    Hongying Mao; Dandan Guan; Meiliang Chen; Weidong Dou; Fei Song; Hanjie Zhang; Haiyang Li; Pimo He; Shining Bao

    2010-01-01

    The growth of tetracene on SiO2\\/Si(111) substrate has been studied by ultraviolet photoemission spectroscopy measurements. Seven emission features of the organic material are located at 2.26, 3.56, 4.77, 5.88, 6.98, 8.18 and 9.90eV, respectively, below the Fermi level. The changes in binding energy and work function during the deposition of tetracene molecules on SiO2 substrate indicate an interaction between tetracene

  9. New insights into intra- and intermolecular interactions of immunoglobulins: crystal structure of mouse IgG2b-Fc at 2·1-Å resolution

    PubMed Central

    Kolenko, Petr; Dohnálek, Jan; Dušková, Jarmila; Skálová, Tereza; Collard, Renata; Hašek, Jind?ich

    2009-01-01

    The structure of the Fc fragment of monoclonal antibody IgG2b from hybridom M75 of Mus musculus has been determined by single crystal X-ray diffraction. This is the first report of the structure of the murine immunoglobulin isotype IgG2b. The structure refined at 2·1 Å resolution provides more detailed structural information about native oligosaccharides than was previously available. High-quality Fourier maps provide a clear identification of ?-l-fucose with partial occupancy in the first branch of the antennary oligosaccharides. A unique Fc:Fc interaction was observed at the CH2-CH3 interface. PMID:18783468

  10. Intermolecular potential energy surfaces for the interaction between H2X (Xdbnd O, S) and a metastable Ne*(3P2,0) atom

    NASA Astrophysics Data System (ADS)

    Falcinelli, Stefano; Bartocci, Alessio; Candori, Pietro; Pirani, Fernando; Vecchiocattivi, Franco

    2014-10-01

    Potential energy surfaces for the interaction of a Ne*(3P2,0) atom with H2O and H2S molecules are obtained on the basis of a semi empirical method that has been previously used for some specific orientations in Ne*(3P2,0)-H2O system. The method is now suitable for all orientations and also for Ne*(3P2,0)-H2S system. Interesting features emerge by comparing the two systems and appear related to different characteristics of the two molecular partners. The potential energy surface for Ne*(3P2,0)-H2S has been also successfully tested for reproducing recent experimental Penning ionization electron spectroscopy data, sensible to some specific orientations of the two colliding partners.

  11. Intermolecular Interaction in the Formaldehyde-Dimethyl Ether and Formaldehyde-Dimethyl Sulfide Complexes Investigated by Fourier Transform Microwave Spectroscopy and ab Initio Calculations.

    PubMed

    Tatamitani, Yoshio; Kawashima, Yoshiyuki; Osamura, Yoshihiro; Hirota, Eizi

    2015-03-12

    The ground-state rotational spectra of the formaldehyde-dimethyl ether (H2CO-DME) and formaldehyde-dimethyl sulfide (H2CO-DMS) complexes have been studied by Fourier transform microwave spectroscopy. The a-type and c-type rotational transitions have been assigned for the normal and deutrated formaldehyde-containing species of both complexes. In the case of H2CO-DME, doublets were observed with the splitting 10-300 kHz, whereas no such splittings were observed for H2CO-DMS, D2CO-DME, and D2CO-DMS. The observed rotational spectra were found consistent with a structure of Cs symmetry with DME or DMS bound to H2CO by two types of hydrogen bonds: C-H(DME/DMS)---O(H2CO) and O(DME)/S(DMS)---H-C(H2CO). The Rcm distances between the centers of mass of the component molecules in the H2CO-DME and H2CO-DMS complexes were determined to be 3.102 and 3.200 Å, respectively, which are shorter than those in most related complexes. The spectral and NBO analyses showed that H2CO-DMS has a stronger charge transfer interaction than H2CO-DME does and that the binding energy of H2CO-DMS is larger than that of H2CO-DME. PMID:25679958

  12. Proton spin dynamics in polymer melts: new perspectives for experimental investigations of polymer dynamics

    E-print Network

    N. Fatkullin; S. Stapf; M. Hofmann; R. Meierc; E. A. Roessler

    2014-05-25

    Significant progress was made in recent years in the understanding of the proton spin kinetics in polymer melts. Generally, the proton spin kinetics is determined by intramolecular and intermolecular magnetic dipole-dipole contributions of proton spins. During many decades it was postulated that the main contribution is a result of intramolecular magnetic dipole-dipole interactions of protons belonging to the same polymer segment. It appears that this postulate is far from reality. The relative weights of intra- and intermolecular contributions are time dependent and sensitive to details of polymer chain dynamics. It is shown that for isotropic models of polymer dynamics the influence of the intermolecular magnetic dipole-dipole interactions increases faster with increasing evolution time (i.e. decreasing frequency) than the corresponding influence of the intramolecular counterpart. On the other hand, an inverted situation is predicted by the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions increases faster with time than the contribution from intermolecular interactions. The intermolecular contribution in the proton relaxation of polymer melts can experimentally be isolated using the isotope dilution technique and this opens a new perspective for experimental investigations of polymer dynamics by proton NMR.

  13. Proton spin dynamics in polymer melts: New perspectives for experimental investigations of polymer dynamics

    NASA Astrophysics Data System (ADS)

    Fatkullin, N.; Stapf, S.; Hofmann, M.; Meier, R.; Rössler, E. A.

    2015-01-01

    Significant progress was made in recent years in the understanding of the proton spin kinetics in polymer melts. Generally, the proton spin kinetics is determined by intramolecular and intermolecular magnetic dipole-dipole contributions of proton spins. During many decades it was postulated that the main contribution is a result of intramolecular magnetic dipole-dipole interactions of protons belonging to the same polymer segment. It appears that this postulate is far from reality. The relative weights of intra- and intermolecular contributions are time dependent and sensitive to details of polymer chain dynamics. It is shown that for isotropic models of polymer dynamics the influence of the intermolecular magnetic dipole-dipole interactions increases faster with increasing evolution time (i.e. decreasing frequency) than the corresponding influence of the intramolecular counterpart. On the other hand, an inverted situation is predicted by the tube-reptation model: here the influence of the intramolecular magnetic dipole-dipole interactions increases faster with time than the contribution from intermolecular interactions. The intermolecular contribution in the proton relaxation of polymer melts can experimentally be isolated using the isotope dilution technique and this opens a new perspective for experimental investigations of polymer dynamics by proton NMR.

  14. Bulk and molecular compressibilities of organic-inorganic hybrids [(CH?)?N]?MnX? (X = Cl, Br); role of intermolecular interactions.

    PubMed

    Barreda-Argüeso, Jose Antonio; Nataf, Lucie; Rodríguez-Lazcano, Yamilet; Aguado, Fernando; González, Jesús; Valiente, Rafael; Rodríguez, Fernando; Wilhelm, Heribert; Jephcoat, Andrew P

    2014-10-01

    This work reports an X-ray diffraction, X-ray absorption, and Raman spectroscopy study of [(CH?)?N]?MnX? (X = Cl, Br) under pressure. We show that both compounds share a similar phase diagram with pressure. A P2?/c monoclinic structure describes precisely the [(CH?)?N]?MnCl? crystal in the 0.1-6 GPa range, prior to crystal decomposition and amorphization, while [(CH?)?N]?MnBr? can be described by a Pmcn orthorhombic structure in its stability pressure range of 0-3 GPa. These materials are attractive systems for pressure studies since they are readily compressible through the weak interaction between organic/inorganic [(CH?)?N?/MnX?²?] tetrahedra through hydrogen bonds and contrast with the small compressibility of both tetrahedra. Here we determine the equation-of-state (EOS) of each crystal and compare it with the corresponding local EOS of the MnX?²? and (CH?)?N? tetrahedra, the compressibility of which is an order and 2 orders of magnitude smaller than the crystal compressibility, respectively, in both chloride and bromide. The variations of the Mn-Cl bond distance obtained by extended X-ray absorption fine structure and the frequency of the totally symmetric ??(A?) Raman mode of MnCl?²? with pressure in [(CH?)?N]?MnCl? allowed us to determine the associated Grüneisen parameter (?(loc) = 1.15) and hence an accurate local EOS. On the basis of a local compressibility model, we obtained the Grüneisen parameters and corresponding variations of the intramolecular Mn–Br and C–N bond distances of MnBr?²? (?(loc) = 1.45) and (CH?)?N? (?(loc) = 3.0) in [(CH?)?N]?MnBr?. PMID:25244664

  15. 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.

  16. A quantum mechanical study of water adsorption on the (110) surfaces of rutile SnO? and TiO?: investigating the effects of intermolecular interactions using hybrid-exchange density functional theory.

    PubMed

    Patel, M; Sanches, F F; Mallia, G; Harrison, N M

    2014-10-21

    Periodic hybrid-exchange density functional theory calculations are used to explore the first layer of water at model oxide surfaces, which is an important step for understanding the photocatalytic reactions involved in solar water splitting. By comparing the structure and properties of SnO2(110) and TiO2(110) surfaces in contact with water, the effects of structural and electronic differences on the water chemistry are examined. The dissociative adsorption mode at low coverage (1/7 ML) up to monolayer coverage (1 ML) on both SnO2 and TiO2(110) surfaces is analysed. To investigate further the intermolecular interactions between adjacent adsorbates, monolayer adsorption on each surface is explored in terms of binding energies and bond lengths. Analysis of the water adsorption geometry and energetics shows that the relative stability of water adsorption on SnO2(110) is governed largely by the strength of the chemisorption and hydrogen bonds at the surface of the adsorbate-substrate system. However on TiO2(110), a more complicated scenario of the first layer of water on its surface arises in which there is an interplay between chemisorption, hydrogen bonding and adsorbate-induced atomic displacements in the surface. Furthermore the projected density of states of each surface in contact with a mixture of adsorbed water molecules and adsorbed hydroxyls is presented and sheds some light on the nature of the crystalline chemical bonds as well as on why adsorbed water has often been reported to be unstable on rutile SnO2(110). PMID:24979063

  17. Librational echo: Subpicosecond intermolecular interactions in liquid

    SciTech Connect

    Nikiforov, V G [E.K.Zavoisky Physical-Technical Institute, Kazan Scientific Center, Russian Academy of Sciences, Kazan (Russian Federation)

    2008-02-28

    The ultrafast optical Kerr effect observed in liquids upon two-pulse laser excitation is studied theoretically. It is shown that a Raman echo on librational frequencies (librational echo) can be excited in liquid. The librational echo has the following features: its shape and amplitude strongly depend on the local inhomogeneity of a medium and the form of local potentials; and the echo signal can be separated into the contributions of the phase and irreversible relaxation of coherent molecular librations. These properties of the librational echo can be used for studying the specific features of the local structure of liquids by the method of selective subpicosecond spectroscopy of molecular librations. (nonlinear optical phenomena)

  18. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

    Busse, James R. (South Fork, CO); Dye, Robert C. (Los Alamos, NM); Foley, Timothy J. (Los Alamos, NM); Higa, Kelvin T. (Ridgecrest, CA); Jorgensen, Betty S. (Jemez Springs, NM); Sanders, Victor E. (White Rock, NM); Son, Steven F. (Los Alamos, NM)

    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.

  19. Interaction induced localization in a gas of pyramidal molecules

    E-print Network

    Giovanni Jona-Lasinio; Carlo Presilla; Cristina Toninelli

    2002-03-07

    We propose a model to describe a gas of pyramidal molecules interacting via dipole-dipole interactions. The interaction modifies the tunneling properties between the classical equilibrium configurations of the single molecule and, for sufficiently high pressure, the molecules become localized in these classical configurations. We explain quantitatively, without free parameters, the shift to zero frequency of the inversion line observed upon increase of the pressure in a gas of ammonia or deuterated ammonia. For sufficiently high pressures, our model suggests the existence of a superselection rule for states of different chirality in substituted derivatives.

  20. 13C NMR Reveals No Evidence of n??* Interactions in Proteins

    PubMed Central

    Worley, Bradley; Richard, Georgia; Harbison, Gerard S.; Powers, Robert

    2012-01-01

    An interaction between neighboring carbonyl groups has been postulated to stabilize protein structures. Such an interaction would affect the C chemical shielding of the carbonyl groups, whose paramagnetic component is dominated by and excitations. Model compound calculations indicate that both the interaction energetics and the chemical shielding of the carbonyl group are instead dominated by a classical dipole-dipole interaction. A set of high-resolution protein structures with associated carbonyl C chemical shift assignments verifies this correlation and provides no evidence for an inter-carbonyl interaction. PMID:22876300

  1. 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

  2. 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

  3. Intramolecular chalcogen-tin interactions in [(o-MeE-C6H4)CH2]2SnPh2-nCln; E = S, O, CH2, n = 0, 1, 2 and intermolecular chlorine-tin interactions in the meta and para-methoxy isomers

    PubMed Central

    Vargas-Pineda, Diana Gabriela; Guardado, Tanya; Cervantes-Lee, Francisco; Metta-Magana, Alejandro J.

    2010-01-01

    Organotin(IV) compounds of the type [(o-MeE-C6H4)CH2]2SnPh2-nCln were synthesized, E = O, n = 0 (1), n = 1 (2), n = 2 (3), E = S, n = 0 (4), n = 1 (5), n = 2 (6) and E = CH2, n = 0 (7), n = 1 (8), n = 2 (9). The dichloro compounds 3 and 6 have been investigated by single crystal X-ray diffraction and exhibit bi-capped tetrahedral geometry at the tin atom as a consequence of significant intramolecular Sn?O (3) and Sn?S (6) secondary bonding, in monomolecular units. Compound 3 when crystallized from a hexane/thf solvent mixture shows two different conformers, 3? and 3?, in the crystal structure, 3? has two equivalent Sn?O interactions, while 3? has two non-equivalent Sn?O interactions. Upon recrystallization of 3 from hexane only a single structural form is observed, 3?. The Sn?E distances in 3?, 3?, and 6 are 71.3; 73.5, 72.9; and 76.3% of the ?vdW radii, respectively. The meta and para-substituted isomers of 3 (10, 11) exhibit a distortion at the tin atom due to self-association via intermolecular Sn?Cl interactions resulting in polymeric structures. 119Sn NMR spectroscopy suggests that the intramolecular Sn?E interactions persist in solution for the dichloride compounds 3 and 6. PMID:20047301

  4. Inelastic x-ray scattering of dense solid oxygen: Evidence for intermolecular bonding

    PubMed Central

    Meng, Yue; Eng, Peter J.; Tse, John S.; Shaw, Dawn M.; Hu, Michael Y.; Shu, Jinfu; Gramsch, Stephen A.; Kao, Chichang; Hemley, Russell J.; Mao, Ho-kwang

    2008-01-01

    The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O2 molecules interact predominantly through the half-filled 1?g* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1?g* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O2 molecules at the transition to the ?-phase. The ?-phase, which consists of (O2)4 clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O2)4 clusters develop upon compression of the ?-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases. PMID:18687889

  5. Charge oscillations and interaction between potassium adatoms on graphene studied by first-principles calculations

    NASA Astrophysics Data System (ADS)

    Liu, Xiaojie; Wang, Cai-Zhuang; Lin, Hai-Qing; Chang, Kai; Chen, Jian; Ho, Kai-Ming

    2015-01-01

    Interaction between K adatoms on graphene is investigated by first-principles calculations based on density function theory and analytical analyses based on the k .p perturbation theory. The calculation shows that there is a strong repulsion between K adatoms. The main origin of this strong repulsion is not from the dipole-dipole interaction as suggested for K adatoms on graphite surface, but comes from the screened Coulomb interaction. Potassium adatom on graphene donates its s electron and becomes K+. The positively charged K adatom induces electron density oscillation on graphene which is responsible for the screened Coulomb repulsion between the K adatoms.

  6. Direct evidence of three-body interactions in a cold Rb85 Rydberg gas

    NASA Astrophysics Data System (ADS)

    Han, Jianing

    2010-11-01

    Cold Rydberg atoms trapped in a magneto-optical trap (MOT) are not isolated and they interact through dipole-dipole and multipole-multipole interactions. First-order dipole-dipole interactions and van der Waals interactions between two atoms have been intensively studied. However, the facts that the first-order dipole-dipole interactions and van der Waals interactions show the same size of broadening [A. Reinhard, K. C. Younge, T. C. Liebisch, B. Knuffman, P. R. Berman, and G. Raithel, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.100.233201 100, 233201 (2008)] and there are transitions between two dimer states [S. M. Farooqi, D. Tong, S. Krishnan, J. Stanojevic, Y. P. Zhang, J. R. Ensher, A. S. Estrin, C. Boisseau, R. Cote, E. E. Eyler, and P. L. Gould, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.91.183002 91, 183002 (2003); K. R. Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.76.011403 76, 011403(R) (2007)] cannot be explained by the two-atom picture. The purpose of this article is to show the few-body nature of a dense cold Rydberg gas by studying the molecular-state microwave spectra. Specifically, three-body energy levels have been calculated. Moreover, the transition from three-body energy levels to two-body coupled molecular energy levels and to isolated atomic energy levels as a function of the internuclear spacing is studied. Finally, single-body, two-body, and three-body interaction regions are estimated according to the experimental data. The results reported here provides useful information for plasma formation, further cooling, and superfluid formation.

  7. Intermolecular contacts within sickle hemoglobin fibers

    NASA Astrophysics Data System (ADS)

    Watowich, Stanley J.; Gross, Leon J.; Josephs, Robert

    1991-03-01

    We have combined x-ray crystallographic coordinates of sickle hemoglobin (HbS) molecules with electron microscopic 3-D reconstruction data of HbS fibers to calculate residues involved in intermolecular contacts within the clinically relevant HbS fiber. The model accounts for the action of 80 of the fifty five point mutations of HbS whose effect on fiber formation has been studied. For instance fiber formation is affected by thirty-three mutants. Of these mutants thirty-one occur at the calculated intermolecular contact sites. Fiber formation is not affected by 28 known HbS mutants 16 of these mutations occur at residues not involved in intermolecular contacts. The 12 mutations that occur at contact sites are postulated to not significantly increase fiber formation energy. The number of intermolecular contacts decreases with radius until at the periphery of the particle there are no contacts. We suggest that this observation accounts for the limited radial growth of the particle and that a similar mechanism may be a factor in limiting the size of other helical particles.

  8. Polynomial identities for ternary intermolecular recombination

    E-print Network

    Murray R. Bremner

    2010-08-11

    The operation of binary intermolecular recombination, originating in the theory of DNA computing, permits a natural generalization to n-ary operations which perform simultaneous recombination of n molecules. In the case n = 3, we use computer algebra to determine the polynomial identities of degree recombination.

  9. Interaction between two spherical particles in a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Fukuda, Jun-Ichi; Stark, Holger; Yoneya, Makoto; Yokoyama, Hiroshi

    2004-04-01

    We numerically investigate the interaction between two spherical particles in a nematic liquid crystal mediated by elastic distortions in the orientational order. We pay attention to the cases where two particles with equal radii R0 impose rigid normal anchoring on their surfaces and carry a pointlike topological defect referred to as a hyperbolic hedgehog. To describe the geometry of our system, we use bispherical coordinates, which prove useful in the implementation of boundary conditions at the particle surfaces and at infinity. We adopt the Landau de Gennes continuum theory in terms of a second-rank tensor order parameter Qij for the description of the orientational order of a nematic liquid crystal. We also utilize an adaptive mesh refinement scheme that has proven to be an efficient way of dealing with topological defects whose core size is much smaller than the particle size. When the two “dipoles,” composed of a particle and a hyperbolic hedgehog, are in parallel directions, the two-particle interaction potential is attractive for large interparticle distances D and proportional to D-3 as expected from the form of the dipole-dipole interaction, until the well-defined potential minimum at D?2.46 R0 is reached. For the antiparallel configuration with no hedgehogs between the two particles, the interaction potential is repulsive and behaves as D-2 for D?10 R0 , which is stronger than the dipole-dipole repulsion ( ˜ D-3 ) expected theoretically as an asymptotic behavior for large D .

  10. Structural analysis of bis-bispidine tetraazamacrocycle: Long-range weak interactions in a channeled organic crystal

    NASA Astrophysics Data System (ADS)

    Wang, Zhuo; Islam, Md. Jahirul; Vukotic, V. Nicholas

    2015-02-01

    A new organic crystal containing one-dimensional channels has been obtained through the synthesis and self-assembly of tetraethoxy bis-bispidine tetraazamacrocycles. The pre-fabricated macrocyclic cavities stack on each other to form ordered channels with highly basic inner cores. Based on the data of the single crystal structure, analysis of a 3D matrix indicates that weak directional interactions such as long-range Csbnd H⋯O hydrogen bonds and Nsbnd C⋯Osbnd C dipole-dipole interactions play an important role in the molecular alignment.

  11. The role of intermolecular interactions in the assemblies of Fe II and Co II tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)-Ru II: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules

    NASA Astrophysics Data System (ADS)

    Ghazzali, Mohamed; Langer, Vratislav; Öhrström, Lars

    2008-09-01

    Two new dual-metal assemblies: 2[Ru(phen) 3] 2+·[Fe(SCN) 4] 2-·2SCN -·4H 2O 1 and [Ru(phen) 3] 2+·[Co(SCN) 4] 2-2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a ????? sequence supported by ?- ? stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O-H⋯O and O-H⋯S hydrogen bonds. In 2, homochiral double helices in the b-direction are revealed, with tetrakis-isothiocyanate Co II anions arranged in the crystal to furnish one-dimensional (1D)-helical chains with S⋯S intermolecular interactions at 3.512(2) and 3.966(2) Å supporting [Ru(phen) 3] 2+?- and ?-helices with Ru⋯Ru shortest distance of 8.676(7) Å. In both 1 and 2, the supramolecular assembly is maintained by C-H⋯S hydrogen bonds extending between the phenanthroline aromatic carbons in the cationic nodes and the sulphur atoms of the isothiocyanates anions. Analysis of S⋯S interactions in isothiocyanate containing compounds using Cambridge structural database (CSD) showed an angle dependence categorizing these interactions into "type-I" and "type-II".

  12. Electromagnetic interaction of split-ring resonators: The role of separation and relative orientation.

    PubMed

    Feth, Nils; König, Michael; Husnik, Martin; Stannigel, Kai; Niegemann, Jens; Busch, Kurt; Wegener, Martin; Linden, Stefan

    2010-03-29

    Extinction cross-section spectra of split-ring-resonator dimers have been measured at near-infrared frequencies with a sensitive spatial modulation technique. The resonance frequency of the dimer's coupled mode as well as its extinction cross-section and its quality factor depend on the relative orientation and separation of the two split-ring resonators. The findings can be interpreted in terms of electric and magnetic dipole-dipole interaction. Numerical calculations based on a Discontinuous Galerkin Time-Domain approach are in good agreement with the experiments and support our physical interpretation. PMID:20389678

  13. Molecular connectivity: intermolecular accessibility and encounter simulation.

    PubMed

    Kier, L B; Hall, L H

    2001-01-01

    The simple molecular connectivity indices are interpreted as summations of bond accessibilities to bimolecular encounters with another, identical molecule. To transcend this model, a molecule is treated as disjecta membra with each bond modeled as a discrete cell in a dynamic simulation of many molecules. Each bond accessibility is transformed into a cellular automata rule. The dynamics are run for each of 38 alkanes, recording the average number of cell encounters, beta. The beta values show a high correlation with the boiling points. The significance of the bond accessibilities and the concept of intermolecular encounters explaining the molecular connectivity indices is supported by these findings. PMID:11760005

  14. n??* Interactions of Amides and Thioamides: Implications for Protein Stability

    PubMed Central

    2014-01-01

    Carbonyl–carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n??* donor–acceptor interaction with an energy of at least 0.27 kcal/mol. The n??* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor–acceptor orbital interactions rather than dipole–dipole interactions. PMID:23663100

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

    SciTech Connect

    Muenter, J.S.

    1992-01-01

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

  16. Some mathematical models of intermolecular autophosphorylation.

    PubMed

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

    2015-04-01

    Intermolecular autophosphorylation refers to the process whereby a molecule of an enzyme phosphorylates another molecule of the same enzyme. The enzyme thereby catalyses its own phosphorylation. In the present paper, we develop two generic models of intermolecular autophosphorylation that also include dephosphorylation by a phosphatase of constant concentration. The first of these, a solely time-dependent model, is written as one ordinary differential equation that relies upon mass-action and Michaelis-Menten kinetics. Beginning with the enzyme in its dephosphorylated state, it predicts a lag before the enzyme becomes significantly phosphorylated, for suitable parameter values. It also predicts that there exists a threshold concentration for the phosphorylation of enzyme and that for suitable parameter values, a continuous or discontinuous switch in the phosphorylation of enzyme are possible. The model developed here has the advantage that it is relatively easy to analyse compared with most existing models for autophosphorylation and can qualitatively describe many different systems. We also extend our time-dependent model of autophosphorylation to include a spatial dependence, as well as localised binding reactions. This spatio-temporal model consists of a system of partial differential equations that describe a soluble autophosphorylating enzyme in a spherical geometry. We use the spatio-temporal model to describe the phosphorylation of an enzyme throughout the cell due to an increase in local concentration by binding. Using physically realistic values for model parameters, our results provide a proof-of-concept of the process of activation by local concentration and suggest that, in the presence of a phosphatase, this activation can be irreversible. PMID:25636493

  17. Quantum Hall effects in fast-rotating Fermi gases with anisotropic dipolar interaction

    SciTech Connect

    Qiu, R.-Z.; Yi, S. [Key Laboratory of Frontiers in Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190 (China); Kou, Su-Peng [Department of Physics, Beijing Normal University, Beijing 100875 (China); Hu, Z.-X. [Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544 (United States); Wan Xin [Zhejiang Institute of Modern Physics, Zhejiang University, Hangzhou 310027 (China)

    2011-06-15

    We investigate fast rotating quasi-two-dimensional dipolar Fermi gases in the quantum Hall regime. By tuning the direction of the dipole moments with respect to the z axis, the dipole-dipole interaction becomes anisotropic in the x-y plane. For a soft confining potential we find that, as we tilt the angle of the dipole moments, the system evolves from a {nu}=1/3 Laughlin state with dipoles being polarized along the z axis to a series of ground states characterized by distinct mean total angular momentum, and finally to an anisotropic integer quantum Hall state. During the transition from the fractional regime to the integer regime, we find that the density profile of the system exhibits crystal-like structures. We map out the ground states as a function of the tilt angle and the confining potential, revealing the competition of the isotropic confining potential and both the isotropic and anisotropic components of the dipole-dipole interaction.

  18. The role of intermolecular interactions in the assemblies of Fe{sup II} and Co{sup II} tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)-Ru{sup II}: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules

    SciTech Connect

    Ghazzali, Mohamed [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)], E-mail: mghazz@chalmers.se; Langer, Vratislav; Ohrstroem, Lars [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

    2008-09-15

    Two new dual-metal assemblies: 2[Ru(phen){sub 3}]{sup 2+}.[Fe(SCN){sub 4}]{sup 2-}.2SCN{sup -}.4H{sub 2}O 1 and [Ru(phen){sub 3}]{sup 2+}.[Co(SCN){sub 4}]{sup 2-}2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a {lambda}{delta}{lambda}{delta}{lambda} sequence supported by {pi}-{pi} stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O-H...O and O-H...S hydrogen bonds. In 2, homochiral double helices in the b-direction are revealed, with tetrakis-isothiocyanate Co{sup II} anions arranged in the crystal to furnish one-dimensional (1D)-helical chains with S...S intermolecular interactions at 3.512(2) and 3.966(2) A supporting [Ru(phen){sub 3}]{sup 2+}{lambda}- and {delta}-helices with Ru...Ru shortest distance of 8.676(7) A. In both 1 and 2, the supramolecular assembly is maintained by C-H...S hydrogen bonds extending between the phenanthroline aromatic carbons in the cationic nodes and the sulphur atoms of the isothiocyanates anions. Analysis of S...S interactions in isothiocyanate containing compounds using Cambridge structural database (CSD) showed an angle dependence categorizing these interactions into 'type-I' and 'type-II'. - Graphical abstract: Side projection in 2 showing the crankshaft caused by S...S interactions in [Co(NCS){sub 4}]{sup 2-} in-between [Ru{sup II}(phen){sub 3}]{sup 2+} helices. Only isothiocyanates arms of [Co(NCS){sub 4}]{sup 2-} that are part of S...S interactions are shown and [Ru{sup II}(phen){sub 3}]{sup 2+} are presented as polyhedra.

  19. Comparison of the local binding motifs in the imidazolium-based ionic liquids [EMIM][BF4] and [EMMIM][BF4] through cryogenic ion vibrational predissociation spectroscopy: Unraveling the roles of anharmonicity and intermolecular interactions.

    PubMed

    Fournier, Joseph A; Wolke, Conrad T; Johnson, Christopher J; McCoy, Anne B; Johnson, Mark A

    2015-02-14

    We clarify the role of the critical imidazolium C(2)H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF4] ionic liquid by analyzing the vibrational spectra of the bare EMIM(+) ion as well as that of the cationic [EMIM]2[BF4](+) (EMIM(+) = 1-ethyl-3-methylimidazolium, C6H11N2 (+)) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D2 molecules formed in a 10 K ion trap. The C(2)H behavior is isolated by following the evolution of key vibrational features when the C(2) hydrogen, the proposed binding location of the anion to the imidazolium ring, is replaced by either deuterium or a methyl group (i.e., in the EMMIM(+) analogue). Strong features in the ring CH stretching region of the bare ion are traced to Fermi resonances with overtones of lower frequency modes. Upon incorporation into the EMIM(+) ? ? ? BF4 (-) ? ? ? EMIM(+) ternary complex, the C(2)H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM(+) ring CH stretches in the light isotopomer, which are strongly suppressed in the deuterated analogue. Further changes in the spectra that occur when the C(2)H is replaced by a methyl group are consistent with BF4 (-) attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions. PMID:25681905

  20. Spectroscopic studies on the intermolecular charge transfer interaction of Fe(II)- and Fe(III)-phthalocyanines with 2,3,5,6-tetrachloro-1,4-benzoquinone and its application in colorimetric sensing of amino acids and amines.

    PubMed

    Balraj, Chellamuthu; Elango, Kuppanagounder P

    2012-02-01

    The interactions of Fe(II)Pc and Fe(III)Pc with ?-acceptor 2,3,5,6-tetrachloro-1,4-benzoquinone (p-chloranil, p-CHL) have been investigated spectroscopically (UV/vis and FT-IR) and spectrofluorimetrically at three different temperatures. The stoichiometry of the complexes was found to be 1:1. The results of electronic spectral studies indicated that the formation constant for Fe(II)Pc-p-CHL system is found to be higher than that for Fe(III)Pc-p-CHL system. This observation is well supported by the results of fluorescence quenching studies and the association constants calculated for Fe(II)Pc-p-CHL system is 4.2 × 10(3) mol L(-1) and that for Fe(III)Pc-p-CHL system is 2.2 × 10(3) mol L(-1). The data are discussed in terms of physico-chemical parameters viz. molar extinction coefficient, oscillator strength, dipole moment, ionization potential, dissociation energy and thermodynamic parameters. The results indicated that the formation of ?-? CT complex is spontaneous and endothermic. Preliminary studies indicated that the CT complex can effectively be used as a colorimetric agent for sensing amino acids and amines. PMID:22074888

  1. Comparison of the local binding motifs in the imidazolium-based ionic liquids [EMIM][BF4] and [EMMIM][BF4] through cryogenic ion vibrational predissociation spectroscopy: Unraveling the roles of anharmonicity and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; McCoy, Anne B.; Johnson, Mark A.

    2015-02-01

    We clarify the role of the critical imidazolium C(2)H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF4] ionic liquid by analyzing the vibrational spectra of the bare EMIM+ ion as well as that of the cationic [EMIM]2[BF4]+ (EMIM+ = 1-ethyl-3-methylimidazolium, C6H11N2+) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D2 molecules formed in a 10 K ion trap. The C(2)H behavior is isolated by following the evolution of key vibrational features when the C(2) hydrogen, the proposed binding location of the anion to the imidazolium ring, is replaced by either deuterium or a methyl group (i.e., in the EMMIM+ analogue). Strong features in the ring CH stretching region of the bare ion are traced to Fermi resonances with overtones of lower frequency modes. Upon incorporation into the EMIM+ ? ? ? BF4- ? ? ? EMIM+ ternary complex, the C(2)H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM+ ring CH stretches in the light isotopomer, which are strongly suppressed in the deuterated analogue. Further changes in the spectra that occur when the C(2)H is replaced by a methyl group are consistent with BF4- attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions.

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

    SciTech Connect

    Son, S. F. (Steven F.); Busse, J. R. (James R.); Asay, B. W. (Blaine W.); Peterson, P. D. (Paul D.); Mang, J. T. (Joseph T.); Bockmon, B. (Bryan); Pantoya, M. (Michelle)

    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.

  3. Control of emission by intermolecular fluorescence resonance energy transfer and intermolecular charge transfer.

    PubMed

    Sun, Mengtao; Pullerits, Tõnu; Kjellberg, Pär; Beenken, Wichard J D; Han, Keli

    2006-05-18

    Control of emission by intermolecular fluorescence resonant energy transfer (IFRET) and intermolecular charge transfer (ICT) is investigated with the quantum-chemistry method using two-dimensional (2D) and three-dimensional (3D) real space analysis methods. The work is based on the experiment of tunable emission from doped 1,3,5-triphenyl-2-pyrazoline (TPP) organic nanoparticles (Peng, A. D.; et al. Adv. Mater. 2005, 17, 2070). First, the excited-state properties of the molecules, which are studied (TPP and DCM) in that experiment, are investigated theoretically. The results of the 2D site representation reveal the electron-hole coherence and delocalization size on the excitation. The results of 3D cube representation analysis reveal the orientation and strength of the transition dipole moments and intramolecular or intermolecular charge transfer. Second, the photochemical quenching mechanism via IFRET is studied (here "resonance" means that the absorption spectrum of TPP overlaps with the fluorescence emission spectrum of DCM in the doping system) by comparing the orbital energies of the HOMO (highest occupied molecular orbital) and the LUMO (lowest unoccupied molecular orbital) of DCM and TPP in absorption and fluorescence. Third, for the DCM-TPP complex, the nonphotochemical quenching mechanism via ICT is investigated. The theoretical results show that the energetically lowest ICT state corresponds to a pure HOMO-LUMO transition, where the densities of the HOMO and LUMO are strictly located on the DCM and TPP moieties, respectively. Thus, the lowest ICT state corresponds to an excitation of an electron from the HOMO of DCM to the LUMO of TPP. PMID:16686468

  4. 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.

  5. Optical evidence for intermolecular coupling in mixed films of pentacene and perfluoropentacene

    NASA Astrophysics Data System (ADS)

    Broch, K.; Heinemeyer, U.; Hinderhofer, A.; Anger, F.; Scholz, R.; Gerlach, A.; Schreiber, F.

    2011-06-01

    We present optical absorption spectra of mixed films of pentacene (PEN) and perfluoropentacene (PFP) grown on SiO2. We investigated the influence of intermolecular coupling between PEN and PFP on the optical spectra by analyzing samples with five different mixing ratios of PFP:PEN with variable angle spectroscopic ellipsometry and differential reflectance spectroscopy. The data show how the spectral shape is influenced by changes in the volume ratio of the two components. By comparison with the pure film spectra an attempt is made to distinguish transitions due to intermolecular coupling between PEN and PFP from transitions caused by interactions of PEN (PFP) with other molecules of the same type. We observe a new transition at 1.6 eV which is not found in the pure film spectra and which we assign to the coupling of PFP and PEN.

  6. Investigations of Diffuse Intermolecular Electronic Systems

    NASA Astrophysics Data System (ADS)

    Muguet, Francis Fabien Michel

    1992-01-01

    Diffuse intermolecular electronic systems, such as the hydrated electron or the ammonia and water dimers, present both a theoretical and a practical computational challenge. The hydrated electron was discovered more than 25 years ago, yet there is still no consensus on an explanation of this phenomenon. A novel model is presented here, whereby the hydrated electron consists in an itinerant diHydronium radical structure. Although electrostatically neutral, the itinerant radical is shown to behave as a negative charge carrier under the influence of an electric field. Within this perspective, the hydrated electron may be considered a quasiparticle. Contrary to the absence of agreement between many experiments and the old but still popular cavity model description, the energetics in the new model are shown to be consistent with photophysical experimental data. In order to understand negatively charged water clusters, it is also proposed that a metastable bifurcated water dimer structure is able to bind an extra electron. Prior to our studies, no ab initio computations had been able to reproduce the experimental geometry of the ammonia dimer or to predict any water dimer anion with the Franck-Condon factors agreeing with those recently found in molecular beam experiments. In both cases the potential energy surface is determined by attractors corresponding to nonlinear and linear hydrogen bonded geometries, respectively. One attractor receives an unfair advantage in the computational procedure mainly because of the basis set superposition error (BSSE). There is still no agreement on a scheme for correcting the BSSE. A widely employed error estimation method is the counterpoise correction. A completely different new method is proposed using reorthonormalization of purified localized molecular orbitals. In terms of a BSSE corrected potential energy surface of the water dimer, a multi-attractor model of liquid water is briefly discussed. For further water molecular dynamics studies, we offer a new algorithm which we have developed specifically for a massively parallel computer.

  7. Nonperturbative calculation of the London-van der Waals interaction potential

    NASA Astrophysics Data System (ADS)

    Berman, P. R.; Ford, G. W.; Milonni, P. W.

    2014-02-01

    The so-called remarkable formula [G. W. Ford, J. T. Lewis, and R. F. O'Connell, Phys. Rev. Lett. 55, 2273 (1985), 10.1103/PhysRevLett.55.2273] for the Helmholtz free energy is applied to the problem of determining the interaction potential to all orders in the coupling strength of a pair of oscillator dipoles interacting through the familiar dipole-dipole interaction of electrodynamics. Simple, straightforward calculations lead to expressions for (1) the London short-range potential, (2) the Casimir-Polder long-range potential, and (3) the potential at high temperature. Explicit results are shown for both the temperature dependence of the interaction potential and its deviation from the weak-coupling limit. It is stressed that the interaction potential is a change in free energy, not the energy; in particular, in the high temperature case, the change of energy is zero.

  8. 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)

  9. Theory of elastic interaction between colloidal particles in the nematic cell in the presence of the external electric or magnetic field

    E-print Network

    S. B. Chernyshuk; O. M. Tovkach; B. I. Lev

    2011-09-14

    The Green function method developed in Ref.[S. B. Chernyshuk and B. I. Lev, Phys. Rev. E \\textbf{81}, 041707 (2010)] is used to describe elastic interactions between axially symmetric colloidal particles in the nematic cell in the presence of the external electric or magnetic field. General formulas for dipole-dipole, dipole-quadrupole and quadrupole-quadrupole interactions in the homeotropic and planar nematic cells with parallel and perpendicular field orientations are obtained. A set of new results has been predicted: 1) \\textit{Deconfinement effect} for dipole particles in the homeotropic nematic cell with negative dielectric anisotropy $\\Delta\\epsilonelectric field, when electric field is approaching it's Frederiks threshold value $E\\Rightarrow E_{c}$. This means cancellation of the confinement effect found in Ref. [M.Vilfan et al. Phys.Rev.Lett. {\\bf 101}, 237801, (2008)] for dipole particles near the Frederiks transition while it remains for quadrupole particles. 2) New effect of \\textit{attraction and stabilization} of the particles along the electric field parallel to the cell planes in the homeotropic nematic cell with $\\Delta\\epsilon<0$ . The minimun distance between two particles depends on the strength of the field and can be ordinary for . 3) Attraction and repulsion zones for all elastic interactions are changed dramatically under the action of the external field.

  10. Higher-order electric multipole contributions to retarded non-additive three-body dispersion interaction energies between atoms: Equilateral triangle and collinear configurations

    SciTech Connect

    Salam, A., E-mail: salama@wfu.edu [Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109 (United States)

    2013-12-28

    The theory of molecular quantum electrodynamics (QED) is used to calculate higher electric multipole contributions to the dispersion energy shift between three atoms or molecules arranged in a straight line or in an equilateral triangle configuration. As in two-body potentials, three-body dispersion interactions are viewed in the QED formalism to arise from exchange of virtual photons between coupled pairs of particles. By employing an interaction Hamiltonian that is quadratic in the electric displacement field means that third-order perturbation theory can be used to yield the energy shift for a particular combination of electric multipole polarizable species, with only six time-ordered diagrams needing to be summed over. Specific potentials evaluated include dipole-dipole-quadrupole (DDQ), dipole-quadrupole-quadrupole (DQQ), and dipole-dipole-octupole (DDO) terms. For the geometries of interest, near-zone limiting forms are found to exhibit an R{sup ?11} dependence on separation distance for the DDQ interaction, and an R{sup ?13} behaviour for DQQ and DDO shifts, agreeing with an earlier semi-classical computation. Retardation weakens the potential in each case by R{sup ?1} in the far-zone. It is found that by decomposing the octupole moment into its irreducible components of weights-1 and -3 that the former contribution to the DDO potential may be taken to be a higher-order correction to the leading triple dipole energy shift.

  11. Higher-order electric multipole contributions to retarded non-additive three-body dispersion interaction energies between atoms: Equilateral triangle and collinear configurations

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2013-12-01

    The theory of molecular quantum electrodynamics (QED) is used to calculate higher electric multipole contributions to the dispersion energy shift between three atoms or molecules arranged in a straight line or in an equilateral triangle configuration. As in two-body potentials, three-body dispersion interactions are viewed in the QED formalism to arise from exchange of virtual photons between coupled pairs of particles. By employing an interaction Hamiltonian that is quadratic in the electric displacement field means that third-order perturbation theory can be used to yield the energy shift for a particular combination of electric multipole polarizable species, with only six time-ordered diagrams needing to be summed over. Specific potentials evaluated include dipole-dipole-quadrupole (DDQ), dipole-quadrupole-quadrupole (DQQ), and dipole-dipole-octupole (DDO) terms. For the geometries of interest, near-zone limiting forms are found to exhibit an R-11 dependence on separation distance for the DDQ interaction, and an R-13 behaviour for DQQ and DDO shifts, agreeing with an earlier semi-classical computation. Retardation weakens the potential in each case by R-1 in the far-zone. It is found that by decomposing the octupole moment into its irreducible components of weights-1 and -3 that the former contribution to the DDO potential may be taken to be a higher-order correction to the leading triple dipole energy shift.

  12. Higher-order electric multipole contributions to retarded non-additive three-body dispersion interaction energies between atoms: equilateral triangle and collinear configurations.

    PubMed

    Salam, A

    2013-12-28

    The theory of molecular quantum electrodynamics (QED) is used to calculate higher electric multipole contributions to the dispersion energy shift between three atoms or molecules arranged in a straight line or in an equilateral triangle configuration. As in two-body potentials, three-body dispersion interactions are viewed in the QED formalism to arise from exchange of virtual photons between coupled pairs of particles. By employing an interaction Hamiltonian that is quadratic in the electric displacement field means that third-order perturbation theory can be used to yield the energy shift for a particular combination of electric multipole polarizable species, with only six time-ordered diagrams needing to be summed over. Specific potentials evaluated include dipole-dipole-quadrupole (DDQ), dipole-quadrupole-quadrupole (DQQ), and dipole-dipole-octupole (DDO) terms. For the geometries of interest, near-zone limiting forms are found to exhibit an R(-11) dependence on separation distance for the DDQ interaction, and an R(-13) behaviour for DQQ and DDO shifts, agreeing with an earlier semi-classical computation. Retardation weakens the potential in each case by R(-1) in the far-zone. It is found that by decomposing the octupole moment into its irreducible components of weights-1 and -3 that the former contribution to the DDO potential may be taken to be a higher-order correction to the leading triple dipole energy shift. PMID:24387355

  13. Theory of elastic interaction between colloidal particles in a nematic cell in the presence of an external electric or magnetic field

    NASA Astrophysics Data System (ADS)

    Chernyshuk, S. B.; Tovkach, O. M.; Lev, B. I.

    2012-01-01

    The Green's function method developed previously [S. B. Chernyshuk and B. I. Lev, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.81.041701 81, 041701 (2010)] is used to describe elastic interactions between axially symmetric colloidal particles in a nematic cell in the presence of an external electric or magnetic field. Formulas for dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions in the homeotropic and planar nematic cells with parallel and perpendicular field orientations are obtained. A set of predictions has been made: (1) The deconfinement effect for dipole particles in the homeotropic nematic cell when an electric field is approaching its Freedericksz threshold value E?Et. This means cancellation of the confinement effect found in [M. Vilfan , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.101.237801 101, 237801 (2008)] near the Freedericksz transition. In the planar nematic cell this deconfinement effect exists for both dipole and quadrupole particles and depends on the field orientation as well as on the sign of dielectric anisotropy ??. (2) The effect of tunable stabilization of the particles is predicted. The equilibrium distance between two particles, which are attracted along the electric field parallel to the planes of a homeotropic nematic cell with ??<0, depends on the strength of the field. (3) Attraction and repulsion zones for all elastic interactions are changed dramatically under the action of the external field.

  14. Intermolecular interaction in plant oils from refractive and density measurements

    NASA Astrophysics Data System (ADS)

    Andriyevsky, B.; Andriyevska, L.; Piecuch, T.

    2010-12-01

    Refractive indices n and density ? of three plant oils (Anise, Nigelle, and Juniper berries) have been measured in the temperature range of 10-60°C. The model of the effective electric field E' acting on a molecule in the material, E' = E + x4? P, with the unlimited value of the coefficient of polarization input x has been applied to the analysis of the results obtained. The value x of the oils studied have been found to be in the range of 0.193-0.269, which is smaller than a similar value for water ( x water > 0.3), known as a strong polar liquid.

  15. Intermolecular Interactions between Retroviral Gag Proteins in the Nucleus

    Microsoft Academic Search

    Scott P. Kenney; Timothy L. Lochmann; Cullen L. Schmid; Leslie J. Parent

    2008-01-01

    The retroviral Gag polyprotein directs virus particle assembly, resulting in the release of virions from the plasma membranes of infected cells. The earliest steps in assembly, those immediately following Gag synthesis, are very poorly understood. For Rous sarcoma virus (RSV), Gag proteins are synthesized in the cytoplasm and then undergo transient nuclear trafficking before returning to the cytoplasm for transport

  16. An Interpretation for the First- and Second-Order Phase Transitions in Nylon 66 Crystal Based on the Intra- and Intermolecular Energy Calculation

    NASA Astrophysics Data System (ADS)

    Itoh, Takashi; Yamagata, Tetsuya; Ishikawa, Hiroya; Hashimoto, Masato; Konishi, Takashi

    1996-12-01

    Intra- and intermolecular interactions in nylon 66 crystal are calculated mainly using internal rotation and Lennard-Jones potential functions reasonably supposing that the amide planes are fixed and the hexamethylene moiety in the chain has an inversion center. Partition function is formularized on the basis of sum of the intra- and intermolecular interaction potentials in analogy with the Ising model on a rectangular lattice with degeneracy of interaction energy to show that the first-order phase transition occurs when the transition temperature T t is lower than the critical temperature T c and the second-order phase transition does when T t=T c, where T c only depends on the intermolecular interaction and T t on the intramolecular one mainly. The pressure effect on this phenomenon is qualitatively explained from temperature- or ?d (d100-d110,010)-dependence of T c and T t.

  17. Mechanisms of interaction between polycyclic aromatic hydrocarbons and dissolved organic matters.

    PubMed

    Wang, Huan Bo; Zhang, Yu Jun

    2014-01-01

    Binding of phenanthrene and fluorene to a number of humic and fulvic substances isolated from various sources as well as a commercially available humic acid, was investigated using a fluorescence quenching approach. The observed fluorescence quenching indicated by linear Stern-Volmer plots and high bimolecular quenching rate constant was induced by a static interaction process. A significant correlation of binding constants with aromaticity and polarity of dissolved organic matter (DOM) was observed. It is hypothesized that the binding of polycyclic aromatic hydrocarbons (PAHs) by DOM is due to both ?-? interactions and hydrophobic interactions. In addition, energy transfer from PAHs to DOM occurs because of the significant overlap between the absorbance spectra of DOM and emission spectra of PAHs. Thus, dipole-dipole interaction may also play an important role in the binding mechanism between PAHs and DOM. PMID:24117086

  18. Ultrafast intermolecular electron transfer from orthomethoxyaniline to excited coumarin dyes

    NASA Astrophysics Data System (ADS)

    Pal, Haridas; Shirota, Hideaki; Tominaga, Keisuke; Yoshihara, Keitaro

    1999-06-01

    Ultrafast intermolecular electron transfer (ET) from orthomethoxyaniline (orthoanisidine, ANS) to a number of excited (S1) 4-trifluoromethyl-1,2-benzopyrones (coumarins) having differently substituted 7-amino group has been investigated by femtosecond fluorescence up-conversion technique. The ET dynamics in the present systems are nonsingle-exponential and occur faster than the diffusive solvation dynamics. The ET rates are largely dependent on the nature of the substituents at the 7-amino group of the coumarins. This dependence is well correlated with the free energy changes (?G0) for the ET reactions. The ET dynamics become slower on using deuterated ANS as the donor, where the amino group hydrogens of ANS are substituted by deuterium. The deuterium isotope effect, however, gradually reduces as the ET dynamics becomes faster. Conventional ET theories can not explain all the observations. The results are explained on the basis of the two-dimensional ET model, which considers the solvent coordinate and the intramolecular coordinate separately to depict the ET process. It is seen that in coumarin-ANS systems the ET occurs much faster than the coumarin-aniline systems. It is indicated that the electronic coupling matrix element, a parameter which determines the extent of interaction between the reactant and the product states in the ET process, is much larger in the present systems than for the coumarin-aniline systems. The deuterium isotope effect on the ET dynamics is explained in terms of the changes in the ?G0 values on isotopic substitution of the solvent donors.

  19. 1H NMR Relaxation Investigation of Inhibitors Interacting with Torpedo californica Acetylcholinesterase

    NASA Astrophysics Data System (ADS)

    Delfini, Maurizio; Gianferri, Raffaella; Dubbini, Veronica; Manetti, Cesare; Gaggelli, Elena; Valensin, Gianni

    2000-05-01

    Two naphthyridines interacting with Torpedo californica acetylcholinesterase (AChE) were investigated. 1H NMR spectra were recorded and nonselective, selective, and double-selective spin-lattice relaxation rates were measured. The enhancement of selective relaxation rates could be titrated by different ligand concentrations at constant AChE (yielding 0.22 and 1.53 mM for the dissociation constants) and was providing evidence of a diverse mode of interaction. The double-selective relaxation rates were used to evaluate the motional correlation times of bound ligands at 34.9 and 36.5 ns at 300 K. Selective relaxation rates of bound inhibitors could be interpreted also in terms of dipole-dipole interactions with protons in the enzyme active site.

  20. Intermolecular symmetry-adapted perturbation theory study of large organic complexes

    NASA Astrophysics Data System (ADS)

    Heßelmann, Andreas; Korona, Tatiana

    2014-09-01

    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.

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

    PubMed

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

    2014-12-01

    We have investigated the physical stability of amorphous curcumin dispersions and the role of curcumin-polymer intermolecular interactions in delaying crystallization. Curcumin is an interesting model compound as it forms both intra and intermolecular hydrogen bonds in the crystal. A structurally diverse set of amorphous dispersion polymers was investigated; poly(vinylpyrrolidone), Eudragit E100, carboxymethyl cellulose acetate butyrate, hydroxypropyl methyl cellulose (HPMC) and HPMC-acetate succinate. Mid-infrared spectroscopy was used to determine and quantify the extent of curcumin-polymer interactions. Physical stability under different environmental conditions was monitored by powder X-ray diffraction. Curcumin chemical stability was monitored by UV-Vis spectroscopy. Isolation of stable amorphous curcumin was difficult in the absence of polymers. Polymers proved to be effective curcumin crystallization inhibitors enabling the production of amorphous solid dispersions; however, the polymers showed very different abilities to inhibit crystallization during long-term storage. Curcumin intramolecular hydrogen bonding reduced the extent of its hydrogen bonding with polymers; hence most polymers were not highly effective crystallization inhibitors. Overall, polymers proved to be crystallization inhibitors, but inhibition was limited due to the intramolecular hydrogen bonding in curcumin, which leads to a decrease in the ability of the polymers to interact at a molecular level. PMID:24192454

  2. 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…

  3. Breaking news on the enantioselective intermolecular Heck reaction.

    PubMed

    Oestreich, Martin

    2014-02-24

    Glowing results with less phosphorus: Tremendous progress has been made recently in asymmetric intermolecular Heck chemistry. Previously unprecedented enantioselective Heck-Matsuda reactions have been accomplished, and mixed phosphine/phosphine oxides have been shown to be superior ligands in enantioselective Mizoroki-Heck reactions. All of this was achieved with chiral ligands containing few or even no phosphorus donors (see scheme). PMID:24481834

  4. Resonant intermolecular transfer of vibrational energy in liquid water

    Microsoft Academic Search

    Sander Woutersen; Huib J. Bakker

    1999-01-01

    Many biological, chemical and physical processes involve the transfer of energy. In the case of electronic excitations, transfer between molecules is rapid, whereas for vibrations in the condensed phase, resonant energy transfer is an unlikely process because the typical timescale of vibrational relaxation (a few picoseconds) is much shorter than that of resonant intermolecular vibrational energy transfer. For the OH-stretch

  5. 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.

  6. Intermolecular reaction screening as a tool for reaction evaluation.

    PubMed

    Collins, Karl D; Glorius, Frank

    2015-03-17

    Synthetic organic chemistry underpins many scientific disciplines. The development of new synthetic methods proceeds with the ultimate intention of providing access to novel structural motifs or providing safer, increasingly efficient, or more economical chemical reactions. To facilitate the identification and application of new methods in solving real synthetic problems, this Account will highlight the benefits of providing a fuller picture of both the scope and limitations of new reactions, with a primary focus on the evaluation of functional group tolerance and stability of a reaction using intermolecular screens. This Account will begin with a discussion on reaction evaluation, specifically considering the suitability of a given reaction for application in target-oriented synthesis. A comparison of desirable and essential criteria when choosing a reaction is given, and a short discussion on the value of negative and qualitative data is provided. The concept of intermolecular reaction screening will be introduced, and a direct comparison with a traditional substrate scope highlights the benefits and limitations of each and thus the complementary nature of these approaches. In recent years, a number of ad hoc applications of intermolecular screens to evaluate the functional group tolerance of a reaction or the stability of functional groups to a given set of reaction conditions have been reported, and will be discussed. More recently, we have developed a formal high-throughput intermolecular screening protocol that can be utilized to rapidly evaluate new chemical reactions. This simple and rapid protocol enables a much broader evaluation of a reaction in terms of functional group tolerance and the stability of chemical motifs to the reaction conditions than is feasible with a typical reaction scope. The development, evaluation, and application of this method within our group will be discussed in detail, with both the potential benefits and limitations highlighted and discussed. In addition, we will discuss more recent applications of intermolecular screens from both industrial and academic groups. Modifications in protocols and applications will be highlighted, including problem based evaluations, assessment of biomolecule compatibility, establishment of relative rate data, and the identification of new reactivity. Such screens have been applied in diverse chemistries including C-H functionalization reactions, frustrated Lewis-pair-catalyzed hydrogenations, heterogeneous catalysis, photoredox catalysis, enantioselective organocatalysis, and polymer science. We feel that the application of intermolecular screens to such a diversity of reactions highlights the practical simplicity of such screens. A summary of the applications and potential utility of intermolecular reaction evaluation is provided. PMID:25699585

  7. Precision measurement of electronic ion-ion interactions between neighboring Eu3+ optical centers.

    PubMed

    Ahlefeldt, R L; McAuslan, D L; Longdell, J J; Manson, N B; Sellars, M J

    2013-12-13

    We report measurements of discrete excitation-induced frequency shifts on the 7F0?5D0 transition of the Eu+ center in La:Lu:EuCl3·6D2O resulting from the optical excitation of neighboring Eu3+ ions. Shifts of up to 46.081±0.005??MHz were observed. The magnitude of the interaction between neighboring ions was found to be significantly larger than expected from the electric dipole-dipole mechanism often observed in rare earth systems. We show that a large network of interacting and individually addressable centers can be created by lightly doping crystals otherwise stoichiometric in the optically active rare earth ion, and that this network could be used to implement a quantum processor with more than ten qubits. PMID:24483634

  8. Ultracold atom-dimer long-range interactions beyond the $1/R^{n}$ expansion

    E-print Network

    Maxence Lepers; Olivier Dulieu

    2011-02-07

    We investigate theoretically the combination of first-order quadrupole-quadrupole and second-order dipole-dipole effects on the long-range electrostatic interactions between a ground-state homonuclear alkali-metal dimer and an excited alkali-metal atom. As the electrostatic energy is comparable to the dimer rotational structure, we develop a general description of the long-range interactions which allows for couplings between the dimer rotational levels. The resulting adiabatic potential energy curves, which exhibit avoided crossings, cannot be expanded on the usual $1/R^{n}$ series. We study in details the breakdown of this approximation in the particular case Cs$_{2}+$Cs. Our results are found promising in the prospect of accomplishing the photoassociation of ultracold trimers.

  9. Ultracold atom-dimer long-range interactions beyond the $1/R^{n}$ expansion

    E-print Network

    Lepers, Maxence

    2011-01-01

    We investigate theoretically the combination of first-order quadrupole-quadrupole and second-order dipole-dipole effects on the long-range electrostatic interactions between a ground-state homonuclear alkali-metal dimer and an excited alkali-metal atom. As the electrostatic energy is comparable to the dimer rotational structure, we develop a general description of the long-range interactions which allows for couplings between the dimer rotational levels. The resulting adiabatic potential energy curves, which exhibit avoided crossings, cannot be expanded on the usual $1/R^{n}$ series. We study in details the breakdown of this approximation in the particular case Cs$_{2}+$Cs. Our results are found promising in the prospect of accomplishing the photoassociation of ultracold trimers.

  10. Controlling the self-assembly of magnetic nanoparticles by competing dipolar and isotropic particle interactions.

    PubMed

    Hod, Manuela; Dobbrow, Celin; Vaidyanathan, Mukanth; Guin, Debanjan; Belkoura, Lhoussaine; Strey, Reinhard; Gottlieb, Moshe; Schmidt, Annette M

    2014-12-15

    Control over the self-assembly of magnetic nanoparticles (MNP) into superstructures due to different types of coupling is of interest in the development of "bottom-up" fabrication schemes. Here we realize a simple strategy for the systematic variation of particle interaction potential in magnetic nanoparticles. This is achieved by varying the effective surface potential by means of a co-surfactant introduced in the course of the synthesis process. As a consequence, the ability to form chain-like assemblies is affected by the resulting balance of attractive and repulsive forces. We use electron microscopy, electron diffraction, and light scattering methods to study a series of cobalt nanoparticles as a characteristic example of ferromagnetic MNP. We demonstrate experimentally and substantiate theoretically that the observed behavior results from a balance between magnetic dipole-dipole, steric, and electrostatic interactions. PMID:25265589

  11. Anisotropic and long-range vortex interactions in two-dimensional dipolar Bose gases

    E-print Network

    Mulkerin, B C; O'Dell, D H J; Martin, A M; Parker, N G

    2013-01-01

    We perform a theoretical study into how dipole-dipole interactions modify the properties of superfluid vortices within the context of a two-dimensional atomic Bose gas of co-oriented dipoles. The reduced density at a vortex acts like a giant anti-dipole, changing the density profile and generating an effective dipolar potential centred at the vortex core whose most slowly decaying terms go as $1/\\rho^2$ and $\\ln(\\rho)/\\rho^3$. These effects modify the vortex-vortex interaction which, in particular, becomes anisotropic for dipoles polarized in the plane. Striking modifications to vortex-vortex dynamics are demonstrated, i.e. anisotropic co-rotation dynamics and the suppression of vortex annihilation.

  12. The effects of changes of intermolecular coupling on glass transition dynamics in polymer thin films and glass-formers confined in nanometer pores

    NASA Astrophysics Data System (ADS)

    Ngai, K. L.

    2003-09-01

    Intermolecular coupling plays an important role in determining the dynamics and the mobility of polymeric and non-polymeric glass-formers. The breadth of the dispersion is an indicator of the intermolecular coupling strength. The coupling model relates intermolecular coupling through the breadth of the dispersion to the dynamics of bulk glass-formers. When a glass-former is confined in nanometer pores or in thin films and if there is absence of chemical and physical interactions with the wall, intermolecular coupling is reduced, resulting in an increase of mobility. The coupling model is used to account for such changes of relaxation time of 1) ortho-terphenyl and poly(dimethyl siloxane) confined in nanometer pores, 2) polymer thin film confined between two impenetrable walls from Monte Carlo simulation, and 3) polymer film confined by perfectly smooth and purely repulsive potential acting on the repeat units from molecular-dynamics simulation. The model continues to explain the opposite effects observed when there is an increase of intermolecular coupling due to the presence of chemical or physical interaction with the walls.

  13. Controlling the interactions of a few cold Rb Rydberg atoms by radio-frequency-assisted Förster resonances

    NASA Astrophysics Data System (ADS)

    Tretyakov, D. B.; Entin, V. M.; Yakshina, E. A.; Beterov, I. I.; Andreeva, C.; Ryabtsev, I. I.

    2014-10-01

    Long-range interactions between cold Rydberg atoms, which are used in many important applications, can be enhanced using Förster resonances between collective many-body states controlled by an external electric field. Here we report on the first experimental observation of highly resolved radio-frequency-assisted Förster resonances in a few cold Rb Rydberg atoms. We also observed radio-frequency-induced Förster resonances which cannot be tuned by a dc electric field. They imply an efficient transition from van der Waals to resonant dipole-dipole interaction due to Floquet sidebands of Rydberg levels appearing in the rf field. This method can be applied to enhance the interactions of almost arbitrary Rydberg atoms with large principal quantum numbers.

  14. 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

  15. Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes

    PubMed Central

    Xie, Wangshen; Pu, Jingzhi; MacKerell, Alexander D.; Gao, Jiali

    2008-01-01

    A polarizable intermolecular potential function (PIPF) employing the Thole interacting dipole (TID) polarization model has been developed for liquid alkanes and amides. In connection with the internal bonding terms of the CHARMM22 force field, the present PIPF-CHARMM potential provides an adequate description of structural and thermodynamic properties for liquid alkanes and for liquid amides through molecular dynamics simulations. The computed heats of vaporization and liquid density are within 1.4% of experimental values. Polarization effects play a major role in liquid amides, which are reflected by an increase of 1.5 to 1.8 D in molecular dipole moment for primary and secondary amides. Furthermore, the computed polarization energies contribute to the total intermolecular interaction energy by 6 to 24%. The ability of the PIPF-CHARMM force field to treat protein backbone structures is tested by examining the potential energy surface of the amide bond rotation in N-methylacetamide and the Ramachandran surface for alanine dipeptide. The agreement with ab initio MP2 results and with the original CHARMM22 force field is encouraging, suggesting the PIPF-CHARMM potential can be used as a starting point to construct a complete polarizable force field for proteins. PMID:18958290

  16. Gas-phase intermolecular phosphate transfer within a phosphohistidine phosphopeptide dimer

    PubMed Central

    Gonzalez-Sanchez, Maria-Belen; Lanucara, Francesco; Hardman, Gemma E.; Eyers, Claire E.

    2014-01-01

    The hydrogen bonds and electrostatic interactions that form between the protonated side chain of a basic residue and the negatively charged phosphate of a phosphopeptide can play crucial roles in governing their dissociation pathways under low-energy collision-induced dissociation (CID). Understanding how phosphoramidate (i.e. phosphohistidine, phospholysine and phosphoarginine), rather than phosphomonoester-containing peptides behave during CID is paramount in investigation of these problematic species by tandem mass spectrometry. To this end, a synthetic peptide containing either phosphohistidine (pHis) or phospholysine (pLys) was analyzed by ESI-MS using a Paul-type ion trap (AmaZon, Bruker) and by traveling wave ion mobility-mass spectrometry (Synapt G2-Si, Waters). Analysis of the products of low-energy CID demonstrated formation of a doubly ‘phosphorylated’ product ion arising from intermolecular gas-phase phosphate transfer within a phosphopeptide dimer. The results are explained by the formation of a homodimeric phosphohistidine (pHis) peptide non-covalent complex (NCX), likely stabilized by the electrostatic interaction between the pHis phosphate group and the protonated C-terminal lysine residue of the peptide. To the best of our knowledge this is the first report of intermolecular gas-phase phosphate transfer from one phosphopeptide to another, leading to a doubly phosphorylated peptide product ion.

  17. Direct detection of intermolecular forces by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Skulason, Hjalti

    The phenomenon of adhesion appears in various applications of everyday life, ranging from PostIt Notes(TM) and Scotch Tape(TM), to the assembly of aircraft and space shuttles. However, adhesion on the molecular scale is fundamentally different from the adhesion that we experience in the macroscopic world. While macroscopic objects require special adhesives or glues to bind them together, microscale and nanoscale objects and molecules commonly have a high affinity to adhere to each other. A detailed description of intermolecular forces is therefore of key importance in order to understand a wide range of phenomena, ranging from macroscopic properties of materials to molecular recognition. Two key aspects of the atomic force microscope (AFM), namely its sensitivity to sub-nanoNewton forces and its very sharp probe, offer the opportunity to measure interactions between very small numbers of molecules. Through chemical tailoring of both substrates and AFM probes with self-assembled monolayers (SAMs), measurements of forces acting between specific functional groups can be measured. Furthermore, the force required to rupture a single chemical bond can be obtained by a detailed analysis of the histograms of rupture forces. A new model was derived to examine the relationship between the various experimental variables and the shape of histograms of rupture forces when discrete chemical bonds are formed between the AFM probe and substrate. Calculations based on the model demonstrated that in measurements aimed at detecting single bond rupture forces, strict limits are put on the size of the AFM probe, the relative magnitude of the interfacial energies and the bond formation probability. These results were used in two experimental systems where the single bond rupture force was successfully measured: (i) the abstraction of a single Au-S complex from an Au coated AFM probe; and (ii) the rupture of a single charge-transfer (CT) complex between tetramethylphenylenediamine (TMPD) and tetracyanoquinodimethane (TCNQ). Measurements involving only one molecule at a time were conducted using polymer chains chemically grafted to the AFM probe and substrate. In these measurements, the effect of the solvent on the elasticity of the poly-ethylene-propylene oligomers was directly observed in the force-elongation profile.

  18. Diastereoselective Intermolecular Rhodium-Catalyzed [4 + 2 + 2] Carbocyclization Reactions: Computational and Experimental Evidence for

    E-print Network

    Baik, Mu-Hyun

    Diastereoselective Intermolecular Rhodium-Catalyzed [4 + 2 + 2] Carbocyclization Reactions@indiana.edu (M.-H.B.); paevans@indiana.edu (P.A.E.) Intermolecular rhodium-catalyzed [m + n + o] reactions of 1-directed synthesis.1 We recently reported a diastereoselective intermolecular rhodium-catalyzed [4 + 2 + 2

  19. Intermolecular cross-links mediate aggregation of phospholipid vesicles by pulmonary surfactant protein SP-A.

    PubMed

    Ross, G F; Sawyer, J; O'Connor, T; Whitsett, J A

    1991-01-22

    As the most abundant glycoprotein component of pulmonary surfactant, SP-A (Mr = 30,000-36,000) plays a central role in the organization of phospholipid bilayers in the alveolar air space. SP-A, isolated from lung lavage, exists in oligomeric forms (N = 6, 12, 18, ...), mediated by collagen-like triple helices and intermolecular disulfide bonds. These protein-protein interactions, involving the amino-terminal domain of SP-A, are hypothesized to facilitate the alignment of surfactant lipid bilayers into unique tubular myelin structures. SP-A reorganization of surfactant lipid was assessed in vitro by quantitating the calcium-dependent light scattering properties of lipid vesicle suspensions induced by SP-A. Accelerated aggregation of unilamellar vesicles required SP-A and at least 3 mM free calcium. The initial rate of aggregation was proportional to the concentration of canine SP-A over lipid:protein molar ratios ranging from 200:1 to 5000:1. Digestion with bacterial collagenase or incubation with dithiothreitol (DTT) completely blocked lipid aggregation activity. Both treatments decreased the binding of SP-A to phospholipids. The conditions used in the DTT experiments (10 mM DTT, nondenaturing Tris buffer, 37 degrees C) resulted in the selective reduction and 14C-alkylation of the intermolecular disulfide bond involving residue 9Cys, whereas the four cysteines found in the noncollagenous domain of SP-A were inefficiently alkylated with [14C]-iodoacetate. HPLC analysis of tryptic SP-A peptides revealed that these four cysteine residues participate in intramolecular disulfide bond formation (138Cys-229Cys and 207Cys-221Cys). Our data demonstrate the importance of the quaternary structure (triple helix and intermolecular disulfide bond) of SP-A for the aggregation of unilamellar phospholipid vesicles. PMID:1988071

  20. ChemTeacher Resource: Flash Interactive Digital Overheads

    NSDL National Science Digital Library

    2012-08-01

    Allows the user to interactively and visually learn chemistry. Subtopics include Microscpic World, Atomic Structure, Molecular Structure, Intermolecular Forces, Chemical Reactions, Chemical Kinetics, Chemical Equilibrium

  1. An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties.

    PubMed

    Lin, Jr-Hung; Clark, Timothy

    2005-01-01

    A fully analytical description of molecular shape, as defined by the shrink-wrap isodensity or solvent-excluded surfaces and local properties related to Coulomb, donor/acceptor, and polarizability (dispersion) interactions is described. The molecular surface and four local properties adequate for describing intermolecular interactions (the molecular electrostatic potential and the local ionization energy, electron affinity, and polarizability) are fitted to spherical-harmonic expansions, which provide a compact and information-rich description of the properties of the static molecule. The resolution of the description can be varied from isotropic to near atomistic detail by adjusting the order of the individual spherical-harmonic expansions. Examples are given to illustrate the effect of truncating the different spherical-harmonic approximations. PMID:16045295

  2. Magnetothermodynamics of single crystal CuSO4.5H2O. VI. Properties below 0.5 °K by heat introduction with constant fields to 33 kG along the gamma axis. The initial T5 dependence of entropy and heat capacity for dipole-dipole magnetic interactions

    Microsoft Academic Search

    R. A. Fisher; G. E. Brodale; E. W. Hornung; W. F. Giauque

    1975-01-01

    The magnetic and thermodynamic properties of a 3.700 cm diam spherical single crystal of CuSO4.5H2O have been investigated from 0.02 to 0.5 °K with various constant fields from 0 to 33 000 G along the gamma axis. Heat introduction was used at fields of 0, 1000, 3000, 5000, 10 000, 20 000, 30 000, and 33 000 G, in combination

  3. Gibb's energy and intermolecular free length of 'Borassus Flabellifier' (BF) and Adansonia digitata (AnD) aqueous binary mixture

    NASA Astrophysics Data System (ADS)

    Phadke, Sushil; Darshan Shrivastava, Bhakt; Ujle, S. K.; Mishra, Ashutosh; Dagaonkar, N.

    2014-09-01

    One of the potential driving forces behind a chemical reaction is favourable a new quantity known as the Gibbs free energy (G) of the system, which reflects the balance between these forces. Ultrasonic velocity and absorption measurements in liquids and liquid mixtures find extensive application to study the nature of intermolecular forces. Ultrasonic velocity measurements have been successfully employed to detect weak and strong molecular interactions present in binary and ternary liquid mixtures. After measuring the density and ultrasonic velocity of aqueous solution of 'Borassus Flabellifier' BF and Adansonia digitata And, we calculated Gibb's energy and intermolecular free length. The velocity of ultrasonic waves was measured, using a multi-frequency ultrasonic interferometer with a high degree of accuracy operating Model M-84 by M/s Mittal Enterprises, New Delhi, at a fixed frequency of 2MHz. Natural sample 'Borassus Flabellifier' BF fruit pulp and Adansonia digitata AnD powder was collected from Dhar, District of MP, India for this study.

  4. Van der Waals interactions in density functional theory by combining the quantum harmonic oscillator-model with localized Wannier functions

    NASA Astrophysics Data System (ADS)

    Silvestrelli, Pier Luigi

    2013-08-01

    We present a new scheme to include the van der Waals (vdW) interactions in approximated Density Functional Theory (DFT) by combining the quantum harmonic oscillator model with the maximally localized Wannier function technique. With respect to the recently developed DFT/vdW-WF2 method, also based on Wannier Functions, the new approach is more general, being no longer restricted to the case of well separated interacting fragments. Moreover, it includes higher than pairwise energy contributions, coming from the dipole-dipole coupling among quantum oscillators. The method is successfully applied to the popular S22 molecular database, and also to extended systems, namely graphite and H2 adsorbed on the Cu(111) metal surface (in this case metal screening effects are taken into account). The results are also compared with those obtained by other vdW-corrected DFT schemes.

  5. Temperature dependence of magnetic moments of nanoparticles and their dipole interaction in magnetic fluids

    NASA Astrophysics Data System (ADS)

    Lebedev, A. V.

    2015-01-01

    Magnetic susceptibility measurements were carried out for magnetite-based fluids over a wide temperature range. The fluids were stabilized with commonly used surfactants (fatty acids) and new surfactants (polypropylene glycol and tallow acids). The coefficients of temperature dependence of the particle magnetic moments were determined by fitting of the measured and calculated values of magnetic susceptibility. The influence of the inter-particle dipole-dipole interaction on the susceptibility was taken into account in the framework of A.O. Ivanov's model. The corrections for thermal expansion were determined by density measurements of the carrier fluid. The obtained values of temperature coefficients correlate to the solidification temperature of the fluid samples. For fluids with a low solidification temperature the value of the temperature coefficient of particle magnetization coincides with its value for bulk magnetite.

  6. Pressure and temperature effects on intermolecular vibrational dynamics of ionic liquids

    NASA Astrophysics Data System (ADS)

    Penna, Tatiana C.; Faria, Luiz F. O.; Matos, Jivaldo R.; Ribeiro, Mauro C. C.

    2013-03-01

    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.

  7. 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 ?-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

  8. Intermolecular ?-strand networks avoid hub residues and favor low interconnectedness: a potential protection mechanism against chain dissociation upon mutation.

    PubMed

    Feverati, Giovanni; Achoch, Mounia; Vuillon, Laurent; Lesieur, Claire

    2014-01-01

    Altogether few protein oligomers undergo a conformational transition to a state that impairs their function and leads to diseases. But when it happens, the consequences are not harmless and the so-called conformational diseases pose serious public health problems. Notorious examples are the Alzheimer's disease and some cancers associated with a conformational change of the amyloid precursor protein (APP) and of the p53 tumor suppressor, respectively. The transition is linked with the propensity of ?-strands to aggregate into amyloid fibers. Nevertheless, a huge number of protein oligomers associate chains via ?-strand interactions (intermolecular ?-strand interface) without ever evolving into fibers. We analyzed the layout of 1048 intermolecular ?-strand interfaces looking for features that could provide the ?-strands resistance to conformational transitions. The interfaces were reconstructed as networks with the residues as the nodes and the interactions between residues as the links. The networks followed an exponential decay degree distribution, implying an absence of hubs and nodes with few links. Such layout provides robustness to changes. Few links per nodes do not restrict the choices of amino acids capable of making an interface and maintain high sequence plasticity. Few links reduce the "bonding" cost of making an interface. Finally, few links moderate the vulnerability to amino acid mutation because it entails limited communication between the nodes. This confines the effects of a mutation to few residues instead of propagating them to many residues via hubs. We propose that intermolecular ?-strand interfaces are organized in networks that tolerate amino acid mutation to avoid chain dissociation, the first step towards fiber formation. This is tested by looking at the intermolecular ?-strand network of the p53 tetramer. PMID:24733378

  9. EPR and magnetic susceptibility studies of the interaction between Cu 2+ and Mn 2+ ions in x(CuO·MnO)(1-x)[2B 2O 3·K 2O] glasses

    NASA Astrophysics Data System (ADS)

    Cozar, O.; Ardelean, I.; Ilonca, Gh.

    1982-11-01

    EPR and magnetic susceptibility experiments have been performed on x(CuO·MnO)(1- x)[2B 2O 3·K 2O] glasses with x varying in the range 0? x?50 mol.%. For x?3 mol.% both Cu 2+ and Mn 2+ ions are present mostly as the isolated species. The increase of the g-tensor values and bonding parameters (? 2, ? 2, ? 2) for Cu 2+ ions together with the increase of TM ions concentration in the 0.2-1 mol.% range was noticed. In the case of 5 ? x ? 30 mol.% the dipole-dipole and superexchange interactions occur between transition metal ions, the first type of interactions prevailing in this range of concentration. For x30 mol.% the superexchange interaction prevail. The strong interaction between Cu 2+ and Mn 2+ gives rise to the exchange coupled Cu 2+?Mn 2+ pairs in the studied glasses with x 3 mol.%.

  10. Importance of the donor:fullerene intermolecular arrangement for high-efficiency organic photovoltaics.

    PubMed

    Graham, Kenneth R; Cabanetos, Clement; Jahnke, Justin P; Idso, Matthew N; El Labban, Abdulrahman; Ngongang Ndjawa, Guy O; Heumueller, Thomas; Vandewal, Koen; Salleo, Alberto; Chmelka, Bradley F; Amassian, Aram; Beaujuge, Pierre M; McGehee, Michael D

    2014-07-01

    The performance of organic photovoltaic (OPV) material systems are hypothesized to depend strongly on the intermolecular arrangements at the donor:fullerene interfaces. A review of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis of reported polymer donor materials wherein the same conjugated backbone was used with varying alkyl substituents, supports this hypothesis. Specifically, the literature shows that higher-performing donor-acceptor type polymers generally have acceptor moieties that are sterically accessible for interactions with the fullerene derivative, whereas the corresponding donor moieties tend to have branched alkyl substituents that sterically hinder interactions with the fullerene. To further explore the idea that the most beneficial polymer:fullerene arrangement involves the fullerene docking with the acceptor moiety, a family of benzo[1,2-b:4,5-b']dithiophene-thieno[3,4-c]pyrrole-4,6-dione polymers (PBDTTPD derivatives) was synthesized and tested in a variety of PV device types with vastly different aggregation states of the polymer. In agreement with our hypothesis, the PBDTTPD derivative with a more sterically accessible acceptor moiety and a more sterically hindered donor moiety shows the highest performance in bulk-heterojunction, bilayer, and low-polymer concentration PV devices where fullerene derivatives serve as the electron-accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solid-state two-dimensional (2D) (13)C{(1)H} heteronuclear correlation (HETCOR) NMR analyses support that a specific polymer:fullerene arrangement is present for the highest performing PBDTTPD derivative, in which the fullerene is in closer proximity to the acceptor moiety of the polymer. This work demonstrates that the polymer:fullerene arrangement and resulting intermolecular interactions may be key factors in determining the performance of OPV material systems. PMID:24932575

  11. Effect of spatial confinement on magnetic hyperthermia via dipolar interactions in Fe3O4 nanoparticles for biomedical applications

    SciTech Connect

    Sadat, M E [University of Cincinnati; Patel, Ronak [University of Cincinnati; Sookoor, Jason [University of Cincinnati; Bud'ko, Sergey L [Ames Laboratory; Ewing, Rodney C [Stanford University; Zhang, Jiaming [Stanford University; Xu, Hong [Shanghai Jiao Tong University; Wang, Yilong [Tongji University School of Medicine; Pauletti, Giovanni M [University of Cincinnati; Mast, David B [University of Cincinnati; Shi, Donglu [University of Cincinnati

    2014-09-01

    In this work, the effect of nanoparticle confinement on the magnetic relaxation of iron oxide (Fe3O4) nanoparticles (NP) was investigated by measuring the hyperthermia heating behavior in high frequency alternating magnetic field. Three different Fe3O4 nanoparticle systems having distinct nanoparticle configurations were studied in terms of magnetic hyperthermia heating rate and DC magnetization. All magnetic nanoparticle (MNP) systems were constructed using equivalent ~10nm diameter NP that were structured differently in terms of configuration, physical confinement, and interparticle spacing. The spatial confinement was achieved by embedding the Fe3O4 nanoparticles in the matrices of the polystyrene spheres of 100 nm, while the unconfined was the free Fe3O4 nanoparticles well-dispersed in the liquid via PAA surface coating. Assuming the identical core MNPs in each system, the heating behavior was analyzed in terms of particle freedom (or confinement), interparticle spacing, and magnetic coupling (or dipole-dipole interaction). DC magnetization data were correlated to the heating behavior with different material properties. Analysis of DC magnetization measurements showed deviation from classical Langevin behavior near saturation due to dipole interaction modification of the MNPs resulting in a high magnetic anisotropy. It was found that the Specific Absorption Rate (SAR) of the unconfined nanoparticle systems were significantly higher than those of confined (the MNPs embedded in the polystyrene matrix). This increase of SAR was found to be attributable to high Néel relaxation rate and hysteresis loss of the unconfined MNPs. It was also found that the dipole-dipole interactions can significantly reduce the global magnetic response of the MNPs and thereby decrease the SAR of the nanoparticle systems.

  12. Effect of spatial confinement on magnetic hyperthermia via dipolar interactions in Fe?O? nanoparticles for biomedical applications.

    PubMed

    Sadat, M E; Patel, Ronak; Sookoor, Jason; Bud'ko, Sergey L; Ewing, Rodney C; Zhang, Jiaming; Xu, Hong; Wang, Yilong; Pauletti, Giovanni M; Mast, David B; Shi, Donglu

    2014-09-01

    In this work, the effect of nanoparticle confinement on the magnetic relaxation of iron oxide (Fe3O4) nanoparticles (NP) was investigated by measuring the hyperthermia heating behavior in high frequency alternating magnetic field. Three different Fe3O4 nanoparticle systems having distinct nanoparticle configurations were studied in terms of magnetic hyperthermia heating rate and DC magnetization. All magnetic nanoparticle (MNP) systems were constructed using equivalent ~10nm diameter NP that were structured differently in terms of configuration, physical confinement, and interparticle spacing. The spatial confinement was achieved by embedding the Fe3O4 nanoparticles in the matrices of the polystyrene spheres of 100 nm, while the unconfined was the free Fe3O4 nanoparticles well-dispersed in the liquid via PAA surface coating. Assuming the identical core MNPs in each system, the heating behavior was analyzed in terms of particle freedom (or confinement), interparticle spacing, and magnetic coupling (or dipole-dipole interaction). DC magnetization data were correlated to the heating behavior with different material properties. Analysis of DC magnetization measurements showed deviation from classical Langevin behavior near saturation due to dipole interaction modification of the MNPs resulting in a high magnetic anisotropy. It was found that the Specific Absorption Rate (SAR) of the unconfined nanoparticle systems were significantly higher than those of confined (the MNPs embedded in the polystyrene matrix). This increase of SAR was found to be attributable to high Néel relaxation rate and hysteresis loss of the unconfined MNPs. It was also found that the dipole-dipole interactions can significantly reduce the global magnetic response of the MNPs and thereby decrease the SAR of the nanoparticle systems. PMID:25063092

  13. 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 ?_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.

  14. Ab initio long-range interaction and adiabatic channel capture model for ultracold reactions between the KRb molecules

    NASA Astrophysics Data System (ADS)

    Buchachenko, A. A.; Stolyarov, A. V.; Szcz??niak, M. M.; Cha?asi?ski, G.

    2012-09-01

    The coefficients at the lowest-order electrostatic, induction, and dispersion terms of the anisotropic long-range potential between the two KRb(1?+) molecules are evaluated through the static and dynamic molecular properties using the ab initio coupled cluster techniques. Adiabatic channel potentials for the ground-state molecules are obtained and used for the numerical quantum capture probability calculations in the spirit of the statistical adiabatic channel models. Capture rate coefficients for indistinguishable (polarized) and distinguishable (unpolarized) molecules at temperatures below 10 ?K agree well with those computed with the simple isotropic dispersion R-6 potential, but underestimate the measured ones [Ospelkaus et al., Science 327, 853 (2010), 10.1126/science.1184121] up to a factor of 3. Preliminary assessment of the effects of higher-order long-range terms, retardation of dispersion forces, and magnetic dipole-dipole interaction does not offer any clear perspectives for drastic improvement of the capture approximation for the reactions studied.

  15. Conformational diversity in prion protein variants influences intermolecular ?-sheet formation

    PubMed Central

    Lee, Seungjoo; Antony, Lizamma; Hartmann, Rune; Knaus, Karen J; Surewicz, Krystyna; Surewicz, Witold K; Yee, Vivien C

    2010-01-01

    A conformational transition of normal cellular prion protein (PrPC) to its pathogenic form (PrPSc) 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 ?-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 ?-sheets involving the M/V129 polymorphic residue. PMID:19927125

  16. Topological Defects and Interactions in Nematic Emulsions

    E-print Network

    T. C. Lubensky; David Pettey; Nathan Currier; Holger Stark

    1997-07-12

    Inverse nematic emulsions in which surfactant-coated water droplets are dispersed in a nematic host fluid have distinctive properties that set them apart from dispersions of two isotropic fluids or of nematic droplets in an isotropic fluid. We present a comprehensive theoretical study of the distortions produced in the nematic host by the dispersed droplets and of solvent mediated dipolar interactions between droplets that lead to their experimentally observed chaining. A single droplet in a nematic host acts like a macroscopic hedgehog defect. Global boundary conditions force the nucleation of compensating topological defects in the nematic host. Using variational techniques, we show that in the lowest energy configuration, a single water droplet draws a single hedgehog out of the nematic host to form a tightly bound dipole. Configurations in which the water droplet is encircled by a disclination ring have higher energy. The droplet-dipole induces distortions in the nematic host that lead to an effective dipole-dipole interaction between droplets and hence to chaining.

  17. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures

    NASA Astrophysics Data System (ADS)

    Stiegler, Thomas; Sadus, Richard J.

    2015-02-01

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form.

  18. Molecular simulation of fluids with non-identical intermolecular potentials: Thermodynamic properties of 10-5 + 12-6 Mie potential binary mixtures.

    PubMed

    Stiegler, Thomas; Sadus, Richard J

    2015-02-28

    General methods for combining interactions between particles characterised by non-identical intermolecular potentials are investigated. The combination methods are tested by performing molecular dynamics simulations to determine the pressure, energy, isochoric and isobaric heat capacities, thermal expansion coefficient, isothermal compressibility, Joule-Thomson coefficient, and speed of sound of 10-5 + 12-6 Mie potential binary mixtures. In addition to the two non-identical Mie potentials, mixtures are also studied with non-identical intermolecular parameters. The combination methods are compared with results obtained by simply averaging the Mie exponents. When either the energy or size parameters are non-identical, very significant differences emerge in the thermodynamic properties predicted by the alternative combination methods. The isobaric heat capacity is the thermodynamic property that is most affected by the relative magnitude of the intermolecular potential parameters and the method for combining non-identical potentials. Either the arithmetic or geometric combination of potentials provides a simple and effective way of performing simulations involving mixtures of components characterised by non-identical intermolecular potentials, which is independent of their functional form. PMID:25725742

  19. Understanding antibody-antigen associations by molecular dynamics simulations: detection of important intra- and inter-molecular salt bridges.

    PubMed

    Sinha, Neeti; Li, Yili; Lipschultz, Claudia A; Smith-Gill, Sandra J

    2007-01-01

    1 NSec molecular dynamics (MD) simulation of anti-hen egg white antibody, HyHEL63 (HH63), complexed with HEL reveals important molecular interactions, not revealed in its X-ray crystal structure. These molecular interactions were predicted to be critical for the complex formation, based on structure-function studies of this complex and 3-other anti-HEL antibodies, HH8, HH10 and HH26, HEL complexes. All four antibodies belong to the same structural family, referred to here as HH10 family. Ala scanning results show that they recognize 'coincident epitopes'. 1 NSec explicit, with periodic boundary condition, MD simulation of HH63- HEL reveals the presence of functionally important saltbridges. Around 200 ps in vacuo and an additional 20 ps explicit simulation agree with the observations from 1 Nsec simulation. Intra-molecular salt-bridges predicted to play significant roles in the complex formation, were revealed during MD simulation. A very stabilizing saltbridge network, and another intra-molecular salt-bridge, at the binding site of HEL, revealed during the MD simulation, is proposed to predipose binding site geometry for specific binding. All the revealed saltbridges are present in one or more of the other three complexes and/or involve \\"hot-spot\\" epitope and paratope residues. Most of these charged epitope residues make large contribution to the binding free energy. The "hot spot" epitope residue Lys97Y, which significantly contributes to the free energy of binding in all the complexes, forms an intermolecular salt-bridge in several MD conformers. Our earlier computations have shown that this inter-molecular salt-bridge plays a significant role in determining specificity and flexibility of binding in the HH8-HEL and HH26-HEL complexes. Using a robust criterion of salt-bridge detection, this intermolecular salt-bridge was detected in the native structures of the HH8-HEL and HH26-HEL complexes, but was not revealed in the crystal structure of HH63-HEL complex. The electrostatic strength of this revealed saltbridge was very strong. During 1 Nsec MD simulation this salt-bridge networks with another inter-molecular salt-bridge to form an inter-molecular salt-bridge triad. Participation of Lys97Y in the formation of inter-molecular triad further validates the functional importance of Lys97Y in HH63-HEL associations. These results demonstrate that many important structural details of biomolecular interactions can be better understood when studied in a dynamic environment, and that MD simulations can complement and expand information obtained from static X-ray structure. This study also highlights "hot-spot" molecular interactions in HyHEL63-HEL complex. PMID:17652781

  20. Intermolecular cycloaddition of N-boranonitrone with alkenes.

    PubMed

    Morita, Nobuyoshi; Fukui, Kenji; Irikuchi, Jinshi; Sato, Hiroshi; Takano, Yuu; Okamoto, Iwao; Ishibashi, Hiroyuki; Tamura, Osamu

    2008-09-19

    Ethyl glyoxylate O-tert-butyldimethylsilyloxime (8), on treatment with 2.2 equiv of BF3 x OEt2, generated N-boranonitrone E, which underwent intermolecular cycloaddition with alkenes 18 to afford isoxazolidines 19 in moderate to high yields. The cycloaddition of N-boranonitrone E with most of the alkenes gave 3,5-trans isoxazolidines as the major isomers via a concerted mechanism. However, in the case of 1-methylated cyclic alkenes (18j and 18l), the cycloaddition surprisingly furnished the 3,3a-cis-cycloadducts (19j and 19l) as major isomers. A possible explanation is that the reaction of 1-methylated cyclic alkenes proceeds mainly via a stepwise mechanism. This reaction of terminal alkenes is very useful for synthesis of 1,3-anti aminoalcohol derivatives by reductive cleavage of an N-O bond. PMID:18720968

  1. A new intermolecular mechanism to selectively drive photoinduced damages

    E-print Network

    Gokhberg, Kirill; Kuleff, Alexander I; Cederbaum, Lorenz S

    2014-01-01

    Low-energy electrons (LEEs) are known to be effective in causing strand breaks in DNA. Recent experiments show that an important direct source of LEEs is the intermolecular Coulombic decay (ICD) process. Here we propose a new cascade mechanism initiated by core excitation and terminated by ICD and demonstrate its properties. Explicit calculations show that the energies of the emitted ICD-electrons can be controlled by selecting the initial atomic excitation. The properties of the cascade may have interesting applications in the fields of electron spectroscopy and radiation damage. Initiating such a cascade by resonant X-ray absorption from a high-Z element embedded in a cancerous cell nucleus, ICD will deliver genotoxic particles \\textit{locally} at the absorption site, increasing in that way the controllability of the induced damage.

  2. Palladium-Catalyzed Intermolecular Aminocarbonylation of Alkenes: Efficient Access of ?-Amino Acid Derivatives.

    PubMed

    Cheng, Jiashun; Qi, Xiaoxu; Li, Ming; Chen, Pinhong; Liu, Guosheng

    2015-02-25

    A novel palladium-catalyzed intermolecular aminocarbonylation of alkenes has been developed in which the employment of hypervalent iodine reagent can accelerate the intermolecular aminopalladation, which thus provides the successful catalytic transformation. The current transformation presents one of the most convenient methods to generate ?-amino acid derivatives from simple alkenes. PMID:25676745

  3. Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes

    E-print Network

    Minnesota, University of

    Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes Received June 17, 2007 Abstract: A polarizable intermolecular potential function (PIPF) employing the Thole. In connection with the internal bonding terms of the CHARMM22 force field, the present PIPF- CHARMM potential

  4. The assembly and intermolecular properties of the Hsp70-Tomm34-Hsp90 molecular chaperone complex.

    PubMed

    Trcka, Filip; Durech, Michal; Man, Petr; Hernychova, Lenka; Muller, Petr; Vojtesek, Borivoj

    2014-04-01

    Maintenance of protein homeostasis by molecular chaperones Hsp70 and Hsp90 requires their spatial and functional coordination. The cooperation of Hsp70 and Hsp90 is influenced by their interaction with the network of co-chaperone proteins, some of which contain tetratricopeptide repeat (TPR) domains. Critical to these interactions are TPR domains that target co-chaperone binding to the EEVD-COOH motif that terminates Hsp70/Hsp90. Recently, the two-TPR domain-containing protein, Tomm34, was reported to bind both Hsp70 and Hsp90. Here we characterize the structural basis of Tomm34-Hsp70/Hsp90 interactions. Using multiple methods, including pull-down assays, fluorescence polarization, hydrogen/deuterium exchange, and site-directed mutagenesis, we defined the binding activities and specificities of Tomm34 TPR domains toward Hsp70 and Hsp90. We found that Tomm34 TPR1 domain specifically binds Hsp70. This interaction is partly mediated by a non-canonical TPR1 two-carboxylate clamp and is strengthened by so far unidentified additional intermolecular contacts. The two-carboxylate clamp of the isolated TPR2 domain has affinity for both chaperones, but as part of the full-length Tomm34 protein, the TPR2 domain binds specifically Hsp90. These binding properties of Tomm34 TPR domains thus enable simultaneous binding of Hsp70 and Hsp90. Importantly, we provide evidence for the existence of an Hsp70-Tomm34-Hsp90 tripartite complex. In addition, we defined the basic conformational demands of the Tomm34-Hsp90 interaction. These results suggest that Tomm34 represents a novel scaffolding co-chaperone of Hsp70 and Hsp90, which may facilitate Hsp70/Hsp90 cooperation during protein folding. PMID:24567332

  5. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase.

    PubMed

    Wong, Jaslyn E M M; Midtgaard, Søren Roi; Gysel, Kira; Thygesen, Mikkel B; Sørensen, Kasper K; Jensen, Knud J; Stougaard, Jens; Thirup, Søren; Blaise, Mickaël

    2015-03-01

    LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed. PMID:25760608

  6. An intermolecular binding mechanism involving multiple LysM domains mediates carbohydrate recognition by an endopeptidase

    PubMed Central

    Wong, Jaslyn E. M. M.; Midtgaard, Søren Roi; Gysel, Kira; Thygesen, Mikkel B.; Sørensen, Kasper K.; Jensen, Knud J.; Stougaard, Jens; Thirup, Søren; Blaise, Mickaël

    2015-01-01

    LysM domains, which are frequently present as repetitive entities in both bacterial and plant proteins, are known to interact with carbohydrates containing N-acetylglucosamine (GlcNAc) moieties, such as chitin and peptidoglycan. In bacteria, the functional significance of the involvement of multiple LysM domains in substrate binding has so far lacked support from high-resolution structures of ligand-bound complexes. Here, a structural study of the Thermus thermophilus NlpC/P60 endopeptidase containing two LysM domains is presented. The crystal structure and small-angle X-ray scattering solution studies of this endopeptidase revealed the presence of a homodimer. The structure of the two LysM domains co-crystallized with N-acetyl-chitohexaose revealed a new intermolecular binding mode that may explain the differential interaction between LysM domains and short or long chitin oligomers. By combining the structural information with the three-dimensional model of peptidoglycan, a model suggesting how protein dimerization enhances the recognition of peptidoglycan is proposed. PMID:25760608

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  8. 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.

  9. A STM perspective on covalent intermolecular coupling reactions on surfaces

    NASA Astrophysics Data System (ADS)

    Lackinger, M.; Heckl, W. M.

    2011-11-01

    'Covalent self-assembly', i.e. the on-surface synthesis of covalent organic aggregates and networks, has received considerable attention. This review covers recent scanning tunnelling microscopy (STM) based studies on intermolecular reactions carried out on solid substrates that resulted in surface-confined covalently interlinked organic nanostructures. Experiments showed that their defect density crucially depends on the targeted dimensionality: while zero-dimensional aggregates and one-dimensional chains and ribbons can be synthesized on surfaces with utmost structural perfection, i.e. without any topological defects, realization of long-range ordered two-dimensional (2D) covalently interlinked organic networks has revealed itself as a paramount challenge for on-surface chemists. Different types of reactions, foremost condensation and addition reactions have been proven suitable as polymerization reactions for 2D cross-linked covalent networks. Yet, the emergence of topological defects during the polymerization is difficult to avoid. However, the combined experience and creativity of chemists and surface scientists has yielded encouraging first results which may open up ways for realization of extended, long-range ordered 2D polymers. This review summarizes and compares different approaches, i.e. reaction types, monomers, environments and conditions, for the on-surface synthesis of covalent organic nanostructures. The focus on STM as an analytical tool appears justified, since its unique capabilities render the STM an ideal instrument to study and even control covalent coupling reactions of organic molecules on surfaces.

  10. Viscosity dependence of intra- and intermolecular Diels-Alder reactions.

    PubMed

    Tiwari, Shraeddha; Kumar, Anil

    2012-02-01

    The kinetics of the bimolecular Diels-Alder reaction between anthracene-9-carbinol and N-ethyl maleimide have been studied in a series of pyridinium-based ionic liquids with the tetrafluoroborate ([BF(4)](-)) and the bis(trifluorosulfonimide) ([NTf(2)](-)) anions and the viscosity dependence of the rate constants have been compared with the results for the intramolecular Diels-Alder reaction of (E)-1-phenyl-4-[2-(3-methyl-2-butenyloxy)benzylidene]-5-pyrazolone. The comparison leads to the surprising observation that the intermolecular reaction is less susceptible to viscosity variations of the ionic liquids as compared to the intramolecular reaction. The observed similarities and differences emphasize the complicated nature of solvent friction on the kinetics of cycloaddition reactions. The results are explained by considering the bimolecular and intramolecular processes as cases of translational and rotational diffusion, respectively. Plausible indicators of microviscosity consistent with the kinetic data for the Diels-Alder reactions are briefly discussed along with the constraints involved in designing a general microviscosity scale. PMID:22224461

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

    PubMed

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

    2011-02-01

    We describe the application of a new class of ligands--the phosphite-oxazole/imidazole (L1-L5a-g)--in asymmetric intermolecular Pd-catalyzed Heck reactions under thermal and microwave conditions. These ligands combine the advantages of the oxazole/imidazole moiety with those of the phosphite moiety: they are more stable than their oxazoline counterparts, less sensitive to air and other oxidizing agents than phosphines and phosphinites, and easy to synthesize from readily available alcohols. The results indicate that activities, regio- and enantioselectivities, are highly influenced by the type of nitrogen donor group (oxazole or imidazole), the oxazole and biaryl-phosphite substituents and the axial chirality of the biaryl moiety of the ligand. By carefully selecting the ligand components, we achieved high activities, regio- (up to 99%) and enantioselectivities (up to 99%) using several triflate sources. Under microwave-irradiation conditions, reaction times were considerably shorter (from 24 h to 30 min) and regio- and enantioselectivities were still excellent. PMID:21152643

  12. Structure and intermolecular vibrations of perylene·trans-1,2-dichloroethene, a weak charge-transfer complex.

    PubMed

    Balmer, Franziska A; Ottiger, Philipp; Pfaffen, Chantal; Leutwyler, Samuel

    2013-10-17

    The vibronic spectra of strong charge-transfer complexes are often congested or diffuse and therefore difficult to analyze. We present the spectra of the ?-stacked complex perylene trans-1,2-dichloroethene, which is in the limit of weak charge transfer, the electronic excitation remaining largely confined to the perylene moiety. The complex is formed in a supersonic jet, and its S0 ? S1 spectra are investigated by two-color resonant two-photon ionization (2C-R2PI) and fluorescence spectroscopies. Under optimized conditions, vibrationally cold (T(vib) ? 9 K) and well resolved spectra are obtained. These are dominated by vibrational progressions in the “hindered-rotation” Rc intermolecular vibration with very low frequencies of 11 (S0) and 13 cm(–1) (S1). The intermolecular Tz stretch and the Ra and Rb bend vibrations are also observed. The normally symmetry-forbidden intramolecular 1a(u) “twisting” vibration of perylene also appears, showing that the ?- stacking interaction deforms the perylene moiety, lowering its local symmetry from D2h to D2. We calculate the structure and vibrations of this complex using six different density functional theory (DFT) methods (CAM-B3LYP, BH&HLYP, B97-D3, ?B97X-D, M06, and M06-2X) and compare the results to those calculated by correlated wave function methods (SCS-MP2 and SCS-CC2). The structures and vibrational frequencies predicted with the CAM-B3LYP and BH&HLYP methods disagree with the other calculations and with experiment. The other four DFT and the ab initio methods all predict a ?-stacked “centered” structure with nearly coplanar perylene and dichloroethene moieties and intermolecular binding energies of D(e) = ?20.8 to ?26.1 kJ/mol. The 000 band of the S0 ? S1 transition is red-shifted by ?? = ?301 cm(–1) relative to that of perylene, implying that the D(e) increases by 3.6 kJ/mol or 15% upon electronic excitation. The intermolecular vibrational frequencies are assigned to the calculated Rc, Tz, Ra, and Rb vibrations by comparing to the observed/calculated frequencies and S0 ? S1 Franck–Condon factors. Of the three TD-DFT methods tested, the hybrid-meta-GGA functional M06-2X shows the best agreement with the experimental electronic transition energies, spectral shifts, and vibronic spectra, closely followed by the ?B97X-D functional, while the M06 functional gives inferior results. PMID:24063531

  13. Spectral Moments of Collision-Induced Absorption of CO2 Pairs: The Role of the Intermolecular Potential

    NASA Technical Reports Server (NTRS)

    Gruszka, Marcin; Borysow, Aleksandra

    1994-01-01

    In this paper we examine the role of the anisotropy of the intermolecular potential in the rototranslational collision-induced absorption of the CO2 pairs. Using newly developed formulas that include the effects of anisotropy of the potential to all orders, we calculate the two lowest spectral moments gamma(prime), and alpha(prime), for four different classes of C02 pair potentials and compare the results with the experimental values. We assumed only multipolar induction in the process of forming the induced dipole, with the second-order contributions included. Using a site-site LJ and a site-site semi-ab initio intermolecular potentials we were able to reproduce the experimental values of gamma(prime), and alpha(prime) moments over entire temperature range from 230 to 330 K. Also, the role of an electrostatic interaction between two C02 molecules and its impact on the spectral moments is thoroughly investigated. An isotropic core with a point quadrupole centered at each molecule is shown to be an inadequate representation of the C02-CO2 potential. Additionally, we show the results obtained with the first- and second-order perturbation theory to be more than twice too small.

  14. A Molecular Based Model for Polymer Viscoelasticity: Intra-and Inter-Molecular

    E-print Network

    A Molecular Based Model for Polymer Viscoelasticity: Intra- and Inter-Molecular Variability H by the configuration of the CC-system, its own configuration and confirma- tion, and external force fields. Conversely

  15. 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)

  16. Structure and polarization properties of water: Molecular dynamics with a nonadditive intermolecular potential

    NASA Astrophysics Data System (ADS)

    Shvab, I.; Sadus, Richard J.

    2012-05-01

    The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li , J. Chem. Phys.JCPSA60021-960610.1063/1.2786449 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm3 and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm3 isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models.

  17. Spatiotemporal patterns enhanced by intra- and inter-molecular fluctuations in arrays of allosterically regulated enzymes

    NASA Astrophysics Data System (ADS)

    Togashi, Yuichi; Casagrande, Vanessa

    2015-03-01

    Enzymatic reactions often involve slow conformational changes, with reaction cycles that sometimes require milliseconds or seconds to complete. The dynamics are strongly affected by fluctuations at the nanoscale. However, such enzymes often occur in small numbers in a cell; hence, the fluctuations caused by finite numbers of molecules should also be substantial. Because of these factors, the behavior of the system is likely to deviate from that of classical reaction–diffusion equations, in which immediate reaction events are assumed to occur without memory and between a huge number of molecules. In this work, we model each enzyme as a unit represented by a phase variable to investigate the effects of fluctuations in arrays of enzymes. Using an analysis based on partial differential equations and stochastic simulations, we show that fluctuations arising from internal states of enzymes (intramolecular fluctuations) and those arising from the stochastic nature of interactions between molecules (intermolecular fluctuations) have distinctive effects on spatiotemporal patterns; the former generally disturb synchronization at high frequencies, whereas the latter can enhance synchronization. The balance of the two types of fluctuations may determine the spatiotemporal behavior of biochemical processes.

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

    PubMed

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

    2014-01-28

    In recent years, dendriplexes, complexes of cationic dendrimers with DNA, have become attractive DNA delivery vehicles due to their well-defined chemistries. To better understand the nature of the forces condensing dendriplexes, we studied low generation poly(amidoamine) (PAMAM) dendrimer-DNA complexes and compared them to comparably charged linear arginine peptides. Using osmotic stress coupled with X-ray scattering, we have investigated the effect of molecular chain architecture on DNA-DNA intermolecular forces that determine the net attraction and equilibrium interhelical distance within these polycation condensed DNA arrays. In order to compact DNA, linear cations are believed to bind in DNA grooves and to interact with the phosphate backbone of apposing helices. We have previously shown a length dependent attraction resulting in higher packaging densities with increasing charge for linear cations. Hyperbranched polycations, such as polycationic dendrimers, presumably would not be able to bind to DNA and correlate their charges in the same manner as linear cations. We show that attractive and repulsive force amplitudes in PAMAM-DNA assemblies display significantly different trends than comparably charged linear arginines resulting in lower DNA packaging densities with increasing PAMAM generation. The salt and pH dependencies of packaging in PAMAM dendrimer-DNA and linear arginine-DNA complexes were also investigated. Significant differences in the force curve behaviour and salt and pH sensitivities suggest that different binding modes may be present in DNA condensed by dendrimers when compared to linear polycations. PMID:24651934

  19. Arginine-phosphate salt bridges between histones and DNA: Intermolecular actuators that control nucleosome architecture

    NASA Astrophysics Data System (ADS)

    Yusufaly, Tahir I.; Li, Yun; Singh, Gautam; Olson, Wilma K.

    2014-10-01

    Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies.

  20. Modeling and simulation of magnetic resonance imaging based on intermolecular multiple quantum coherences

    NASA Astrophysics Data System (ADS)

    Cai, Congbo; Dong, Jiyang; Cai, Shuhui; Cheng, En; Chen, Zhong

    2006-11-01

    Intermolecular multiple quantum coherences (iMQCs) have many potential applications since they can provide interaction information between different molecules within the range of dipolar correlation distance, and can provide new contrast in magnetic resonance imaging (MRI). Because of the non-localized property of dipolar field, and the non-linear property of the Bloch equations incorporating the dipolar field term, the evolution behavior of iMQC is difficult to deduce strictly in many cases. In such cases, simulation studies are very important. Simulation results can not only give a guide to optimize experimental conditions, but also help analyze unexpected experimental results. Based on our product operator matrix and the K-space method for dipolar field calculation, the MRI simulation software was constructed, running on Windows operation system. The non-linear Bloch equations are calculated by a fifth-order Cash-Karp Runge-Kutta formulism. Computational time can be efficiently reduced by separating the effects of chemical shifts and strong gradient field. Using this software, simulation of different kinds of complex MRI sequences can be done conveniently and quickly on general personal computers. Some examples were given. The results were discussed.

  1. Intermolecularly-induced conformational disorder in ferrocene, 1-bromoferrocene and 1,1?-dibromoferrocene

    NASA Astrophysics Data System (ADS)

    Silva, Patrícia A.; Maria, Teresa M. R.; Nunes, Cláudio M.; Eusébio, Maria Ermelinda S.; Fausto, Rui

    2014-12-01

    Conformational preferences for isolated molecules of ferrocene, 1-bromoferrocene and 1,1?-dibromoferrocene were obtained by combined use of matrix-isolation infrared spectroscopy and quantum chemical calculations. Monomeric ferrocene and 1-dibromoferrocene were found to exist in a low temperature argon matrix (T = 15 K) exclusively in the eclipsed configuration, which corresponds to their most stable conformation in gas phase. On the other hand, for the neat compounds in crystalline phase, intermolecular interactions induce conformational disorder, leading to presence in the room temperature polymorphic forms of monomeric units with the staggered (or nearly staggered) conformation. 1,1?-Dibromoferrocene exists in both gas phase and low temperature argon matrix in two conformers of C2 symmetry (C2-I and C2-II), with eclipsed cyclopentadienyl moieties and Br atoms opposed to H atoms. The populations of the two conformers trapped in the as-deposited matrix were found to correspond to those estimated from theory for the room temperature equilibrium gas phase. By increasing the temperature of the matrix (up to 35 K), the gas phase lower energy form (C2-I) converted to the C2-II form. Besides allowing the precise structural and spectroscopic characterization of the two forms, these studies also revealed that the C2-II conformer (having a largest dipole moment) is stabilized in the matrix media, thus becoming more stable than the C2-I form under these conditions. Very interestingly, the room temperature stable polymorph of the compound (Tfus = 325.4 ± 0.1 K) is composed by 1,1?-dibromoferrocene units exhibiting the C2v symmetry eclipsed conformation with opposed bromine atoms, which for the isolated molecule corresponds to the highest energy conformation along the ring torsional coordinate and is the transition state structure between the two symmetry equivalent C2-II minima. Differential scanning calorimetry, polarized light thermomicroscopy and infrared measurements on 1,1?-dibromoferrocene allowed to identify a new polymorph of the compound, with Tfus = 320.2 ± 0.1 K. On the whole, the results presented in this article represent illuminating examples of intermolecularly-induced conformational disorder in solid phase and of its relevance to polymorphism.

  2. Improving activity of minicellulosomes by integration of intra- and intermolecular synergies

    PubMed Central

    2013-01-01

    Background Complete hydrolysis of cellulose to glucose requires the synergistic action of three general types of glycoside hydrolases; endoglucanases, exoglucanases, and cellobiases. Cellulases that are found in Nature vary considerably in their modular diversity and architecture. They include: non-complexed enzymes with single catalytic domains, independent single peptide chains incorporating multiple catalytic modules, and complexed, scaffolded structures, such as the cellulosome. The discovery of the latter two enzyme architectures has led to a generally held hypothesis that these systems take advantage of intramolecular and intermolecular proximity synergies, respectively, to enhance cellulose degradation. We use domain engineering to exploit both of these concepts to improve cellulase activity relative to the activity of mixtures of the separate catalytic domains. Results We show that engineered minicellulosomes can achieve high levels of cellulose conversion on crystalline cellulose by taking advantage of three types of synergism; (1) a complementary synergy produced by interaction of endo- and exo-cellulases, (2) an intramolecular synergy of multiple catalytic modules in a single gene product (this type of synergism being introduced for the first time to minicellulosomes targeting crystalline cellulose), and (3) an intermolecular proximity synergy from the assembly of these cellulases into larger multi-molecular structures called minicellulosomes. The binary minicellulosome constructed in this study consists of an artificial multicatalytic cellulase (CBM4-Ig-GH9-X11-X12-GH8-Doc) and one cellulase with a single catalytic domain (a modified Cel48S with the structure CBM4-Ig-GH48-Doc), connected by a non-catalytic scaffoldin protein. The high level endo-exo synergy and intramolecular synergies within the artificial multifunctional cellulase have been combined with an additional proximity-dependent synergy produced by incorporation into a minicellulosome demonstrating high conversion of crystalline cellulose (Avicel). Our minicellulosome is the first engineered enzyme system confirmed by test to be capable of both operating at temperatures as high as 60°C and converting over 60% of crystalline cellulose to fermentable sugars. Conclusion When compared to previously reported minicellulosomes assembled from cellulases containing only one catalytic module each, our novel minicellulosome demonstrates a method for substantial reduction in the number of peptide chains required, permitting improved heterologous expression of minicellulosomes in microbial hosts. In addition, it has been shown to be capable of substantial conversion of actual crystalline cellulose, as well as of the less-well-ordered and more easily digestible fraction of nominally crystalline cellulose. PMID:23987588

  3. Supramolecular step in design of nonlinear optical materials: Effect of ?…? stacking aggregation on hyperpolarizability

    NASA Astrophysics Data System (ADS)

    Suponitsky, Kyrill Yu; Masunov, Artëm E.

    2013-09-01

    Theoretical estimation of nonlinear optical (NLO) properties is an important step in systematic search for optoelectronic materials. Density functional theory methods are often used to predict first molecular hyperpolarizability for compounds in advance of their synthesis. However, design of molecular NLO materials require an estimation of the bulk properties, which are often approximated as additive superposition of molecular tensors. It is therefore important to evaluate the accuracy of this additive approximation and estimate the extent by which intermolecular interactions influence the first molecular hyperpolarizability ?. Here we focused on the stacking aggregates, including up to 12 model molecules (pNA and ANS) and observed enhancement and suppression of molecular hyperpolarizability relative to the additive sum. We found that degree of nonadditivity depends on relative orientation of the molecular dipole moments and does not correlate with intermolecular interaction energy. Frenkel exciton model, based on dipole-dipole approximation can be used for qualitative prediction of intermolecular effects. We report on inaccuracy of this model for the molecules with long ?-systems that are significantly shifted relative to each other, when dipole-dipole approximation becomes inaccurate. To obtain more detailed information on the effect of intermolecular interactions on ? we proposed electrostatic approach which accounts for the mutual polarization of the molecules by each other. We measure the induced polarization of each molecule in the aggregate by the charge of its donor (or acceptor) group. The proposed approach demonstrates linear correlation ?FF vs ?elm (estimated by finite field theory and electrostatic model, respectively) and allows decomposition of the hyperpolarizability for a molecular aggregate into separate molecular contributions. We used this decomposition to analyze the reasons of deviation of aggregate ? from additivity, as well as the cooperative effect of intermolecular interactions on hyperpolarizability for stacks of growing size. In cases of positive cooperativity (enhancement), we found 6-8 molecules to be necessary to reach the asymptotic limit. In more frequent cases of negative cooperativity two opposite factors play role. The first one consists of direct lowering of ? due to repulsive dipole-dipole interactions. The second factor is originated in a decrease of molecular dipole moments, which in turn leads to a decrease of dipole-dipole repulsion, and therefore increases ?. For strong intermolecular repulsive dipole-dipole interactions these effects nearly cancel each other. In such cases the trimers and even dimers are sufficient to reach the asymptotic limit of the infinite stacks. Based on the observed trends we estimated non-additive correction to ? for well known NLO crystals NPAN and MNMA. In the case of NPAN, stacking effect on molecular hyperpolarizability represents the leading component of the crystal packing effect and improves the agreement between calculated and experimental data which is further improved when frequency dependence is taken in account.

  4. Size calibration of strained epitaxial islands due to dipole–monopole interaction

    NASA Astrophysics Data System (ADS)

    Tokar, V. I.; Dreyssé, H.

    2015-02-01

    Irreversible growth of strained epitaxial nanoislands has been studied with the use of the kinetic Monte Carlo (KMC) technique. It has been shown that the strain-inducing size misfit between the substrate and the overlayer produces long range dipole–monopole (d–m) interaction between the mobile adatoms and the islands. To simplify the account of the long range interactions in the KMC simulations, use has been made of a modified square island model. An analytic formula for the interaction between the point surface monopole and the dipole forces has been derived and used to obtain a simple expression for the interaction between the mobile adatom and the rectangular island. The d–m interaction was found to be longer ranged than the conventional dipole–dipole potential. The narrowing of the island size distributions (ISDs) observed in the simulations was shown to be a consequence of a weaker repulsion of adatoms from small islands than from large ones which led to the preferential growth of the former. Furthermore, similar to the unstrained case, the power-law behavior of the average island size and of the island density on the coverage has been found. In contrast to the unstrained case, the value of the scaling exponent was not universal but strongly dependent on the strength of the long range interactions. Qualitative agreement of the simulation results with some previously unexplained behaviors of experimental ISDs in the growth of semiconductor quantum dots was observed.

  5. Interaction of localized surface plasmons with chiral molecules

    NASA Astrophysics Data System (ADS)

    Davis, T. J.; Gómez, D. E.

    2014-12-01

    We analyze theoretically the interaction between chiral molecules and localized surface plasmons in subwavelength metallic structures of arbitrary shape. The chiral molecule is modeled using Condon's classical description of the molecular dipole moment that depends on the magnetic field [E. U. Condon, Rev. Mod. Phys. 9, 432 (1937), 10.1103/RevModPhys.9.432]. This model is included in an eigenmode theory of coupled plasmonic systems. In the limit of dipole-dipole interactions, the theory predicts there is no change in the resonance frequency of the surface plasmon in the presence of a chiral molecule and there is no change in the amplitude of the resonance in the presence of a uniform distribution of chiral molecules. This implies that to observe the effects of the chirality of molecules it may be necessary to form localized surface plasmons with more complex charge distributions. We also examine the absorption of light of the combined system of the metal structure and chiral molecule. The theory predicts that the chirality-dependent absorption in the metal structure averages to zero for a uniform distribution of molecules, with the observed absorption occurring entirely within the molecule due to excitation by the incident light and the fields from the surface plasmon. Apart from the expected circular dichroism, the theory also predicts a chirality-dependent absorption arising from a metal nanostructure illuminated with linearly polarized light and an absorption arising from those chiral properties of the molecule usually associated with optical activity.

  6. Estrogen Receptor Alpha/Co-activator Interaction Assay: TR-FRET.

    PubMed

    Moore, Terry W; Gunther, Jillian R; Katzenellenbogen, John A

    2015-01-01

    Time-resolved fluorescence resonance energy transfer, TR-FRET, is a time-gated fluorescence intensity measurement which defines the relative proximity of two biomolecules (e.g., proteins, peptides, or DNA) based on the extent of non-radiative energy transfer between two fluorophores with overlapping emission/excitation spectra. In these assays, an excited lanthanide ion acts as a "donor" that transfers energy to an "acceptor" fluorophore through dipole-dipole interactions. A FRET signal is reported as the ratio of acceptor to donor emission following donor excitation. When a donor-conjugated protein interacts with an acceptor-conjugated protein, the donor and acceptor fluorophores are brought in close proximity allowing energy transfer from the donor to the acceptor resulting in a FRET signal. Because the lanthanide donors have a long emission half-life, the energy transfer measurement can be time-gated, which dramatically reduces assay interference (due to background autofluorescence and direct acceptor excitation) and thereby increases data quality. Here, we describe a TR-FRET assay that monitors the interaction of the estrogen receptor (ER) ? ligand binding domain (labeled with a terbium chelate via a streptavidin-biotin interaction) with a sequence of coactivator protein SRC3 (labeled directly with fluorescein) and the disruption of this interaction with a peptide and a small molecule inhibitor. PMID:25859975

  7. 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) is a particularly interesting (and exotic) system in which ICD was detected. It was employed in several publications to elucidate the strong impact of nuclear motion on ICD and its longrange-character. The review will present these findings and their initial theoretical predictions and give insight into most recent time-resolved measurements of ICD.

  8. Concentration-dependent reversible self-oligomerization of serum albumins through intermolecular ?-sheet formation.

    PubMed

    Bhattacharya, Arpan; Prajapati, Roopali; Chatterjee, Surajit; Mukherjee, Tushar Kanti

    2014-12-16

    Proteins inside a cell remain in highly crowded environments, and this often affects their structure and activity. However, most of the earlier studies involving serum albumins were performed under dilute conditions, which lack biological relevance. The effect of protein-protein interactions on the structure and properties of serum albumins at physiological conditions have not yet been explored. Here, we report for the first time the effect of protein-protein and protein-crowder interactions on the structure and stability of two homologous serum albumins, namely, human serum albumin (HSA) and bovine serum albumin (BSA), at physiological conditions by using spectroscopic techniques and scanning electron microscopy (SEM). Concentration-dependent self-oligomerization and subsequent structural alteration of serum albumins have been explored by means of fluorescence and circular dichroism spectroscopy at pH 7.4. The excitation wavelength (?ex) dependence of the intrinsic fluorescence and the corresponding excitation spectra at each emission wavelength indicate the presence of various ground state oligomers of serum albumins in the concentration range 10-150 ?M. Circular dichroism and thioflavin T binding assay revealed formation of intermolecular ?-sheet rich interfaces at high protein concentration. Excellent correlations have been observed between ?-sheet content of both the albumins and fluorescence enhancement of ThT with protein concentrations. SEM images at a concentration of 150 ?M revealed large dispersed self-oligomeric states with sizes vary from 330 to 924 nm and 260 to 520 nm for BSA and HSA, respectively. The self-oligomerization of serum albumins is found to be a reversible process; upon dilution, these oligomers dissociate into a native monomeric state. It has also been observed that synthetic macromolecular crowder polyethylene glycol (PEG 200) stabilizes the self-associated state of both the albumins which is contrary to expectations that the macromolecular crowding favors compact native state of proteins. PMID:25409497

  9. Amorphous drug-PVP dispersions: application of theoretical, thermal and spectroscopic analytical techniques to the study of a molecule with intermolecular bonds in both the crystalline and pure amorphous state.

    PubMed

    Tobyn, Michael; Brown, Jonathan; Dennis, Andrew B; Fakes, Michael; Gao, Qi; Gamble, John; Khimyak, Yaroslav Z; McGeorge, Gary; Patel, Chhaya; Sinclair, Wayne; Timmins, Peter; Yin, Shawn

    2009-09-01

    We report the case of BMS-488043-PVP solid dispersions which when analysed using modulated DSC showed compliance with the Gordon-Taylor model, confirming ideal mixing behaviour of the two components. The nature or presence of stabilising interactions between drug and PVP could not be confirmed using this technique. Use of FT-IR, Raman and solid-state NMR spectroscopy confirmed the presence of stabilising hydrogen bond interactions between the drug and PVP. Similar interactions are present as intermolecular bonds in the crystalline and pure amorphous drug system. The Gordon-Taylor equation, as it is not predictive of the presence of intermolecular bonds such as hydrogen bonding in an amorphous dispersion, may underestimate the likely physical stability of solid dispersions which are produced and stabilised by these interactions. PMID:19603506

  10. Intra- and intermolecular hydrogen bonding and conformation in 1-acyl thioureas: An experimental and theoretical approach on 1-(2-chlorobenzoyl)thiourea.

    PubMed

    Saeed, Aamer; Khurshid, Asma; Bolte, Michael; Fantoni, Adolfo C; Erben, Mauricio F

    2015-05-15

    The vibrational analysis (FT-IR and FT-Raman) for the new 1-(2-chlorobenzoyl)thiourea species suggests that strong intramolecular interactions affect the conformational properties. The X-ray structure determination corroborates that an intramolecular N-H?OC hydrogen bond occurs between the carbonyl (-CO) and thioamide (-NH2) groups. Moreover, periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Extended N-H?SC hydrogen-bonding networks between both the thioamide (N-H) and carbamide (NH2) groups and the thiocarbonyl bond (CS) determine the crystal packing. The Natural Bond Orbital (NBO) population analysis demonstrates that strong hyperconjugative remote interactions are responsible for both, intra and intermolecular interactions. The Atom in Molecule (AIM) results also show that the N-H?Cl intramolecular hydrogen bond between the 2-Cl-phenyl ring and the amide group characterized in the free molecule changes to an N?Cl interaction as a consequence of crystal packing. PMID:25710115

  11. The role of intermolecular interactions in the assemblies of Fe{sup II} and Co{sup II} tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)Ru{sup II}: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules

    Microsoft Academic Search

    Mohamed Ghazzali; Vratislav Langer; Lars Ohrstroem

    2008-01-01

    Two new dual-metal assemblies: 2[Ru(phen)]{sup 2+}.[Fe(SCN)]².2SCN.4HO 1 and [Ru(phen)]{sup 2+}.[Co(SCN)]²2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a sequence supported by - stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O-H...O and O-H...S

  12. The role of intermolecular interactions in the assemblies of Fe II and Co II tetrakis-isothiocyanatometalates with tris(1,10-phenanthroline)Ru II: Crystal structures of two dual-metal assemblies featuring octahedral cationic and tetrahedral anionic modules

    Microsoft Academic Search

    Mohamed Ghazzali; Vratislav Langer; Lars Öhrström

    2008-01-01

    Two new dual-metal assemblies: 2[Ru(phen)3]2+·[Fe(SCN)4]2?·2SCN?·4H2O 1 and [Ru(phen)3]2+·[Co(SCN)4]2?2, (phen:1,10-phenanthroline), have been prepared and their structures were characterized by X-ray diffraction. In 1, the cationic octahedral enantiomers are arranged with a ????? sequence supported by ?–? stacking and the anionic inorganic tetrahedral units are oriented between these stacks by interacting with the nearby water molecules through strong O–H?O and O–H?S hydrogen

  13. Effects of a perpendicular magnetic field in the dipolar Heisenberg model with dominant exchange interaction.

    PubMed

    Abu-Labdeh, A M; MacIsaac, A B; De'Bell, K

    2011-07-27

    The effects of a uniform magnetic field on the phase diagram of the dipolar Heisenberg model with a dominant antiferromagnetic exchange interaction have been investigated. The model consists of a square lattice of classical spin vectors, where the spins interact through an antiferromagnetic exchange interaction of strength J and a dipole-dipole interaction of strength g. The spins couple to a magnetic surface anisotropy of strength ? and to an applied external magnetic field of strength H. The external field is applied perpendicular to the plane of the lattice. From extensive Monte Carlo simulations, representative magnetic phase diagrams have been determined as a function of the ratios ?/g and T/g, where T is temperature, and at three different ratios of H/g (H/g = 10, 20, 27). These results are compared to the previously investigated case of H/g = 0 and to analytic calculations for the ground state energies. The nature of the equilibrium phases and order of the phase boundaries separating them are considered and changes due to the strength of the applied field are highlighted. PMID:21737865

  14. Enhanced hole carrier transport due to increased intermolecular contacts in small molecule based field effect transistors.

    PubMed

    Dharmapurikar, Satej S; Arulkashmir, Arulraj; Das, Chayanika; Muddellu, Pooja; Krishnamoorthy, Kothandam

    2013-08-14

    Small molecules and oligomers can be synthesized with very high purity and precise molecular weights, but they often do not form uniform thin films while processed from solution. Decreased intermolecular contacts between the small molecules are another disadvantage. To increase the intermolecular contacts in small molecules, we have chosen i-indigo, as one of the conjugated molecular units. The electron poor i-indigo has been connected with electron rich triphenylamine to synthesize a donor-acceptor-donor type small molecule. The propeller shaped triphenylamine helps to increase the solubility of the small molecule as well as isotropic charge transport. The intermolecular spacing between the molecules has been found to be low and did not vary as a function of thermal annealing. This implies that the intermolecular contacts between the small molecules are enhanced, and they do not vary as a function of thermal annealing. Organic field effect transistors (OFET) fabricated using a small molecule exhibited a hole carrier mobility (?) of 0.3 cm(2)/(V s) before thermal annealing. A marginal increase in ? was observed upon thermal annealing at 150 °C, which has been attributed to changes in thin film morphology. The morphology of the thin films plays an important role in charge transport in addition to the intermolecular spacing that can be modulated with a judicious choice of the conjugated molecular unit. PMID:23808768

  15. Intermolecular transmission of superoxide dismutase 1 misfolding in living cells

    E-print Network

    Plotkin, Steven S.

    ­protein interaction. neurodegeneration | protein misfolding | prion | template-directed misfolding | seeded, swallowing, and respiration. ALS is re- sponsible for approximately 1 in 1,000 adult deaths, with 80

  16. Intermolecular Casimir-Polder forces in water and near surfaces

    NASA Astrophysics Data System (ADS)

    Thiyam, Priyadarshini; Persson, Clas; Sernelius, Bo E.; Parsons, Drew F.; Malthe-Sørenssen, Anders; Boström, Mathias

    2014-09-01

    The Casimir-Polder force is an important long-range interaction involved in adsorption and desorption of molecules in fluids. We explore Casimir-Polder interactions between methane molecules in water, and between a molecule in water near SiO2 and hexane surfaces. Inclusion of the finite molecular size in the expression for the Casimir-Polder energy leads to estimates of the dispersion contribution to the binding energies between molecules and between one molecule and a planar surface.

  17. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  18. Novel Intermolecular Iterative Mechanism for Biosynthesis of Mycoketide Catalyzed by a Bimodular Polyketide Synthase

    PubMed Central

    Chopra, Tarun; Banerjee, Srijita; Gupta, Sarika; Yadav, Gitanjali; Anand, Swadha; Surolia, Avadhesha; Roy, Rajendra P; Mohanty, Debasisa; Gokhale, Rajesh S

    2008-01-01

    In recent years, remarkable versatility of polyketide synthases (PKSs) has been recognized; both in terms of their structural and functional organization as well as their ability to produce compounds other than typical secondary metabolites. Multifunctional Type I PKSs catalyze the biosynthesis of polyketide products by either using the same active sites repetitively (iterative) or by using these catalytic domains only once (modular) during the entire biosynthetic process. The largest open reading frame in Mycobacterium tuberculosis, pks12, was recently proposed to be involved in the biosynthesis of mannosyl-?-1-phosphomycoketide (MPM). The PKS12 protein contains two complete sets of modules and has been suggested to synthesize mycoketide by five alternating condensations of methylmalonyl and malonyl units by using an iterative mode of catalysis. The bimodular iterative catalysis would require transfer of intermediate chains from acyl carrier protein domain of module 2 to ketosynthase domain of module 1. Such bimodular iterations during PKS biosynthesis have not been characterized and appear unlikely based on recent understanding of the three-dimensional organization of these proteins. Moreover, all known examples of iterative PKSs so far characterized involve unimodular iterations. Based on cell-free reconstitution of PKS12 enzymatic machinery, in this study, we provide the first evidence for a novel “modularly iterative” mechanism of biosynthesis. By combination of biochemical, computational, mutagenic, analytical ultracentrifugation and atomic force microscopy studies, we propose that PKS12 protein is organized as a large supramolecular assembly mediated through specific interactions between the C- and N-terminus linkers. PKS12 protein thus forms a modular assembly to perform repetitive condensations analogous to iterative proteins. This novel intermolecular iterative biosynthetic mechanism provides new perspective to our understanding of polyketide biosynthetic machinery and also suggests new ways to engineer polyketide metabolites. The characterization of novel molecular mechanisms involved in biosynthesis of mycobacterial virulent lipids has opened new avenues for drug discovery. PMID:18613748

  19. Photoinduced intermolecular electron transfer from aromatic amines to coumarin dyes in sodium dodecyl sulphate micellar solutions

    NASA Astrophysics Data System (ADS)

    Kumbhakar, Manoj; Nath, Sukhendu; Pal, Haridas; Sapre, Avinash V.; Mukherjee, Tulsi

    2003-07-01

    Photoinduced intermolecular electron transfer interaction between coumarin dyes and aromatic amines has been investigated in sodium dodecyl sulphate micellar solutions using steady-state and time-resolved fluorescence quenching measurements. Steady-state fluorescence quenching of the coumarin dyes by the amine quenchers always shows a positive deviation from linear Stern-Volmer relationship, which arises due to the localized high quencher concentrations at the micellar Stern layer. In time-resolved fluorescence measurements, the analysis of the fluorescence decays following a micellar quenching kinetics model assuming a unified quenching constant (kq') per quencher occupancy does not give satisfactory results, especially for the higher quencher concentrations used. The observed fluorescence decays are, however, seen to fit reasonably well following a bi-exponential analysis for all the quencher concentrations used. The average fluorescence lifetimes of the coumarin dyes in the micellar solution as estimated from the bi-exponential decay analysis are seen to undergo a systematic reduction with the effective mean quencher concentrations. The bimolecular quenching constants (kq) thus estimated are seen to be much smaller than those reported in the homogeneous solutions (e.g., in acetonitrile), indicating that the electron transfer in the micellar media is inherently inefficient. Correlation of the observed kq values in the micellar solutions with the free-energy changes (?G0) for electron transfer reactions show an inversion in the observed rates as predicted by Marcus' outer sphere electron transfer theory at exergonicities more that ˜0.65 eV. To the best of our knowledge this is the first report on the Marcus inverted region observed for the electron transfer reactions in micellar solution.

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

    PubMed

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

    2012-05-10

    We present a definition of intermolecular surface contact by applying weighted Voronoi tessellations to configurations of various organic liquids and water obtained from molecular dynamics simulations. This definition of surface contact is used to link the COSMO-RS model and molecular dynamics simulations. We demonstrate that additively weighted tessellation is the superior tessellation type to define intermolecular surface contact. Furthermore, we fit a set of weights for the elements C, H, O, N, F, and S for this tessellation type to obtain optimal agreement between the models. We use these radii to successfully predict contact statistics for compounds that were excluded from the fit and mixtures. The observed agreement between contact statistics from COSMO-RS and molecular dynamics simulations confirms the capability of the presented method to describe intermolecular contact. Furthermore, we observe that increasing polarity of the surfaces of the examined molecules leads to weaker agreement in the contact statistics. This is especially pronounced for pure water. PMID:22480253

  1. Intermolecular potential functions from spectroscopic properties of weakly bound complexes. Third progress report, July 1, 1991--June 30, 1992

    SciTech Connect

    Muenter, J.S.

    1992-08-01

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

  2. Chemical cross-linking with thiol-cleavable reagents combined with differential mass spectrometric peptide mapping--a novel approach to assess intermolecular protein contacts.

    PubMed Central

    Bennett, K. L.; Kussmann, M.; Björk, P.; Godzwon, M.; Mikkelsen, M.; Sørensen, P.; Roepstorff, P.

    2000-01-01

    The intermolecular contact regions between monomers of the homodimeric DNA binding protein ParR and the interaction between the glycoproteins CD28 and CD80 were investigated using a strategy that combined chemical cross-linking with differential MALDI-MS analyses. ParR dimers were modified in vitro with the thiol-cleavable cross-linker 3,3'-dithio-bis(succinimidylproprionate) (DTSSP), proteolytically digested with trypsin and analyzed by MALDI-MS peptide mapping. Comparison of the peptide maps obtained from digested cross-linked ParR dimers in the presence and absence of a thiol reagent strongly supported a "head-to-tail" arrangement of the monomers in the dimeric complex. Glycoprotein fusion constructs CD28-IgG and CD80-Fab were cross-linked in vitro by DTSSP, characterized by nonreducing SDS-PAGE, digested in situ with trypsin and analyzed by MALDI-MS peptide mapping (+/- thiol reagent). The data revealed the presence of an intermolecular cross-link between the receptor regions of the glycoprotein constructs, as well as a number of unexpected but nonetheless specific interactions between the fusion domains of CD28-IgG and the receptor domain of CD80-Fab. The strategy of chemical cross-linking combined with differential MALDI-MS peptide mapping (+ thiol reagent) enabled localization of the interface region(s) of the complexes studied and clearly demonstrates the utility of such an approach to obtain structural information on interacting noncovalent complexes. PMID:10975572

  3. Intermolecular potential energy surface and thermophysical properties of ethylene oxide.

    PubMed

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide. PMID:25362314

  4. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    SciTech Connect

    Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  5. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    NASA Astrophysics Data System (ADS)

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-01

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  6. Synthesis of Acyclic r, -Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction of Alkynamides and Alkenes

    E-print Network

    Liu, David R.

    Synthesis of Acyclic r, -Unsaturated Ketones via Pd(II)-Catalyzed Intermolecular Reaction ketone.3 Here we describe the development of an analogous intermolecular oxidative coupling reaction between alkynamides and terminal alkenes to generate acyclic R, -unsat- urated ketones4 (eq 1). Our

  7. Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from

    E-print Network

    Clore, G. Marius

    Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance ambiguous, intermolecular distance restraints (comprising between 400 and 3000 individual distances) to avoid expansion at the protein-protein interface, and a torsion angle database potential of mean force

  8. Interaction

    NSDL National Science Digital Library

    Wolfgang Christian

    Set values for the initial position, velocity, and mass of the two particles, and click on the button "Initialize Animation" to play the animation using your specified values. Note, if m or v are too large, the particles may actually pass through one another which will seem a little strange. Note: the interaction between the particles is a "non-contact" interaction, much like the electrostatic force on two charges. Mathematically, it is actually a Hooke's law interaction.

  9. Anion of the formic acid dimer as a model for intermolecular proton transfer induced by a *

    E-print Network

    Simons, Jack

    , Pozna 60-780, Poland and Chemical Sciences Division, Fundamental Sciences Directorate, Pacific Northwest of Chemistry, University of Gdask, Gdask 80-952, Poland Maciej Gutowskia Chemical Sciences Division proton transfer between carbon and oxygen nitrogen atoms. Intermolecular proton transfer is involved

  10. 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.

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

    PubMed

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

    2013-11-28

    By exploiting the instantaneous normal mode (INM) analysis for models of flexible molecules, we investigate intermolecular and intramolecular vibrations of water from the atomic point of view. With two flexible SPC/E models, our investigations include three aspects about their INM spectra, which are separated into the unstable, intermolecular, bending, and stretching bands. First, the O- and H-atom contributions in the four INM bands are calculated and their stable INM spectra are compared with the power spectra of the atomic velocity autocorrelation functions. The unstable and intermolecular bands of the flexible models are also compared with those of the SPC/E model of rigid molecules. Second, we formulate the inverse participation ratio (IPR) of the INMs, respectively, for the O- and H-atom and molecule. With the IPRs, the numbers of the three species participated in the INMs are estimated so that the localization characters of the INMs in each band are studied. Further, by the ratio of the IPR of the H atom to that of the O atom, we explore the number of involved OH bond per molecule participated in the INMs. Third, by classifying simulated molecules into subensembles according to the geometry of their local environments or their H-bond configurations, we examine the local-structure effects on the bending and stretching INM bands. All of our results are verified to be insensible to the definition of H-bond. Our conclusions about the intermolecular and intramolecular vibrations in water are given. PMID:24289362

  12. 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.

  13. Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

    ERIC Educational Resources Information Center

    Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

    2010-01-01

    This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

  14. Intramolecular and Intermolecular Signatures of Incipient Ordering in a Multicomponent Polymer Blend

    NASA Astrophysics Data System (ADS)

    Jeon, H. S.; Lee, J. H.; Balsara, N. P.

    1997-10-01

    Neutron scattering experiments were performed on a homogeneous blend of two homopolymers and a block copolymer, in the vicinity of an ordering transition. The concentration fluctuations of individual components were examined in separate experiments on contrast matched systems. The homopolymers exhibit intermolecular aggregation, while the block copolymer exhibits intramolecular segregation.

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

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China)] [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China); Wu, Ten-Ming, E-mail: tmw@faculty.nctu.edu.tw [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China) [Institute of Physics, National Chiao-Tung University, Hsinchu 300, Taiwan (China); National Center for Theoretical Sciences, Hsinchu 300, Taiwan (China)

    2013-11-28

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

  16. Stress acidulated amphoteric molecules and mechanochromism via reversible intermolecular proton transfer.

    PubMed

    Wang, Yi; Li, Minjie; Zhang, Yumo; Yang, Jin; Zhu, Shaoyin; Sheng, Lan; Wang, Xudong; Yang, Bing; Zhang, Sean Xiao-An

    2013-07-28

    Stress has been proved to acidulate amphoteric molecules and promote an intermolecular proton transfer, which results in a significant absorption and emission change. The stress acidulated amphoteric molecules open a new avenue for developing mechanochromic materials and anticipate many broad applications such as stress/pressure sensors and rewritable media. PMID:23712461

  17. Practical, modular, and general synthesis of 3-coumaranones through gold-catalyzed intermolecular alkyne oxidation strategy.

    PubMed

    Shu, Chao; Liu, Rongfu; Liu, Shuang; Li, Jian-Qiao; Yu, Yong-Fei; He, Qiao; Lu, Xin; Ye, Long-Wu

    2015-01-01

    A gold-catalyzed intermolecular alkyne oxidation for the preparation of 3-coumaranones has been developed. Using 8-isopropylquinoline N-oxides as oxidants, the reactions of o-ethynylanisoles afford versatile 3-coumaranones in moderate to good isolated yields. The synthetic utility of this chemistry is also indicated by the synthesis of the natural product sulfuretin. PMID:25287758

  18. Cell Adhesion Strength Is Controlled by Intermolecular Spacing of Adhesion Receptors

    E-print Network

    Schwarz, Ulrich

    Cell Adhesion Strength Is Controlled by Intermolecular Spacing of Adhesion Receptors C. Selhuber numerous cellular processes such as spreading, adhesion, migration, and proliferation. Using force forces as well as the stiffness of the cell body were significantly decreased compared to spacings %50 nm

  19. 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…

  20. Visible light mediated intermolecular [3 + 2] annulation of cyclopropylanilines with alkynes

    PubMed Central

    Nguyen, Theresa H; Maity, Soumitra

    2014-01-01

    Summary Intermolecular [3 + 2] annulation of cyclopropylanilines with alkynes is realized using visible light photoredox catalysis, yielding a variety of cyclic allylic amines in fair to good yields. This method exhibits significant group tolerance particularly with heterocycles. It can also be used to prepare complex heterocycles such as fused indolines. PMID:24991247

  1. Investigations of the intermolecular forces between RDX and polyethylene by force-distance spectroscopy and molecular dynamics simulations.

    PubMed

    Taylor, D E; Strawhecker, K E; Shanholtz, E R; Sorescu, D C; Sausa, R C

    2014-07-10

    The development of novel nanoenergetic materials with enhanced bulk properties requires an understanding of the intermolecular interactions occurring between molecular components. We investigate the surface interactions between 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) and polyethylene (PE) crystals on the basis of combined use of molecular dynamics (MD) simulations and force-distance spectroscopy, in conjunction with Lifshitz macroscopic theory of van der Waals forces between continuous materials. The binding energy in the RDX-PE system depends both on the degree of PE crystallinity and on the RDX crystal face. Our MD simulations yield binding energies of approximately 132 and 120 mJ/m(2) for 100% amorphous and 100% crystalline PE on RDX (210), respectively. The average value is about 36% greater than our experimental value of 81 ± 15 mJ/m(2) for PE (?48% amorphous) on RDX (210). By comparison, Liftshitz theory predicts a value of about 79 mJ/m(2) for PE interacting with RDX. Our MD simulations also predict larger binding energies for both amorphous and crystalline PE on RDX (210) compared to the RDX (001) surface. Analysis of the interaction potential indicates that about 60% of the binding energy in the PE-RDX system is due to attractive interactions between HPE-ORDX and CPE-NRDX pairs of atoms. Further, amorphous PE shows a much longer interaction distance than crystalline PE with the (210) and (001) RDX surfaces due to the possibility of larger polymer elongations in the case of amorphous PE as strain is applied. Also, we report estimates of the binding energies of energetic materials RDX and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) with PE, propylene, polystyrene, and several fluorine-containing polymers using Lifshitz theory and compare these with reported MD calculations. PMID:24922563

  2. Multiple-scattering approach to interatomic interactions and superradiance in inhomogeneous dielectrics

    NASA Astrophysics Data System (ADS)

    Wubs, Martijn; Suttorp, L. G.; Lagendijk, A.

    2004-11-01

    The dynamics of a collection of resonant atoms embedded inside an inhomogeneous nondispersive and lossless dielectric is described with a dipole Hamiltonian that is based on a canonical quantization theory. The dielectric is described macroscopically by a position-dependent dielectric function and the atoms as microscopic harmonic oscillators. We identify and discuss the role of several types of Green tensors that describe the spatio-temporal propagation of field operators. After integrating out the atomic degrees of freedom, a multiple-scattering formalism emerges in which an exact Lippmann-Schwinger equation for the electric field operator plays a central role. The equation describes atoms as point sources and point scatterers for light. First, single-atom properties are calculated such as position-dependent spontaneous-emission rates as well as differential cross sections for elastic scattering and for resonance fluorescence. Secondly, multiatom processes are studied. It is shown that the medium modifies both the resonant and the static parts of the dipole-dipole interactions. These interatomic interactions may cause the atoms to scatter and emit light cooperatively. Unlike in free space, differences in position-dependent emission rates and radiative line shifts influence cooperative decay in the dielectric. As a generic example, it is shown that near a partially reflecting plane there is a sharp transition from two-atom superradiance to single-atom emission as the atomic positions are varied.

  3. Electronic energy transfer between fluorescent dyes with inter- and intramicellar interactions

    NASA Astrophysics Data System (ADS)

    de Oliveira, Hueder P. M.; Gehlen, Marcelo H.

    2003-05-01

    Energy transfer by dipole-dipole interaction between cationic dyes solubilized in micelles of sodium dodecyl sulfate (SDS) in aqueous solution was studied in the particular case where donor-acceptor Förster critical radius ( R0) is larger than the micelle diameter ( dm). Using the donor-acceptor dye pairs acridine/Nile blue ( R 0=68 Å), and 9-aminoacridine/Nile blue ( R 0=36 Å), long range interaction allows energy transfer from a survival isolated excited donor to an acceptor solubilized in a neighboring micelle. The efficiency of intramicellar energy transfer in steady-state measurements was proportional to the product of micelle concentration and average acceptor occupancy, being more pronounced in the case of the pair with large R0 value. In these situations with R0> dm, the distribution analysis of decay times recovers two well separated contributions where the short-lived components are related to fast intramicellar quenching, and the long-lived components are ascribed to long range intermicellar energy transfer.

  4. Solitons in quasi-one-dimensional Bose-Einstein condensates with competing dipolar and local interactions

    SciTech Connect

    Cuevas, J. [Departamento de Fisica Aplicada I, Grupo de Fisica No Lineal, Escuela Universitaria Politecnica, C/Virgen de Africa, 7, 41011 Sevilla (Spain); Malomed, Boris A. [Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978 (Israel); Kevrekidis, P. G. [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003-4515 (United States); Frantzeskakis, D. J. [Department of Physics, University of Athens, Panepistimiopolis, Zografos, Athens 15784 (Greece)

    2009-05-15

    We study families of one-dimensional matter-wave bright solitons supported by the competition of contact and dipole-dipole (DD) interactions of opposite signs. Soliton families are found, and their stability is investigated in the free space and in the presence of an optical lattice (OL). Free-space solitons may exist with an arbitrarily weak local attraction if the strength of the DD repulsion is fixed. In the case of the DD attraction, solitons do not exist beyond a maximum value of the local-repulsion strength. In the system which includes the OL, a stability region for subfundamental solitons is found in the second finite band gap. For the existence of gap solitons (GSs) under the attractive DD interaction, the contact repulsion must be strong enough. In the opposite case of the DD repulsion, GSs exist if the contact attraction is not too strong. Collisions between solitons in the free space are studied too. In the case of the local attraction, they merge or pass through each other at small and large velocities, respectively. In the presence of the local repulsion, slowly moving solitons bounce from each other.

  5. Modeling and measurement of intermolecular interaction forces between cartilage ECM macromolecules

    E-print Network

    Dean, Delphine Marguerite Denise, 1978-

    2005-01-01

    The mechanical properties of cartilage tissue depend largely on the macromolecules that make up its extracellular matrix (ECM). Aggrecan is the most abundant proteoglycan in articular cartilage. It is composed of a core ...

  6. Study of intermolecular interaction of allyl chloride with acetone through dielectric and volumetric properties

    NASA Astrophysics Data System (ADS)

    Sudake, Y. S.; Kamble, S. P.; Maharolkar, A. P.; Patil, S. S.; Khirade, P. W.

    2012-06-01

    The static dielectric constant (?s)and relaxation time (?) are determined from complex permittivity spectra of Allyl Chloride (ALC) with Acetone (ACE), which are obtained using the Time Domain Reflectometry (TDR) technique in microwave frequency range 10 MHz to 10 GHz. Density (?) and refractive index (nD) were also measured. These parameters are used to determine excess dielectric constant, excess molar volume, and excess molar refraction. The excess parameter is fitted to Redlich-Kister(RK) equation. The values of excess parameters are positive in ALC rich region whereas in ACE rich region are negative.

  7. Intermolecular interactions in soybean oil + different organic solvents by ultrasonic velocity measurements

    Microsoft Academic Search

    C. González; J. M. Resa; J. Lanz; M. Iglesias

    2006-01-01

    Ultrasonic velocity measurement is a reliable procedure that allows a quick and easy determination of solvent concentrations in the micelle structures that appear in oil technology, as well as a theoretical analysis to understand the solvation process. This paper presents data of ultrasonic velocities and isentropic compressibilities of mixtures enclosing soybean oil and different solvents such as short aliphatic alkanols

  8. Self-assembly of pyrene derivatives on Au(111): substituent effects on intermolecular interactions.

    PubMed

    Pham, Tuan Anh; Song, Fei; Nguyen, Manh-Thuong; Stöhr, Meike

    2014-11-25

    The adsorption behaviour as well as the influence of bromine substituents on the formation of highly-ordered two-dimensional structures of pyrene derivatives on Au(111) are studied by a combination of scanning tunnelling microscopy (STM) and density functional theory (DFT) calculations. PMID:24905327

  9. HIGH SENSITIVITY FOURIER TRANSFORM NMR. INTERMOLECULAR INTERACTIONS BETWEEN ENVIRONMENTAL TOXIC SUBSTANCES AND BIOLOGICAL MACROMOLECULES

    EPA Science Inventory

    This project explored the feasibility of developing new techniques for evaluation of the effects of environmental toxic materials on complex biopolymer systems using high sensitivity Fourier transform nuclear magnetic resonance (nmr) spectroscopy. Commercial instrumentation avail...

  10. Laboratory-Frame Photoelectron Angular Distributions in Anion Photodetachment: Insight into Electronic Structure and Intermolecular Interactions

    NASA Astrophysics Data System (ADS)

    Sanov, Andrei

    2014-04-01

    This article provides an overview of some recent advances in the modeling of photoelectron angular distributions in negative-ion photodetachment. Building on the past developments in threshold photodetachment spectroscopy that first tackled the scaling of the partial cross sections with energy, depending on the angular momentum quantum number ?, it examines the corresponding formulation of the central potential model and extends it to the more general case of hybrid molecular orbitals. Several conceptual approaches to understanding photoelectron angular distributions are discussed. In one approach, the angular distributions are examined based on the contributions of the symmetry-allowed s and p partial waves of the photodetached electron. In another related approach, the parent molecular orbitals are described based on their dominant s and p characters, whereas the continuum electron is described in terms of interference of the corresponding ? = ±1 photodetachment channels.

  11. Intermolecular interactions in adsorbate-carbon systems of various nano- and adsorption textures

    Microsoft Academic Search

    V. I. Zheivot; E. M. Moroz; V. I. Zaikovskii; V. V. Chesnokov; V. Yu. Gavrilov

    1997-01-01

    Carbon materials possessing various nano- and adsorption textures have been investigated using adsorption, X-ray diffraction, electron microscopy and gas molecular chromatography. They were systematized according to their substructure characteristics and orientation of carbon layers. Substructure characteristics and carbon layer orientation essentially affect the adsorption and gas chromatography behavior of adsorbates. Carbons' application in molecular gas chromatography is discussed.

  12. Intermolecular Interaction Between R Domains of Cystic Fibrosis Transmembrane Conductance Regulator

    Microsoft Academic Search

    Sanhita Gupta; Junxia Xie; Jianjie Ma; Pamela B. Davis

    The function of the R domain of cystic fibrosis transmembrane conductance regulator (CFTR) has not yet been fully estab- lished. The cis-trans proline isomerase cyclophilin A stimulates channel activity, and stimulation depends on the presence of highly conserved prolines at positions 740, 750, and 759. When the prolines at these positions, which normally exist in the cis conformation, are locked

  13. Intermolecular potential parameters and combining rules determined from viscosity data

    SciTech Connect

    Bastien, Lucas A.J.; Price, Phillip N.; Brown, Nancy J.

    2010-05-07

    The Law of Corresponding States has been demonstrated for a number of pure substances and binary mixtures, and provides evidence that the transport properties viscosity and diffusion can be determined from a molecular shape function, often taken to be a Lennard-Jones 12-6 potential, that requires two scaling parameters: a well depth {var_epsilon}{sub ij} and a collision diameter {sigma}{sub ij}, both of which depend on the interacting species i and j. We obtain estimates for {var_epsilon}{sub ij} and {sigma}{sub ij} of interacting species by finding the values that provide the best fit to viscosity data for binary mixtures, and compare these to calculated parameters using several 'combining rules' that have been suggested for determining parameter values for binary collisions from parameter values that describe collisions of like molecules. Different combining rules give different values for {sigma}{sub ij} and {var_epsilon}{sub ij} and for some mixtures the differences between these values and the best-fit parameter values are rather large. There is a curve in ({var_epsilon}{sub ij}, {sigma}{sub ij}) space such that parameter values on the curve generate a calculated viscosity in good agreement with measurements for a pure gas or a binary mixture. The various combining rules produce couples of parameters {var_epsilon}{sub ij}, {sigma}{sub ij} that lie close to the curve and therefore generate predicted mixture viscosities in satisfactory agreement with experiment. Although the combining rules were found to underpredict the viscosity in most of the cases, Kong's rule was found to work better than the others, but none of the combining rules consistently yields parameter values near the best-fit values, suggesting that improved rules could be developed.

  14. Intermolecular reactivity study to scale adsorption property of para- and meta-substituted nitrobenzene over 2:1 dioctahedral smectite

    NASA Astrophysics Data System (ADS)

    Chatterjee, Abhijit; Ebina, Takeo; Iwasaki, Takashi; Mizukami, Fujio

    2003-06-01

    Substituted nitrobenzene, a toxic series of molecules with its wide application in pesticides needs to be removed by a suitable sorbent, whose characteristic is to be determined using the reactivity index theory within the helm of the density-functional theory and as well inside the broad subject range of the hard-soft acid-base (HSAB) principle. We studied a series of meta- and para-substituted nitrobenzene molecules (NBMs) starting from -NH2, -OH, -OCH3, -CHO, -OCOCH3, -COCH3, -CF3, -CN, and -COOCH3 to monitor the effect of electrophilicity and nucleophilicity in their adsorption properties. From the values of the local softness and the charge on the hydrogen atom of the bridging/structural (occurring on the surface) hydroxyl attached to the octahedral/tetrahedral metal site present in smectite, it is concluded that the local acidities of the inorganic material systems are dependent on several characteristics which are of importance within the framework of HSAB principle. We used "group softness" for the interacting molecules, whose values were generated by adding the local softness values of constituent atoms of the respective group and found it can be a better descriptor for intermolecular interactions occurring in these NBMs. A semiquantitave scale is proposed from the group reactivity index present in NBM and the clay cluster.

  15. The inter-adsorbate interaction mediated by Shockley-type surface state electrons and dipole moment: Cs and Ba atoms absorbed on Ag (1 1 1) films

    NASA Astrophysics Data System (ADS)

    Zhang, Shuyuan; Zhang, Hong; Miyamoto, Yoshiyuki

    2014-01-01

    Through first-principles investigation, we display the formation process of Shockley-type surface states which emerges on silver thin films along Ag (1 1 1) orientation with increasing thicknesses from 6 to 21 layers. We look at the surface state band for various adatoms adsorbed on 6, 12, 18 layers strained Ag (1 1 1) films with different coverage, and discuss the long range interaction mediated by surface state electrons. We discovered that film's thickness can modulate the surface state mediated interaction drastically, but the dipole-dipole repulsive interaction is not affected by slab thickness. This factor had never been discussed in detail. Therefore, adatoms adsorbed on thin films have strong attractive interaction which leads to small adsorption separation and the tendency of island formation. For different coverage or different adsorbate types, both surface states and dipole moment are modulated. The three factors, film's thickness, adsorbate coverage and adatoms types, could help us learn more about the interactions between adatoms and exploit advanced ways to control surface geometry structures of self-assembly.

  16. C60 chain phases on ZnPc/Ag(111) surfaces: Supramolecular organization driven by competing interactions

    NASA Astrophysics Data System (ADS)

    Jin, W.; Liu, Q.; Dougherty, D. B.; Cullen, W. G.; Reutt-Robey, J. E.; Weeks, J.; Robey, S. W.

    2015-03-01

    Serpentine chain C60 phases were observed in scanning tunneling microscopy (STM) images of C60 layers on zinc phthalocyanine (ZnPc) or pentacene covered Ag(111) and Au(111) surfaces. This low-density, quasi-one-dimensional organization contrasts starkly with the close-packed hexagonal phases observed for C60 layers on bare metal substrates. STM was employed to perform a detailed investigation of these chain structures for C60/ZnPc/Ag(111) heterolayers. Motivated by the similarity of these chain phases, and the chain and stripe organization occurring in dipole-fluid systems, we investigated a model based on competing van der Waals attractions and electrostatic repulsions between C60 molecules as an explanation for the driving force behind these monolayer phases. Density functional theory (DFT) calculations revealed significant charge transfer to C60 from the Ag(111) substrate, through the intervening ZnPc layer, inducing electrostatic interactions between C60 molecules. Molecular dynamics simulations performed with attractive van der Waals interactions plus repulsive dipole-dipole interactions reproduced the C60 chain phases with dipole magnitudes consistent with DFT calculations.

  17. C60 chain phases on ZnPc/Ag(111) surfaces: Supramolecular organization driven by competing interactions.

    PubMed

    Jin, W; Liu, Q; Dougherty, D B; Cullen, W G; Reutt-Robey, J E; Weeks, J; Robey, S W

    2015-03-14

    Serpentine chain C60 phases were observed in scanning tunneling microscopy (STM) images of C60 layers on zinc phthalocyanine (ZnPc) or pentacene covered Ag(111) and Au(111) surfaces. This low-density, quasi-one-dimensional organization contrasts starkly with the close-packed hexagonal phases observed for C60 layers on bare metal substrates. STM was employed to perform a detailed investigation of these chain structures for C60/ZnPc/Ag(111) heterolayers. Motivated by the similarity of these chain phases, and the chain and stripe organization occurring in dipole-fluid systems, we investigated a model based on competing van der Waals attractions and electrostatic repulsions between C60 molecules as an explanation for the driving force behind these monolayer phases. Density functional theory (DFT) calculations revealed significant charge transfer to C60 from the Ag(111) substrate, through the intervening ZnPc layer, inducing electrostatic interactions between C60 molecules. Molecular dynamics simulations performed with attractive van der Waals interactions plus repulsive dipole-dipole interactions reproduced the C60 chain phases with dipole magnitudes consistent with DFT calculations. PMID:25770499

  18. Optical activity enhanced by strong inter-molecular coupling in planar chiral metamaterials.

    PubMed

    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

  19. Kinetic characterization of intramolecular and intermolecular hammerhead RNAs with stem II deletions.

    PubMed Central

    Long, D M; Uhlenbeck, O C

    1994-01-01

    A method is described to obtain intramolecular cleavage rates for the hammerhead ribozyme during in vitro transcription. By avoiding RNA purification and renaturation, the potential for formation of inactive conformations of the RNA is minimized. By showing that an intramolecular hammerhead and a closely related intermolecular hammerhead cleave at the same rate under a given set of conditions, we confirm that both reactions probably have the same rate-limiting step. An in vitro selection strategy was used to isolate active hammerheads from a library of molecules where six randomized nucleotides replaced stem-loop II. The sequence and number of nucleotides which replace stem-loop II have large effects on hammerhead cleavage activity. The relative activities of three sequences selected from the intramolecular library are the same when the sequences are transferred into an intermolecular hammerhead background. PMID:7518924

  20. 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

  1. Transferable intermolecular potential functions. Application to liquid methanol including internal rotation

    Microsoft Academic Search

    Jorgensen

    1981-01-01

    Two transferable intermolecular potential functions for the methanol dimer have been used in Monte Carlo statistical mechanics simulations of liquid methanol at 25°C. One function employs the three-site TIP model for a monomer, while the other retains the methyl hydrogens explicitly in a six-site model. The sampling with the latter potential included the internal rotation for the first time in

  2. Determination of the intermolecular potential energy surface for (HCl)2 from vibration–rotation–tunneling spectra

    Microsoft Academic Search

    M. J. Elrod; R. J. Saykally

    1995-01-01

    An accurate and detailed semiempirical intermolecular potential energy surface for (HCl)2 has been determined by a direct nonlinear least-squares fit to 33 microwave, far-infrared and near-infrared spectroscopic quantities using the analytical potential model of Bunker etal. [J. Mol. Spectrosc. 146, 200 (1991)] and a rigorous four-dimensional dynamical method (described in the accompanying paper). The global minimum (De=?692 cm?1) is located

  3. Vibrational Analysis and Intermolecular Hydrogen Bonding of Azodicarbonamide in the Pentamer Cluster

    Microsoft Academic Search

    Choongkeun Lee; Sun-Kyung Park; Kyung-Chul Min; Yunsoo Kim; Nam-Soo Lee

    Pentamer cluster of azodicarbonamide (ADA) based on the crystalline structure was investigated for the equilibrium structure, the stabilization energies, and the vibrational properties at various levels of the density functional theory. Stretching force constants of N…H or O…H, and angle-bending force constants of N-H…N or N-H…O for intermolecular hydrogen bonds in the pentamer cluster were obtained in 0.2-0.5 mdyn\\/Å and

  4. Chain-length-dependent intermolecular packing in polyphenylenes: a high pressure study

    Microsoft Academic Search

    G. Heimel; P. Puschnig; M. Oehzelt; K. Hummer; B. Koppelhuber-Bitschnau; F. Porsch; C. Ambrosch-Draxl; R. Resel

    2003-01-01

    We report on pressure-induced structural changes in crystalline oligo(para-phenylenes) containing two to six phenyl rings. The results are discussed with particular emphasis put on the implications these changes in intermolecular distances and molecular arrangement have on important bulk properties of this class of materials, such as optical response and charge transport. We performed energy dispersive x-ray diffraction in a systematic

  5. Estimation of Some Parameters from Morse-Morse-Spline-Van Der Waals Intermolecular Potential

    SciTech Connect

    Coroiu, I. [Technical University, Physics Department, C. Daicoviciu St., Nr. 15, 400084, Cluj-Napoca 3400 (Romania)

    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.

  6. Intermolecular recombination assay for mammalian cells that produces recombinants carrying both homologous and nonhomologous junctions.

    PubMed Central

    Brouillette, S; Chartrand, P

    1987-01-01

    We present an intermolecular recombination assay for mammalian cells that does not involve the reconstitution of a selectable marker. It is based on the generation of a shuttle vector by recombination between a bacterial and a mammalian vector. The recombinants can thus be amplified in mammalian cells, isolated by plasmid rescue in an Escherichia coli RecA- host, and identified by in situ hybridization, by using mammalian vector sequences as probes. Since both parental molecules can share defined lengths of homology, this assay permits a direct comparison between homologous and nonhomologous intermolecular recombination. Our results indicate that the dominant intermolecular recombination mechanism is a nonhomologous one. The relative frequency of homologous to nonhomologous recombination was influenced by the length of shared homology between parental molecules and the replicative state of the parental molecules, but not by the introduction of double-strand breaks per se. Finally, almost all of the recombinants with a homologous junction did not have the reciprocal homologous junction but instead had a nonhomologous one. We propose a model to account for the generation of these recombinants. PMID:3037354

  7. The intermolecular hydrogen-hydrogen structure of chain-molecule liquids from neutron diffraction

    NASA Astrophysics Data System (ADS)

    Londono, J. D.; Annis, B. K.; Turner, J. Z.; Soper, A. K.

    1994-11-01

    Neutron diffraction isotopic substitution experiments on liquid n-decane (C10H22) and n-eicosane (C20H42) are described. The intermolecular H-H structure function hHH(Q) and the intermolecular H-H correlation function ginterHH(r) are obtained without recourse to models of the intramolecular structure. The structure of the ginterHH(r) found at 2.5, 5.0, and 7.0 Å corresponds to different shells in the H-H pair correlation function. In addition, ginterHH(r)<1 for a considerable range, due to the screening of intermolecular correlations by intramolecular correlations. This ``correlation hole'' effect is accentuated by extrapolation of the structure functions to the expected infinite wavelength limit, and shows good agreement with values determined from small-angle neutron scattering (SANS) data. All of these features are in good agreement with the results of molecular dynamics simulations for the closely related system C13H28.

  8. Dzyaloshinskii-Moriya interactions and adiabatic magnetization dynamics in molecular magnets H. De Raedt,1,

    E-print Network

    and quantum (de)coherence.1­22 As a result of the very weak intermolecular interactions, experi- ments can-reversal symmetry en- forces at least a twofold degeneracy of the energy levels at zero field. The possibility

  9. Ferroelastic and ferroelectric phase transition in a molecular crystal : tanane From ab initio computation of the intermolecular forces

    E-print Network

    Boyer, Edmond

    ab initio computation of the intermolecular forces to statistical mechanics of the transition J. F, the Van der Waals inter- molecular forces are computed for the 16 nearest neighbours of a given molecule

  10. Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces.

    PubMed Central

    Rau, D C; Parsegian, V A

    1992-01-01

    Rather than acting by modifying van der Waals or electrostatic double layer interactions or by directly bridging neighboring molecules, polyvalent ligands bound to DNA double helices appear to act by reconfiguring the water between macromolecular surfaces to create attractive long range hydration forces. We have reached this conclusion by directly measuring the repulsive forces between parallel B-form DNA double helices pushed together from the separations at which they have self organized into hexagonal arrays of parallel rods. For all of the wide variety of "condensing agents" from divalent Mn to polymeric protamines, the resulting intermolecular force varies exponentially with a decay rate of 1.4-1.5 A, exactly one-half that seen previously for hydration repulsion. Such behavior qualitatively contradicts the predictions of all electrostatic double layer and van der Waals force potentials previously suggested. It fits remarkably well with the idea, developed and tested here, that multivalent counterion adsorption reorganizes the water at discrete sites complementary to unadsorbed sites on the apposing surface. The measured strength and range of these attractive forces together with their apparent specificity suggest the presence of a previously unexpected force in molecular organization. Images FIGURE 1 PMID:1540693

  11. 1H NMR and DFT studies of steric effects on intermolecular C H···O hydrogen bonding in solution

    NASA Astrophysics Data System (ADS)

    Xiang, Shaoji; Yu, Guiqin; Liang, Yongmin; Wu, Longmin

    2006-05-01

    Significant changes in 1H chemical shifts (? ?s) for H a and H b of L-2( S)-(1-imidazolyl)-3( S)-methylpentanol (IMP) from D 2O to CDCl 3 have been observed. H a and H b of IMP experience deshielding effects in D 2O with respect to in CDCl 3. In order to assess the effects on ? ?s, comparisons of 1H chemical shifts ( ?s) with those for 2-(1-imidazolyl) ethanol (IE) and 1-methyl imidazole (MI) as well as density functional theory (DFT) calculations on IMP· nSol hydrogen-bonded models were performed. By analyzing the values for ? ?(IMP-MI) in both solvents and for structural parameters for IMP, it is indicative of that the main contribution to ? ?s is most likely produced by an intermolecular C-H···O hydrogen bonding, which has been denoted as ? ?(C-H···O). The steric effects arising from the C 2H 5CH(CH 3)-CH-CH 2OH group of IMP favor interactions of IMP molecule with D 2O molecules over CDCl 3. Moreover, ? ?(C-H···O) is suggested to be rationalized by two effects: the electronic effects, ? ?e(C-H···O), and the steric effects, ? ?s(C-H···O). Experiments gave ??sIMP( for H a and H b of IMP 0.354 and 0.396 ppm, respectively. ??sIMP( for H a and H b of IMP are calculated to be 0.347 and 0.369 ppm, respectively, using the IMP·3Sol hydrogen-bonded models. The similarity of ??sIMP( to ??sIMP( encourages the use of IMP·3Sol hydrogen-bonded models as appropriate solution models for ? ?s and the cause of ??s attributing to an intermolecular C-H···O hydrogen bond produced by the steric effects of the C 2H 5CH(CH 3)-CH-CH 2OH group.

  12. PROTEIN-CHEMICAL INTERACTION PREDICTION VIA KERNELIZED SPARSE LEARNING SVM

    E-print Network

    Schuurmans, Dale

    but also pointed to an optimal subset of potential binding regions. Supplementary materials are available al. created a protein-chemical interaction database called STITCH,5 which, up to now, contains-covalent intermolecular interactions, such as hydrogen bonding, electrostatic interactions, hydrophobic and Van der

  13. Insights into hydrogen bonding via ice interfaces and isolated water

    NASA Astrophysics Data System (ADS)

    Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

    2014-11-01

    Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling.

  14. Insights into hydrogen bonding via ice interfaces and isolated water.

    PubMed

    Shultz, Mary Jane; Bisson, Patrick; Vu, Tuan Hoang

    2014-11-14

    Water in a confined environment has a combination of fewer available configurations and restricted mobility. Both affect the spectroscopic signature. In this work, the spectroscopic signature of water in confined environments is discussed in the context of competing models for condensed water: (1) as a system of intramolecular coupled molecules or (2) as a network with intermolecular dipole-dipole coupled O-H stretches. Two distinct environments are used: the confined asymmetric environment at the ice surface and the near-isolated environment of water in an infrared transparent matrix. Both the spectroscopy and the environment are described followed by a perspective discussion of implications for the two competing models. Despite being a small molecule, water is relatively complex; perhaps not surprisingly the results support a model that blends inter- and intramolecular coupling. The frequency, and therefore the hydrogen-bond strength, appears to be a function of donor-acceptor interaction and of longer-range dipole-dipole alignment in the hydrogen-bonded network. The O-H dipole direction depends on the local environment and reflects intramolecular O-H stretch coupling. PMID:25399186

  15. Effect of f-f interactions on quantum tunnelling of the magnetization: mono- and dinuclear Dy(III) phthalocyaninato triple-decker single-molecule magnets with the same octacoordination environment.

    PubMed

    Katoh, Keiichi; Asano, Rina; Miura, Akira; Horii, Yoji; Morita, Takaumi; Breedlove, Brian K; Yamashita, Masahiro

    2014-06-01

    The single-molecule magnet (SMM) behaviour of dinuclear Ln(III)-Pc triple-decker complexes (Dy(III)-Y(III): 1 and Dy(III)-Dy(III): 2) with the same octacoordination environment and slow magnetic relaxation behaviour were explained using X-ray crystallography and static and dynamic susceptibility measurements. In particular, interactions among the 4f electrons of dinuclear Dy(III)-Pc triple-decker type SMMs have never been discussed on the basis of the same octacoordination environment. Our results clearly show that the Dy(III) ion sites of 1 and 2 are equivalent, consistent with the crystal structure. 2 Exhibited ferromagnetic interaction between Dy(III) ions. This is clear evidence that the magnetic relaxation mechanism depends heavily on the dipole-dipole (f-f) interactions between the Dy(III) ions in the dinuclear systems. For both 1 and 2, quantum tunnelling of the magnetization (QTM) was observed. However, the magnetic relaxation time (?) for 2 was one order of magnitude greater than that for 1, and single-component magnetic relaxation behaviour was explained. In other words, it is possible to use f-f interactions to increase ? by one order of magnitude. PMID:24604114

  16. Equalization of the inverted repeat sequences of the pseudorabies virus genome by intermolecular recombination.

    PubMed

    Ben-Porat, T; Deatly, A; Veach, R A; Blankenship, M L

    1984-01-30

    During a study designed to identify changes in the genomes that are observed in mutant populations of pseudorabies virions, a thymidine kinase-defective population of virions which contains genomes that possess inverted repeated sequences of unequal sizes has been identified. This population of virions has been used to ascertain the mechanism and rates of equalization of the repeats. Results showed that when the virions were passed in cell cultures at high multiplicities of infection (either once or several times), one-half of the molecules had repeats of equal size and one-half had repeats of unequal size. This result is to be expected if conditions allowing a high degree of intermolecular recombination involving exchange of repeats exist. The process of intermolecular exchange of inverted repeats is rapid and the DNA molecules were at equilibrium by the time a virion had produced a small plaque. If the virions were passed in cell culture at low multiplicities of infection, they acquired genomes with equal-size repeats. This is probably due to segregation of the virions which had acquired genomes with equal repeats by recombination; in the absence of coinfection of the cells with virions containing genomes with different repeat sizes, heterogeneity of the repeats could not be generated. The fact that virions containing genomes with equal repeats are usually isolated from nature can thus be attributed to equalization of the repeats which results from intermolecular recombination, followed by segregation. A special mechanism ensuring equalization of repeats, such as one repeat acting as a template for the synthesis (or repair) of the other, need therefore not be invoked. PMID:6322414

  17. Joint Experimental and Computational Investigation of the Structural and Spectroscopic Properties of Poly(vinylidene fluoride) Polymorphs.

    PubMed

    Milani, Alberto; Castiglioni, Chiara; Radice, Stefano

    2015-04-01

    State-of-the-art density functional theory calculations are here adopted for the investigation of the crystal structure and of the vibrational properties of ?, ?, ?, and ? phases of poly(vinylidene fluoride) (PVDF), in comparison with IR and Raman measurements. DFT calculations allowed a detailed interpretation of the IR and Raman spectra of ? and ? phases, giving vibrational assignments useful for qualitative and quantitative characterization of these systems. From a molecular perspective, the computational investigation of the crystal structure and the spectra of PVDF polymorphs helped in clarifying the role of supramolecular dipole-dipole interactions, which indeed modulate the vibrational properties of these systems, indicating also that intermolecular interaction could play a significant role in the modulation of ferroelectric properties. Furthermore, the combined experimental and computational approach allowed us to identify and characterize the thermally and mechanically induced ? phase, shedding light on the far-IR marker bands of this elusive phase of PVDF. PMID:25775384

  18. Spectral lineshapes of collision-induced absorption (CIA) and collision-induced light scattering (CILS) for molecular nitrogen using isotropic intermolecular potential. New insights and perspectives

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Mostafa, S. I.; Bancewicz, T.; Maroulis, G.

    2014-08-01

    The rototranslational collision-induced absorption (CIA) at different temperatures and collision-induced light scattering (CILS) at room temperature of nitrogen gas are analyzed in terms of new isotropic intermolecular potential, multipole-induced dipole functions and interaction-induced pair polarizability models, using quantum spectral lineshape computations. The irreducible spherical form for the induced operator of light scattering mechanisms was determined. The high frequency wings are discussed in terms of the collision-induced rotational Rayleigh effect and estimates for the dipole-octopole polarizability E4, is obtained and checked with the ab initio theoretical value. The quality of the present potential has been checked by comparing between calculated and experimental thermo-physical and transport properties over a wide temperature range, which are found to be in good agreement.

  19. Iridium-Catalyzed Intermolecular Dehydrogenative Silylation of Polycyclic Aromatic Compounds without Directing Groups.

    PubMed

    Murai, Masahito; Takami, Keishi; Takai, Kazuhiko

    2015-03-16

    This study describes the iridium-catalyzed intermolecular dehydrogenative silylation of C(sp(2) )?H bonds of polycyclic aromatic compounds without directing groups. The reaction produced various arylsilanes through both Si?H and C?H bond activation, with hydrogen as the sole byproduct. Reactivity was affected by the electronic nature of the aromatic compounds, and silylation of electron-deficient and polycyclic aromatic compounds proceeded efficiently. Site-selectivity was controlled predominantly by steric factors. Therefore, the current functionalization proceeded with opposite chemo- and site-selectivity compared to that observed for general electrophilic functionalization of aromatic compounds. PMID:25677898

  20. Solvent and nuclear dynamics in ultrafast intermolecular electron transfer in a diffusionless, weakly polar system

    NASA Astrophysics Data System (ADS)

    Yartsev, Arkadiy; Nagasawa, Yutaka; Douhal, Abderrazzak; Yoshihara, Keitaro

    1993-05-01

    Femtosecond intermolecular electron (ET) transfer dynamics were studied by time-resolved fluorescence up-conversion technique in contact systems of oxazine dyes in electron-donating solvents. Clearly non-exponential ET time dependence was observed in aniline and explained by the effects of both solvent reorientation and nuclear motion of the reactants. Single exponential processes were measured for nile blue (?160 fs) and oxazine 1 (?280 fs) in N,N-dimethylaniline. The rate of ET is explained to be limited only by ultrafast nuclear relaxation.

  1. Density functional theory calculations on dipeptide gallic acid interaction

    NASA Astrophysics Data System (ADS)

    Madhan, B.; Parthasarathi, R.; Subramanian, V.; Raghava Rao, J.; Nair, Balachandran Unni; Ramasami, T.

    2003-02-01

    In the present investigation, an attempt has been made to study the interaction of dipeptides with gallic acid, using Becke3 parameter Lee Yang Parr (B3LYP) method employing 3-21G*, 6-31G* and 6-31+G* basis sets. The interaction energies of the dipeptide-gallic acid complexes are in the range of -5 to -18 kcal/mol depending on the mode of intermolecular complexation. Calculated molecular electrostatic potential (MESP) for the various intermolecular complexes revealed the electrostatic nature of the interaction. Qualitative estimations based on chemical hardness and chemical potential demonstrated fractional electron transfer from dipeptide to gallic acid.

  2. The dynamics of entanglement in two-atom Tavis-Cummings model with non-degenerate two-photon transitions for four-qubits initial atom-field entangled states

    NASA Astrophysics Data System (ADS)

    Bashkirov, E. K.; Mastyugin, M. S.

    2014-02-01

    The influence of dipole-dipole interaction on the entanglement between two ?-type artificial atoms interacting with two-mode field via non-degenerate two-photon transitions has been investigated. The atom-field system is assumed to be prepared in four-partite atom-field entangled state. The results show that the entanglement between two atoms can be increased by means of dipole-dipole interaction and for some initial states the entanglement sudden death effect can be weakened.

  3. Interaction potential for aluminum nitride: A molecular dynamics study of mechanical and thermal properties of crystalline and amorphous aluminum nitride

    NASA Astrophysics Data System (ADS)

    Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, José Pedro; CollaboratoryAdvanced Computing; Simulations

    2011-02-01

    An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole-dipole (van der Waals) interactions. The covalent characters of the Al-N-Al and N-Al-N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger-Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants (C11, C12, C13, C33, C44, and C66), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.

  4. Hydration and distance dependence of intermolecular shearing between collagen molecules in a model microfibril.

    PubMed

    Gautieri, Alfonso; Pate, Monica I; Vesentini, Simone; Redaelli, Alberto; Buehler, Markus J

    2012-08-01

    In vertebrates, collagen tissues are the main component responsible for force transmission. In spite of the physiological importance of these phenomena, force transmission mechanisms are still not fully understood, especially at smaller scales, including in particular collagen molecules and fibrils. Here we investigate the mechanism of molecular sliding between collagen molecules within a fibril, by shearing a central molecule in a hexagonally packed bundle mimicking the collagen microfibril environment, using varied lateral distance between the molecules in both dry and solvated conditions. In vacuum, the central molecule slides under a stick-slip mechanism that is due to the characteristic surface profile of collagen molecules, enhanced by the breaking and reformation of H-bonds between neighboring collagen molecules. This mechanism is consistently observed for varied lateral separations between molecules. The high shearing force (>7 nN) found for the experimentally observed intermolecular distance (?1.1 nm) suggests that in dry samples the fibril elongation mechanism relies almost exclusively on molecular stretching, which may explain the higher stiffnesses found in dry fibrils. When hydrated, the slip-stick behavior is observed only below 1.3 nm of lateral distance, whereas above 1.3 nm the molecule shears smoothly, showing that the water layer has a strong lubricating effect. Moreover, the average force required to shear is approximately the same in solvated as in dry conditions (?2.5 nN), which suggests that the role of water at the intermolecular level includes the transfer of load between molecules. PMID:22762892

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

    PubMed Central

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

    2014-01-01

    Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase Lpro (Labpro and Lbpro). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4G. During infection, Lbpro removes six residues from its own C-terminus, generating sLbpro. We present the structure of sLbpro bound to the inhibitor E64-R-P-NH2, illustrating how sLbpro can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lbpro was unaffected by P1 or P1? substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLbpro failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lbpro binding site restored cleavage. These data imply that Lbpro and sLbpro may have different functions in infected cells. PMID:25240326

  6. Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics

    NASA Astrophysics Data System (ADS)

    Casey, Ryan E.; Pittman, Faith A.

    2005-02-01

    Environmental education for undergraduate nonscience majors and high school students is key in fostering an increased understanding of environmental issues among the general public. We have developed an environmental chemistry module that can be used in high schools or undergraduate nonscience courses to relate chemical structures and properties to the macroscopic behavior of environmentally relevant organic chemicals like pesticides, PCBs, and solvents. The module introduces the concepts of intermolecular forces, polarity, and partitioning to explain complex phenomena such as environmental transport and biomagnification of xenobiotics (human-made chemicals). The level 1 version 2.11 model, developed by Trent University, is used in a laboratory segment that allows students to explore the relationship between chemical properties and environmental distribution. The initial material on polarity and intermolecular forces can lead to additional applications, including: bioaccumulation and biomagnification of organic chemicals; toxicology or pharmacology (ability of molecules to cross membranes); and groundwater contamination. This module can enhance chemistry courses by presenting detailed applications and allowing students to make powerful, verifiable predictions. See Featured Molecules .

  7. 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. (Case Western); (Cleveland Clinic)

    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.

  8. Kinetic Demonstration of Intermolecular General Acid (GA) Catalysis in Thiolysis of 9-Anilinoacridine

    NASA Astrophysics Data System (ADS)

    Niyaz Khan, Mohammad

    1998-05-01

    All acids other than hydronium ion (known as specific acid) are called general acids (GA) and all bases other than hydroxide ion (known as specific base) are defined as general bases (GB). If a reaction is sensitive to acid catalysis, it may involve both specific acid and GA catalysis. It is now generally believed that most enzyme-catalyzed reactions involve the occurrence of intramolecular and intermolecular general acid-base (GA-GB) catalysis (1). Since this fact was realized a huge amount of work has been carried out using simpler nonenzymatic reactions with the purpose of developing an understanding of the mechanistic aspects of such catalysis (2). After nearly five decades of active research and numerous publications on GA-GB catalysis, introduction of an experiment on GA for students majoring in enzymology/physical organic chemistry at advanced undergraduate/postgraduate level is appropriate. A kinetic experiment involving the reaction of 2-mercaptoethanol (2-ME) with 9-anilinoacridine (9-ANA) is designed to demonstrate intermolecular GA catalysis.

  9. Theoretical studies of molecular interactions

    SciTech Connect

    Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  10. Effects of low symmetry and spin-spin interaction in the centrosymmetric dimer [Cu(PU)5(ClO4)2]2 with out-of-plane bond

    NASA Astrophysics Data System (ADS)

    Voronkova, V. K.; Mosina, L. V.; Yablokov, Yu. V.; Ková?ik, I.; Langfelderová, H.; Kožišek, J.

    Electron paramagnetic resonance (EPR) of single-crystal [Cu(PU)5(ClO4)2]2, built of dimeric fragments with P symmetry, Z = 1, and ClO4 anions, was studied over a range of temperatures at both X and Q band frequencies. EPR spectra show the presence of exchange interaction J(S1 · S2) (J < 0) between two identical Cu2+ ions (S1 = S2 = 1/2) in the dimeric fragment. The single-crystal spectra recorded in three different planes were analysed by diagonalization of the full Hamiltonian matrix. The values of g and D were found to have coincident y axes, with the x and z axes rotated by 45°. The tensor of the dipole-dipole interaction was calculated. Two variants for the anisotropic exchange interaction tensor were determined. The data obtained from the analysis of the single-crystal spectra were used to simulate the polycrystalline spectrum. The peculiarities of the polycrystalline spectra for centres S = 1 with nonparallel g and D tensors and the possibilities of their unambiguous interpretation are discussed. The double-quantum transition in single-crystal and polycrystalline spectra was detected.

  11. Enhancing intermolecular benzoyl-transfer reactivity in crystals by growing a "reactive" metastable polymorph by using a chiral additive.

    PubMed

    Murali, Chebrolu; Shashidhar, Mysore S; Gonnade, Rajesh G; Bhadbhade, Mohan M

    2009-01-01

    Racemic 2,4-di-O-benzoyl-myo-inositol-1,3,5-orthoacetate, which normally crystallizes in a monoclinic form (form I, space group P2(1)/n) could be persuaded to crystallize out as a metastable polymorph (form II, space group C2/c) by using a small amount of either D- or L- 2,4-di-O-benzoyl-myo-inositol-1,3,5-orthoformate as an additive in the crystallization medium. The structurally similar enantiomeric additive was chosen by the scrutiny of previous experimental results on the crystallization of racemic 2,4-di-O-benzoyl-myo-inositol-1,3,5-orthoacetate. Form II crystals can be thermally transformed to form I crystals at about 145 degrees C. The relative organization of the molecules in these dimorphs vary slightly in terms of the helical assembly of molecules, that is, electrophile (El)...nucleophile (Nu) and C-H...pi interactions, but these minor variations have a profound effect on the facility and specificity of benzoyl-group-transfer reactivity in the two crystal forms. While form II crystals undergo a clean intermolecular benzoyl-group-transfer reaction, form I crystals are less reactive and undergo non-specific benzoyl-group transfer leading to a mixture of products. The role played by the additive in fine-tuning small changes that are required in the molecular packing opens up the possibility of creating new polymorphs that show varied physical and chemical properties. Crystals of D-2,6-di-O-benzoyl-myo-inositol-1,3,5-orthoformate (additive) did not show facile benzoyl-group-transfer reactivity (in contrast to the corresponding racemic compound) due to the lack of proper juxtaposition and assembly of molecules. PMID:19035584

  12. Thrombin receptor activation. Confirmation of the intramolecular tethered liganding hypothesis and discovery of an alternative intermolecular liganding mode.

    PubMed

    Chen, J; Ishii, M; Wang, L; Ishii, K; Coughlin, S R

    1994-06-10

    Cleavage of the thrombin receptor's amino-terminal exodomain at the Arg41/Ser42 peptide bond within the sequence ... LDPR41/S42FLLRN ... is necessary and sufficient for receptor activation by proteases. The synthetic peptide SFLLRN activates the receptor independent of proteolysis. We proposed that the SFLLRN sequence is a tethered peptide ligand; receptor cleavage unmasks this agonist which then binds intramolecularly to effect receptor activation. The alternative hypothesis that receptor cleavage or exogenous SFLLRN effect receptor activation by disrupting tonic inhibitory interactions exerted by the receptor's amino-terminal exodomain has not been excluded. We report that delta AMINO, a mutant thrombin receptor lacking the amino-terminal exodomain, was not constitutively active and responded to SFLLRN but not thrombin when expressed in Xenopus oocytes or mammalian cells. Thrombin signaling was restored when delta AMINO was co-expressed with ATE-CD8 which encoded the receptor's amino-terminal exodomain fused to the transmembrane domain of CD8. Co-expression of a thrombin receptor lacking a functional tethered ligand domain ("F43A") with a non-signaling receptor mutant bearing an intact tethered ligand domain ("YYY") also reconstituted thrombin signaling. However, the EC50 for thrombin activation of cells co-expressing F43A and YYY was > 1000-fold that for cells expressing comparable levels of wild type receptor, while EC50s for activation by SFLLRN were similar. These and other data refute the release from inhibition hypothesis and suggest that while intermolecular liganding between two thrombin receptor molecules can occur, the intramolecular tethered liganding mechanism is the predominant mode of thrombin receptor activation. PMID:8206902

  13. Optoelectronic method for analysis of biomolecular interaction dynamics

    NASA Astrophysics Data System (ADS)

    Nepomnyashchaya, E.; Velichko, E.; Aksenov, E.; Bogomaz, T.

    2014-10-01

    Optoelectronic method of laser correlation spectroscopy for study of intermolecular interaction in biomolecular suspension is presented. The method of laser correlation spectroscopy is integrated with orthogonal laser light scattering and ultramicroscopy technique for visual control of biomolecular interactions. The capabilities of the method for analysis of biomolecular conglomerates dynamics are considered.

  14. The dynamics of entanglement in two-atom Tavis-Cummings model with non-degenerate two-photon transitions for tripartite entangled W-like states

    E-print Network

    E. K. Bashkirov; M. S. Mastyugin

    2012-10-13

    The influence of dipole-dipole interaction on the entanglement between two atoms with different initial entangled W-like states in Tavis-Cummings model with degenerate two-photon transitions has been investigated. The results show that the entanglement between two atoms can be increased by means of dipole-dipole interaction and for some initial states the entanglement sudden death effect can be weakened.

  15. Structures of CH 3F⋯CH 3F and CH 3F⋯H 2O complexes in a supersonic jet studied by matrix-isolation infrared spectroscopy and density-functional-theory calculation

    NASA Astrophysics Data System (ADS)

    Futami, Yoshisuke; Kudoh, Satoshi; Takayanagi, Masao; Nakata, Munetaka

    2002-05-01

    The CH 3F⋯CH 3F and CH 3F⋯H 2O complexes produced by supersonic-jet expansion have been deposited on a cold plate using a standard matrix-isolation technique. By comparing the infrared spectra measured with an FTIR spectrophotometer with the results of DFT calculations, the structure of CH 3F⋯CH 3F is estimated to be anti-parallel, while that of CH 3F⋯H 2O has a bent C-F⋯H-O intermolecular hydrogen bonding. The difference in the structure of CH 3F dimer from that of CH 3I dimer is explained in terms of the dipole-dipole interaction of two methyl halide molecules and the dispersion force of halogen atoms.

  16. Non-linear QCD dynamics in two-photon interactions at high energies

    SciTech Connect

    Carvalho, F. [Depto de Ciencias Exatas e da Terra, Universidade Federal de Sao Paulo Rua Arthur Riedel 275, Jd. Eldorado, Cep 09972-270, Diadema, SP (Brazil); Navarra, F. S.; Cazaroto, E. [Instituto de Fisica, Universidade de Sao Paulo, Rua do Matao, Travessa R, 187, 05508-090 Sao Paulo, SP (Brazil); Goncalves, V. P. [Instituto de Fisica e Matematica, Universidade Federal de Pelotas Caixa Postal 354, 96010-900, Pelotas, RS (Brazil)

    2013-03-25

    Assuming that the dipole - dipole cross section can be related with the dipole - proton cross section, we calculate the total {gamma}{gamma}, {gamma}*{gamma}* cross-sections and the real photon structure function F{sup {gamma}}{sub 2}(x,Q{sup 2}) using the recent solution of the BK equation with running coupling constant.

  17. Isotropic and anisotropic spin-spin interactions and a quantum phase transition in a dinuclear Cu(II) compound

    NASA Astrophysics Data System (ADS)

    Napolitano, Lia M. B.; Nascimento, Otaciro R.; Cabaleiro, Santiago; Castro, Jesús; Calvo, Rafael

    2008-06-01

    We report electron-paramagnetic resonance (EPR) studies at ˜9.5GHz ( X band) and ˜34GHz ( Q band) of powder and single-crystal samples of the compound Cu2[TzTs]4 [ N -thiazol-2-yl-toluenesulfonamidatecopper(II)], C40H36Cu2N8O8S8 , having copper(II) ions in dinuclear units. Our data allow determining an antiferromagnetic interaction J0=(-113±1)cm-1 (Hex=-J0S1?S2) between Cu(II) ions in the dinuclear unit and the anisotropic contributions to the spin-spin coupling matrix D(Hani=S1?D?S2) , a traceless symmetric matrix with principal values D/4=(0.198±0.003)cm-1 and E/4=(0.001±0.003)cm-1 arising from magnetic dipole-dipole and anisotropic exchange couplings within the units. In addition, the single-crystal EPR measurements allow detecting and estimating very weak exchange couplings between neighbor dinuclear units, with an estimated magnitude |J'|=(0.060±0.015)cm-1 . The interactions between a dinuclear unit and the “environment” of similar units in the structure of the compound produce a spin dynamics that averages out the intradinuclear dipolar interactions. This coupling with the environment leads to decoherence, a quantum phase transition that collapses the dipolar interaction when the isotropic exchange coupling with neighbor dinuclear units equals the magnitude of the intradinuclear dipolar coupling. Our EPR experiments provide a new procedure to follow the classical exchange-narrowing process as a shift and collapse of the line structure (not only as a change of the resonance width), which is described with general (but otherwise simple) theories of magnetic resonance. Using complementary procedures, our EPR measurements in powder and single-crystal samples allow measuring simultaneously three types of interactions differing by more than three orders of magnitude (between 113cm-1 and 0.060cm-1 ).

  18. Competing intramolecular NH⋯OC hydrogen bonds and extended intermolecular network in 1-(4-chlorobenzoyl)-3-(2-methyl-4-oxopentan-2-yl) thiourea analyzed by experimental and theoretical methods

    NASA Astrophysics Data System (ADS)

    Saeed, Aamer; Khurshid, Asma; Jasinski, Jerry P.; Pozzi, C. Gustavo; Fantoni, Adolfo C.; Erben, Mauricio F.

    2014-03-01

    The synthesis of a novel 1-acyl-thiourea species (C14H17N2O2SCl), has been tailored in such a way that two distinct NH⋯OC intramolecular competing hydrogen bonds are feasible. The X-ray structure analysis as well as the vibrational (FT-IR and FT-Raman) data reveal that the S conformation is preferred, with the CO and CS bonds of the acyl-thiourea group pointing in opposite directions. The preference for the intramolecular NH⋯OC hydrogen bond within the C(O)NHC(S)NH core is confirmed. The Natural Bond Orbital and the Atom in Molecule approaches demonstrate that a strong hyperconjugative lpO ? ??(NH) remote interaction between the acyl and the thioamide NH groups is responsible for the stabilization of the S conformation. Intermolecular interactions have been characterized in the periodic system electron density and the topological analysis reveals the presence of an extended intermolecular network in the crystal, including a Cl⋯N interaction playing a relevant role in crystal packing.

  19. Influence of intermolecular hydrogen bonds on the luminescence properties of {alpha}-substituted cinnamonitriles

    SciTech Connect

    Mikhlina, Ya. A.; Bolotin, B. M., E-mail: bolotin70@yandex.ru [State Research Institute of Chemical Reagents and Especially Pure Chemical Substances (Russian Federation); Uzhinov, B. M., E-mail: uzhinov@light.chem.msu.ru; Volchkov, V. V. [Moscow State University, Faculty of Chemistry (Russian Federation)] [Moscow State University, Faculty of Chemistry (Russian Federation); Kuz'mina, L. G., E-mail: kuzmina@igic.ras.ru [Russian Academy of Sciences, Kurnakov Institute of General and Inorganic Chemistry (Russian Federation)

    2013-03-15

    In view of the dramatic difference in the spectral-luminescence properties of {alpha}-(p-chlorobenzoyl)-4-diethylaminocinnamonitrile and {alpha}-ethoxycarbonyl-4-diethylaminocinnamonitrile in solutions and in the crystalline state, X-ray diffraction analysis has been applied to study crystals of these compounds. The intermolecular C-H...N and C-H...O hydrogen bonds are found to contribute to the quinoidization of molecules, which leads to a bathochromic shift in the absorption and fluorescence spectra. A spectral-luminescence study of the aforementioned compounds has revealed that the solvent temperature and polarity affect the position of absorption and luminescence peaks: a decrease in these parameters causes a hypsochromic shift.

  20. Intermolecular single-quantum coherence sequences for high-resolution NMR spectra in inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Huang, Yuqing; Cai, Shuhui; Chen, Xi; Chen, Zhong

    2010-03-01

    A new pulse sequence based on intermolecular single-quantum coherences (iSQCs) is proposed to obtain high-resolution NMR spectroscopy in inhomogeneous magnetic fields via fast 2D acquisition. Taking the intrinsic properties of iSQCs, the sequence is time-efficient with a narrow spectral width in the indirect dimension. It can recover useful information of chemical shifts, relative peak areas, J coupling constants, and multiplet patterns even when the field inhomogeneity is severe enough to erase almost all spectroscopic information. Moreover, good solvent suppression efficiency can be achieved by this sequence even with imperfect radio-frequency pulse flip angles. Spatially localized iSQC spectroscopy was performed on a sample packed with pig brain tissue and cucumber to show the feasibility of the sequence in in vivo magnetic resonance spectroscopy (MRS). This sequence may provide a promising way for the applications on in vivo and in situ high-resolution NMR spectroscopy.

  1. A study of palladium catalyzed intra/intermolecular cascade cross coupling/cyclizations involving bicyclopropylidene.

    PubMed

    Demircan, Aydin

    2014-01-01

    The compounds [3-(2-Bromocyclohex-2-enyloxy)prop-1-ynyl]-tert-butyl-dimethylsilane 3, [4-(2-bromocyclohex-2-en-1-yloxy)but-2-yn-1-yloxy]tert-butyldimethylsilane 5 and dimethyl 2-(2-bromocyclohex-2-enyl)-2-(3-(tert-butyldimethylsilanyl)prop-2-ynyl)malonate 9 were prepared and subjected to palladium-catalyzed intra-intermolecular cascade cross couplings incorporating bicyclopropylidene 10 under two types of conditions. In the presence of Pd(OAc)2, PPh3 and K2CO3 in acetonitrile at 80 °C, the products were indene analogues, cross-conjugated tetraenes 11, 12 and 13, respectively. The corresponding spirocyclopropanated tricycle 16 in dimethylformamide at 110 °C was obtained, albeit in low yield (24%), and observed as an equimolar mixture of diastereomers, whereas 14, 15 were not fully isolated. PMID:24828378

  2. 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 ?- or ?-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 ?- or ?-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp3 carbons is also realized. PMID:25753366

  3. Anthocyanin color behavior and stability during storage: effect of intermolecular copigmentation.

    PubMed

    Eiro, Maarit J; Heinonen, Marina

    2002-12-01

    Intermolecular copigmentation reactions are significantly responsible for the manifold color expression of fruits, berries, and their products. These reactions were investigated with five anthocyanins and five phenolic acids acting as copigments. The stability of the pigment-copigment complexes formed was studied during a storage period of 6 months. The study was conducted using a UV-visible spectrophotometer to monitor the hyperchromic effect and the bathochromic shift of the complexes. The greatest copigmentation reactions took place in malvidin 3-glucoside solutions. The strongest copigments for all anthocyanins were ferulic and rosmarinic acids. The immediate reaction of rosmarinic acid with malvidin 3-glucoside resulted in the biggest bathochromic shift (19 nm) and the strongest hyperchromic effect, increasing the color intensity by 260%. The color induced by rosmarinic acid was not very stable. The color intensity of pelargonidin 3-glucoside increased greatly throughout the storage period with the addition of ferulic and caffeic acids. PMID:12452676

  4. Brief history of intermolecular and intersurface forces in complex fluid systems.

    PubMed

    Israelachvili, Jacob; Ruths, Marina

    2013-08-01

    We review the developments of ideas, concepts, and theories of intermolecular and intersurface forces and how these were influenced (or ignored) by observations of nature and, later, systematic experimentation. The emphasis of this review is on the way things gradually changed: experimentation replaced rhetoric, measurement and quantification replaced hand waving, energy replaced force in calculations, discrete atoms replaced the (continuum) aether, thermodynamics replaced mechanistic models, randomness and probability replaced certainty, and delicate experiments on the subnanoscale revealed fascinating self-assembling structures and complex behavior of even the simplest systems. We conclude by discussing today's unresolved challenges: how complex "dynamic" multicomponent--especially living biological--systems that receive a continuous supply of energy can be far from equilibrium and not even in any steady state. Such systems, never static but evolving in both space and time, are still far from being understood both experimentally and theoretically. PMID:23659277

  5. Cobalt-catalysed site-selective intra- and intermolecular dehydrogenative amination of unactivated sp(3) carbons.

    PubMed

    Wu, Xuesong; Yang, Ke; Zhao, Yan; Sun, Hao; Li, Guigen; Ge, Haibo

    2015-01-01

    Cobalt-catalysed sp(2) 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 sp(3) carbons. Here we report the cobalt-catalysed site-selective dehydrogenative cyclization of aliphatic amides via a C-H bond functionalization process on unactivated sp(3) carbons with the assistance of a bidentate directing group. This method provides a straightforward synthesis of monocyclic and spiro ?- or ?-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 ?- or ?-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp(3) carbons is also realized. PMID:25753366

  6. 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.

  7. Intermolecular, catalytic asymmetric hydroamination of bicyclic alkenes and dienes in high yield and enantioselectivity.

    PubMed

    Zhou, Jianrong Steve; Hartwig, John F

    2008-09-17

    A set of catalytic, intermolecular hydroaminations of strained bicyclic olefins and dienes are reported that occur in both high yield and high enantioselectivity. These reactions occur with a catalyst generated from [Ir(cyclooctene)Cl]2, sterically hindered and electron-rich derivatives of the Segphos and BIPHEP family of ligands, and a soluble base. This system catalyzes the addition of various anilines to norbornene, norbornadiene, and other bicyclic olefins. The products from addition of p-anisidine can be transformed to BOC-protected norbornylamine and to substituted cyclopentanes in nearly enantiopure form. Mechanistic studies show that addition of aniline-d2 occurs in a syn fashion and suggest that the catalytic cycle comprises oxidative addition of aniline to form a bis-anilide hydride complex, followed by migratory insertion of olefin and reductive elimination of product in a series of steps involving iridium complexes containing ancillary bisphosphine and arylamide ligands. PMID:18715004

  8. Correlation of transducin photoaffinity labeling with the specific formation of intermolecular disulfide linkages in its ?-subunit.

    PubMed

    Perdomo, Deisy; Möller, Carolina; Bubis, José

    2015-01-01

    Transducin (T) is a heterotrimer of T?, T?, and T? subunits. In the presence of light-activated rhodopsin, 8-azidoguanosine triphosphate (8-N3GTP) was covalently incorporated into T in a UV-light photodependent manner, with a low stoichiometry of 0.02 mol of 8-N3GTP per mol of T. Although T? was preferentially labeled by 8-N3GTP, T? and T? were also modified. Photolabeling of T was specifically inhibited by GDP and GTP, but not by ?,?-imido-guanosine 5'-triphosphate (GMP-PNP), indicating that 8-N3GTP was modifying the GDP binding site of the holoenzyme. This was consistent with the observation that the photoaffinity probe was completely hydrolyzed to 8-N3GDP by T activated by illuminated rhodopsin. The formation of intermolecular disulfide associations in T was also determined because photolabeling of T was performed under non-reducing conditions. We established that Cys-347 of T? was the major residue involved in the formation of disulfide-linked T oligomers. Other cysteines of T?, such as Cys-321, also participated in the formation of disulfide bonds, revealing a complex pattern of intermolecular disulfide cross-links that led to the polymerization of T. The spontaneous generation of these cystines in T? inhibited the light-dependent GTPase and GMP-PNP binding activities of T. A model was constructed illustrating that when two heterotrimers dimerize through the formation of disulfide bridges between the Cys-347 of their T? subunits, the guanine ring of the 8-N3GDP bound to one T molecule might approach to the T??-complex of the other heterotrimer. This model provides an explanation for the additional photolabeling of T? and T? by 8-N3GTP. PMID:25450251

  9. Intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization reactions of 1,6-enynes with symmetrical and unsymmetrical alkynes†

    PubMed Central

    Andrew Evans, P.; Sawyer, James R.; Lai, Kwong Wah; Huffman, John C.

    2006-01-01

    The crossed intermolecular rhodium-catalyzed [2 + 2 + 2] carbocyclization of carbon and heteroatom tethered 1,6-enynes can be accomplished with symmetrical and unsymmetrical alkynes, to afford the corresponding bicyclohexadienes in an efficient and highly selective manner. PMID:16075089

  10. Intermolecular sequential [4 + 2]-cycloaddition-aromatization reaction of aryl-substituted allenes with DMAD affording phenanthrene and naphthalene derivatives.

    PubMed

    Jiang, Xuefeng; Kong, Wangqing; Chen, Jie; Ma, Shengming

    2008-10-01

    An efficient entry to phenanthrene and naphthalene derivatives through intermolecular sequential [4 + 2]-cycloaddition-aromatization reactions of aryl-substituted allenes with DMAD in the absence of any catalyst was discovered. In this reaction the aromatic ring and the adjacent carbon-carbon double bond of the allene unit acted as the 1,3-diene. PMID:19082163

  11. Infrared absorption spectroscopy of the CO2–Ar complex in the 2376 cm?1 combination band region: The intermolecular bend

    Microsoft Academic Search

    S. W. Sharpe; D. Reifschneider; C. Wittig; R. A. Beaudet

    1991-01-01

    The rovibrational absorption spectrum of CO2–Ar has been recorded in the 2376 cm?1 region by using a pulsed, slit nozzle expansion and tunable IR diode laser. The spectrum is ascribed to the 410510 combination band, where ?4 corresponds to the asymmetric stretch of the CO2 moiety and ?5 is the intermolecular bend. This combination band is ?102 times less intense

  12. Chemistry of the collagen cross-links. Isolation and characterization of two intermediate intermolecular cross-links in collagen

    PubMed Central

    Bailey, A. J.; Peach, Catherine M.; Fowler, L. J.

    1970-01-01

    This paper describes the isolation from reduced collagen of two new amino acids believed to be involved, in their non-reduced form, as intermolecular cross-links stabilizing the collagen fibre. The reduction of intact collagen fibrils with tritiated sodium borohydride was found to stabilize the aldehyde-mediated cross-links to acid hydrolysis and thus allowed their location and isolation from acid hydrolysates on an automatic amino acid analyser. Comparison of the radioactive elution patterns from the autoanalyser of collagen treated in various ways before reduction permitted a preliminary classification of the peaks into cross-link precursors, intramolecular and intermolecular cross-links. The techniques employed to isolate the purified components on a large scale and to identify them structurally are described in detail. Two labile intermolecular cross-links were isolated in their reduced forms, one of which was identified by high-resolution mass spectrometry as N?-(5-amino-5-carboxypentyl)hydroxylysine. The structure of this compound was confirmed by chemical synthesis. The cross-link precursor ?-aminoadipic ?-semialdehyde was isolated in its reduced form, ?-hydroxynorleucine, together with its acid degradation product ?-chloronorleucine. A relatively stable intermolecular cross-link was isolated and partially characterized by mass spectrometry as an aldol resulting from the reaction of the ?-semialdehyde derived from lysine and hydroxylysine. PMID:5451907

  13. Terahertz phonon modes of an intermolecular network of hydrogen bonds in an anhydrous ?- d-glucopyranose crystal

    Microsoft Academic Search

    Shigeki Saito; Talgat M. Inerbaev; Hiroshi Mizuseki; Nobuaki Igarashi; Yoshiyuki Kawazoe

    2006-01-01

    First-principles calculations of single molecular vibrations and the crystalline phonons of an anhydrous ?-d-glucopyranose monosaccharide crystal in the terahertz region were performed using periodic density functional theory (DFT) calculations. The calculated frequencies and eigenvectors of the phonon modes, which agreed with experimental results, did not correspond to those of the modes of a single molecule, mainly due to intermolecular hydrogen

  14. Intermolecular structure in a single component polymer glass: Towards high resolution measurements of the sidechain pair correlation function

    E-print Network

    Fayer, Michael D.

    as a function of tagged polymer concentration in the polymeric solid. The results are compared to experimental- ing of the polymer segments.t4 In this case, the intermolecu- lar segmental pair distribution functionIntermolecular structure in a single component polymer glass: Towards high resolution measurements

  15. Applications and Analogies: Phototherapy and the Treatment of Hyperbilirubinemia: A Demonstration of Intra- versus Intermolecular Hydrogen Bonding.

    ERIC Educational Resources Information Center

    Wilbraham, Antony C.

    1984-01-01

    Background information and procedures are provided for a demonstration of intramolecular versus intermolecular hydrogen bonding. The demonstration is based on structural changes in bilirubin molecules which lead to changes in physical properties. A list of further investigations to try is included. (JN)

  16. A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex.

    PubMed

    Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

    2012-12-14

    We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H(2)O complex with the H(2)O monomer fixed at its experimental averaged structure. Using the supermolecular approach, the intermolecular potential energies were evaluated at the coupled-cluster singles and doubles level with noniterative inclusion of connected triples with the full counterpoise correction for the basis set superposition error and a large basis set including bond functions. The global minimum corresponding to a planar H-bond configuration was located at the intermolecular distance of 3.82 A? with a well depth of 169.98 cm(-1). In addition, two first-order and one second-order saddle points were also identified. The combined radial discrete variable representation?angular finite basis representation method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for 16 isotopic species of the Kr-H(2)O complexes. The rotational transition frequencies, structure parameters, and nuclear quadrupole coupling constants were also determined for the ground and first intermolecular vibrational excited states and are all in good agreement with the available experimental values. PMID:23249010

  17. The Structure of Water in Crystalline Aluminophosphates: Isolated Water and Intermolecular Clusters Probed by Raman Spectroscopy, NMR and Structural Modeling

    E-print Network

    Goddard III, William A.

    The Structure of Water in Crystalline Aluminophosphates: Isolated Water and Intermolecular Clusters are used to elucidate the properties of water in Metavariscite, AlPO4-H3, AlPO4-8 and VPI-5. The framework density of the aluminophosphates decreases along this sequence, the pore size increases, and the water

  18. Magneto-Dielectric Effects Induced by Optically-Generated Intermolecular Charge-Transfer States in Organic Semiconducting Materials

    PubMed Central

    Zang, Huidong; Yan, Liang; Li, Mingxing; He, Lei; Gai, Zheng; Ivanov, Ilia; Wang, Min; Chiang, Long; Urbas, Augustine; Hu, Bin

    2013-01-01

    Traditionally, magneto-dielectric effects have been developed by combining ferroelectric and magnetic materials. Here, we show a magneto-dielectric effect from optically-generated intermolecular charge-transfer states in an organic semiconducting donor:acceptor (PVK:TCNB) system. We observe in magnetic field effects of photoluminescence that a magnetic field can change singlet/triplet population ratio in intermolecular charge-transfer states. Furthermore, our theoretical analysis and experimental evidence indicate that the singlets and triplets in charge-transfer states have stronger and weaker electrical polarizations, respectively. Therefore, the observed magneto-dielectric effect can be attributed to magnetically-dependent singlet/triplet ratio in intermolecular charge-transfer states. In principle, a magneto-dielectric effect can be generated through two different channels based on magneto-polarization and magneto-current effects when the singlet/triplet ratio in intermolecular charge-transfer states is changed by a magnetic field. We find, from the simulation of dielectric effects, that magneto-polarization and magneto-current effects play primary and secondary roles in the generation of magneto-dielectric effect. PMID:24084983

  19. Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Cai-Guang Yang and Chuan He*

    E-print Network

    He, Chuan

    Gold(I)-Catalyzed Intermolecular Addition of Phenols and Carboxylic Acids to Olefins Cai-Guang Yang 60637 Received January 20, 2005; E-mail: chuanhe@uchicago.edu Gold-catalyzed reactions have emerged as important synthetic methods.1 Cationic gold(I) and gold(III) show exceptional activities to activate alkynes

  20. Identification of molecular-adsorption geometries and intermolecular hydrogen-bonding configurations by in situ STM manipulation.

    PubMed

    Xu, Wei; Kong, Huihui; Zhang, Chi; Sun, Qiang; Gersen, Henkjan; Dong, Liang; Tan, Qinggang; Laegsgaard, Erik; Besenbacher, Flemming

    2013-07-15

    Don't be dim! By combining the technique with DFT calculations, STM manipulation was extended to the probing of intermolecular hydrogen-bonding configurations in self-assembled nanostructures. It was also possible to convert one configuration into another in a controlled fashion through the careful manipulation of a particular structural unit (see picture). PMID:23737128

  1. Nano-structured complexes of reserpine and quinidine drugs with chloranilic acid based on intermolecular H-bond: spectral and surface morphology studies.

    PubMed

    Adam, Abdel Majid A

    2014-06-01

    The study of the drug-acceptor interaction may be useful in understanding the drug-receptor interactions and the mechanism of drug action. Here, complexes of reserpine (Res) and quinidine (Qui) drugs with chloranilic acid (CLA) have been synthesized. Then, these complexes were characterized chemically and structurally using CHN elemental analysis, infrared (IR) and electronic absorption spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). The stoichiometry of the H-bonded complex was found to have a 1:1 ratio, so these complexes can be formulated as [(Drug)(CLA)]. IR measurements confirmed the presence of intermolecular H-bond. Application of Debye-Scherrer equation indicates that the formed complexes are in the range of nano-size. The Res complex exhibits a remarkable crystalline morphology. It was also found that the particle size of Res complex is 1.533 time higher than that of Qui complex. Interestingly, free Res molecular weight is higher than that of free Qui by the same ratio (precisely; 1.525). PMID:24632163

  2. Reactivity trends of Fe phthalocyanines confined on graphite electrodes in terms of donor-acceptor intermolecular hardness: Linear versus volcano correlations

    NASA Astrophysics Data System (ADS)

    Linares-Flores, C.; Espinoza-Vergara, J.; Zagal, J. H.; Arratia-Perez, R.

    2014-10-01

    In this work, we have studied the interaction between the hydrazine N2H4 molecule with several FeN4 macrocyclic complexes (FePc's). In order to modulate the electron density located on the metal center using iron-phthalocyanine (FePc) as the reference, we used substituted iron-phthalocyanines with different types of substituents electron-donating groups such as iron-tetraamino-phthalocyanine (4?(NH2)FePc) and iron-octamethoxyphthalocyanine (8?(OCH3)FePc), and with electron-withdrawing groups such as iron-tetranitrophthalocyanine(4?(NO2)FePc) and iron-hexadecachlorophthalocyanine (16(Cl)FePc), respectively. We have found that the energy of interaction between hydrazine and the Fe center in the macrocycle increases as the electron-withdrawing power of the substituents increases. When rate constants instead of currents are compared in a semilog plot versus ??D-A, a linear correlation is found where log k increases as the intermolecular hardness of the systems decreases.

  3. Nano-structured complexes of reserpine and quinidine drugs with chloranilic acid based on intermolecular H-bond: Spectral and surface morphology studies

    NASA Astrophysics Data System (ADS)

    Adam, Abdel Majid A.

    2014-06-01

    The study of the drug-acceptor interaction may be useful in understanding the drug-receptor interactions and the mechanism of drug action. Here, complexes of reserpine (Res) and quinidine (Qui) drugs with chloranilic acid (CLA) have been synthesized. Then, these complexes were characterized chemically and structurally using CHN elemental analysis, infrared (IR) and electronic absorption spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM). The stoichiometry of the H-bonded complex was found to have a 1:1 ratio, so these complexes can be formulated as [(Drug)(CLA)]. IR measurements confirmed the presence of intermolecular H-bond. Application of Debye-Scherrer equation indicates that the formed complexes are in the range of nano-size. The Res complex exhibits a remarkable crystalline morphology. It was also found that the particle size of Res complex is 1.533 time higher than that of Qui complex. Interestingly, free Res molecular weight is higher than that of free Qui by the same ratio (precisely; 1.525).

  4. Photoassociation and photoinduced charge transfer in bridged diaryl compounds. 6. Intramolecular triplet excimers of dicarbazolylalkanes and their comparison to an intermolecular triplet excimer of carbazole

    SciTech Connect

    Cai, J.; Lim, E.C. (Univ. of Akron, OH (United States))

    1994-03-10

    A time-resolved emission study of intramolecular triplet excimer formation has been carried out for dicarbazolylmethane (DCM) and dicarbazolylpropane (DCP) in fluid solution at room temperature. The triplet excimer formation was deduced from the comparison of the phosphorescence with the corresponding emission from the intermolecular triplet excimer of carbazole. It has been found that whereas the triplet excimer formation in DCP is evident in both polar and nonpolar solvents, the excimer formation in DCM is observed only in polar solvents at longer delay times. The result indicates that the conformation favored by the triplet excimer is more readily attainable in DCP than in DCM. The enhancement of the triplet excimer formation by polar solvent, which is also observed for carbazole, suggests that the triplet excimers are stabilized (at least in part) by charge resonance interactions. Comparison of the temporal characteristics of the normal delayed fluorescence of DCP with those of the corresponding excimer phosphorescence suggests that the delayed fluorescence at long delay times is produced by bimolecular annihilation of the intramolecular triplet excimers. This in turn implies that the excited singlet-state species produced by bimolecular annihilation of the triplet excimers is unstable and rearranges into monomeric (i.e., non-interacting) conformation prior to its decay by emission of radiation. 16 refs., 7 figs.

  5. Effects of intermolecular forces and backbone architecture on the phase behavior of fluorocopolymer-supercritical fluid mixtures

    NASA Astrophysics Data System (ADS)

    Mertdogan, Cynthia Asli

    The impact of polymer backbone architecture on fluorocopolymer solubility in supercritical fluid (SCF) solvents is studied by systematically varying the chemical type of the repeat units in the main chain. The fluorocopolymers investigated include nonpolar copolymers of tetrafluoroethylene with 19 mol% hexafluoropropylene (FEPsb{19}) and 48 mol% hexafluoropropylene (FEPsb{48}) and a polar copolymer of vinylidene fluoride with 22 mol% hexafluoropropylene (Fluorelsp°ler ). The solvents are methodically varied from nonpolar perfluoroalkanes and SFsb6 to polar fluorocarbons and COsb2. Low molecular weight solvents are used to facilitate in interpreting the intermolecular forces that control fluorocopolymer solubility, although pressures in excess of 2,500 bar are sometimes needed to dissolve the fluorocopolymers in these simple solvents. Polarity effects, which vary inversely with temperature, are moderated by operating over a large temperature range from 0 to 300sp° C. A variable-volume view cell, capable of operating to high temperatures and high pressures, was designed and implemented to meet these extreme operating conditions. Increasing the polarizability of nonpolar solvents reduces the pressures required to dissolve FEPsb{19} by as much as 1,500 bar going from perfluoromethane to perfluoropropane. However, in polar solvents, the pressures required for FEPsb{19} solubility rise dramatically as the temperature is decreased due to the increase in polar, solvent-solvent interactions that do not favor the solubility of a nonpolar copolymer. Replacing semi-crystalline FEPsb{19} with amorphous FEPsb{48} yields the same trends in phase behavior. Therefore, crystallinity does not control the shape of these fluorocopolymer-SCF cloud-point curves. Adding a cosolvent to the solution can dramatically lower the pressures needed to dissolve the copolymer. Introducing the "cosolvent" directly into the polymer backbone by changing copolymer architecture is another method of modifying fluorocopolymer solubility as seen with the results for Fluorel-SCF mixtures compared to those for FEPsb{19}-SCF mixtures. A supercritical fractionation of FEPsb{19} provides information on the impact of molecular weight and end-group content on fluorocopolymer solubility. Challenges remain for modeling fluorocopolymer-solvent mixtures. The Sanchez-Lacombe equation cannot capture the characteristics of FEPsb{19}-SCF solvent phase behavior unless two empirical mixture parameters, one of which varies with temperature, are used.

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

    NASA Astrophysics Data System (ADS)

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

    2008-09-01

    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 (?1) is the measure of the fastest ET rate (?1=?ETfast=(kETfast)-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 (Vel). 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 ?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 (xA) is found to be ˜0.4 for aromatic amines and ˜0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the ?1 values are seen to increase very sharply. The large difference in the critical xA 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 (?-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 ?-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 Vel and thus ultrafast ET reaction. In contrary, the HOMO of the ?-type aromatic amines is largely distributed throughout the whole molecule and thus most of the orientations of these amines can give significant Vel for ultrafast ET reactions with close-contact C151 dyes.

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

    SciTech Connect

    Singh, P. K.; Nath, S.; Bhasikuttan, A. C.; Kumbhakar, M.; Mohanty, J.; Sarkar, S. K.; Mukherjee, T.; Pal, H. [Radiation and Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085 (India)

    2008-09-21

    Effect of donor amine orientation on nondiffusive ultrafast intermolecular electron transfer (ET) reactions in coumarin-amine systems has been investigated using femtosecond fluorescence upconversion measurements. Intermolecular ET from different aromatic and aliphatic amines used as donor solvents to the excited coumarin-151 (C151) acceptor occurs with ultrafast rates such that the shortest fluorescence lifetime component ({tau}{sub 1}) is the measure of the fastest ET rate ({tau}{sub 1}={tau}{sub ET}{sup fast}=(k{sub ET}{sup fast}){sup -1}), assigned to the C151-amine contact pairs in which amine donors are properly oriented with respect to C151 to maximize the acceptor-donor electronic coupling (V{sub el}). It is interestingly observed that as the amine solvents are diluted by suitable diluents (either keeping solvent dielectric constant similar or with increasing dielectric constant), the {tau}{sub 1} remains almost in the similar range as long as the amine dilution does not cross a certain critical limit, which in terms of the amine mole fraction (x{sub A}) is found to be {approx}0.4 for aromatic amines and {approx}0.8 for aliphatic amines. Beyond these dilutions in the two respective cases of the amine systems, the {tau}{sub 1} values are seen to increase very sharply. The large difference in the critical x{sub A} values involving aromatic and aliphatic amine donors has been rationalized in terms of the largely different orientational restrictions for the ET reactions as imposed by the aliphatic (n-type) and aromatic ({pi}-type) nature of the amine donors [A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008)]. Since the highest occupied molecular orbital (HOMO) of the n-type aliphatic amines is mostly centralized at the amino nitrogen, only some specific orientations of these amines with respect to the close-contact acceptor dye [also of {pi}-character; A. K. Satpati et al., J. Mol. Struct. 878, 84 (2008) and E. W. Castner et al., J. Phys. Chem. A 104, 2869 (2000)] can give suitable V{sub el} and thus ultrafast ET reaction. In contrary, the HOMO of the {pi}-type aromatic amines is largely distributed throughout the whole molecule and thus most of the orientations of these amines can give significant V{sub el} for ultrafast ET reactions with close-contact C151 dyes.

  8. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the ? and ? polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics. PMID:23879450

  9. Hadamard-encoded high-resolution NMR spectroscopy via intermolecular single-quantum coherences

    NASA Astrophysics Data System (ADS)

    Ke, Hanping; Cai, Honghao; Cai, Shuhui; Chen, Hao; Lin, Yanqin; Chen, Zhong

    2014-11-01

    NMR spectroscopy plays an important role in metabolite studies because it can provide atomic level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues are hampered by the magnetic field inhomogeneities originating from variations in macroscopic magnetic susceptibility, which lead to broad spectral lines and subsequently obscure metabolite signals. A new pulse sequence based on intermolecular single-quantum coherences was proposed to obtain one-dimensional high-resolution NMR spectra in inhomogeneous magnetic fields via Hadamard encoding. The new method can provide resolution-improved spectra directly through one-dimensional acquisition within a relatively short acquisition time. Theoretical derivation was performed and the conclusion was tested by solution samples in purposely de-shimmed magnetic fields and pig brain tissue sample. The experimental results show that this sequence can yield useful structural information, even when the field inhomogeneity is sufficiently severe to erase almost all spectral information with conventional one-dimensional single-quantum coherence techniques. Moreover, good solvent suppression efficiency can be achieved by this sequence. This sequence may provide a promising way for high-resolution NMR spectroscopy of biological tissue.

  10. Laser initiation thresholds of a 'green' aluminum/molybdenum-trioxide metastable intermolecular composite and other pyrotechnics

    NASA Astrophysics Data System (ADS)

    Howard, Stephen L.; Morris, Jeffrey B.; Beyer, Richard A.; Hamlin, Scott J.; Martin, James; Burke, Gregory C.; Doris, Thomas

    2005-09-01

    Metastable intermolecular composites (MIC) consisting of nanometer-scale aluminum and molybdenum trioxide have been proposed as fast initiators. A compound of this class of material was evaluated as a potential environmentally friendly replacement pyrotechnic material for lead styphnate for use in the primer of the M230 medium-caliber automatic cannon. In addition to removing the lead hazard, laser ignition would also reduce or remove certain hazards due to electrostatic or radio frequency radiation. This study was conducted with both a flashlamp-pumped Nd+3:YAG laser and a fiber-coupled diode laser. The measured threshold ignition energies of the MIC and two other inorganic pyrotechnic compounds are presented. The low ignition threshold, advances in diode laser technology, and compact size of the diode laser indicated that laser diode technology could be an ideal candidate ignition source for the M230 cannon. The candidate pyrotechnic compounds were also evaluated for suitability in laser initiation via measurement of time-to-first-light. This metric provided a measurement of the potential for achievement of the necessary action time required for proper cannon operation.

  11. In Vivo Noninvasive Detection of Brown Adipose Tissue through Intermolecular Zero-Quantum MRI

    PubMed Central

    Branca, Rosa T.; Zhang, Le; Warren, Warren S.; Auerbach, Edward; Khanna, Arjun; Degan, Simone; Ugurbil, Kamil; Maronpot, Robert

    2013-01-01

    The recent discovery of active Brown Adipose Tissue (BAT) in adult humans has opened new avenues for obesity research and treatment, as reduced BAT activity seem to be implicated in human energy imbalance, diabetes, and hypertension. However, clinical applications are currently limited by the lack of non-invasive tools for measuring mass and function of this tissue in humans. Here we present a new magnetic resonance imaging method based on the normally invisible intermolecular multiple-quantum coherence 1H MR signal. This method, which doesn’t require special hardware modifications, can be used to overcome partial volume effect, the major limitation of MR-based approaches that are currently being investigated for the detection of BAT in humans. With this method we can exploit the characteristic cellular structure of BAT to selectively image it, even when (as in humans) it is intimately mixed with other tissues. We demonstrate and validate this method in mice using PET scans and histology. We compare this methodology with conventional 1H MR fat fraction methods. Finally, we investigate its feasibility for the detection of BAT in humans. PMID:24040203

  12. Site- and energy-selective slow-electron production through intermolecular Coulombic decay.

    PubMed

    Gokhberg, Kirill; Koloren?, P?emysl; Kuleff, Alexander I; Cederbaum, Lorenz S

    2014-01-30

    Irradiation of matter with light tends to electronically excite atoms and molecules, with subsequent relaxation processes determining where the photon energy is ultimately deposited and electrons and ions produced. In weakly bound systems, intermolecular Coulombic decay (ICD) enables very efficient relaxation of electronic excitation through transfer of the excess energy to neighbouring atoms or molecules that then lose an electron and become ionized. Here we propose that the emission site and energy of the electrons released during this process can be controlled by coupling the ICD to a resonant core excitation. We illustrate this concept with ab initio many-body calculations on the argon-krypton model system, where resonant photoabsorption produces an initial or 'parent' excitation of the argon atom, which then triggers a resonant-Auger-ICD cascade that ends with the emission of a slow electron from the krypton atom. Our calculations show that the energy of the emitted electrons depends sensitively on the initial excited state of the argon atom. The incident energy can thus be adjusted both to produce the initial excitation in a chosen atom and to realize an excitation that will result in the emission of ICD electrons with desired energies. These properties of the decay cascade might have consequences for fundamental and applied radiation biology and could be of interest in the development of new spectroscopic techniques. PMID:24362566

  13. Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

    PubMed

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

    Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials. PMID:24467489

  14. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    SciTech Connect

    Shvab, I.; Sadus, Richard J., E-mail: rsadus@swin.edu.au [Centre for Molecular Simulation, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122 (Australia)

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  15. 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 ?-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.

  16. Pressure waves generated by metastable intermolecular composites in an aqueous environment

    NASA Astrophysics Data System (ADS)

    Maines, G.; Radulescu, M.; Bacciochini, A.; Jodoin, B.; Lee, J. J.

    2014-05-01

    In the present study, pressure waves generated by a metastable intermolecular composite (MIC) have been measured experimentally in an aqueous environment and correlated with flame speed measurements. Underwater experiments were performed in a 1.0 L high-pressure chamber mounted with high-resolution pressure transducers and designed with optical access. Samples consisting of a stoichiometric mixture of aluminium and copper(II)-oxide particles were evaluated. Two types of samples were synthesized; a mixture of micron-sized raw powders, and ball-milled powders with a fine-scale nano-structure. A planetary mill was used to refine reactant powders from micron- to nano-scale dimensions. The dynamics of the pressure wave and high-pressure gas bubble were monitored via pressure histories and high-speed Schlieren visualization. The effect of reactant particle size has been evaluated quantitatively. The dynamics of the pressure wave were correlated with the rate of expansion of the high-pressure gas bubble.

  17. Pin-wheel hexagons: A model for anthraquinone ordering on Cu(111)

    NASA Astrophysics Data System (ADS)

    Šim?nas, M.; Tornau, E. E.

    2013-10-01

    The 4-state model of anthraquinone molecules ordering in a pin-wheel large-pore honeycomb phase on Cu(111) is proposed and solved by Monte Carlo simulation. The model is defined on a rescaled triangular lattice with the lattice constant a being equal to intermolecular distance in the honeycomb phase. The pin-wheel triangle formations are obtained taking into account the elongated shape of the molecules and anisotropic interactions for main two attractive short range (double and single dimeric) H-bond interactions. The long-range intermolecular interactions, corresponding to repulsive dipole-dipole forces, are assumed to be isotropic. Also, a very small (compared to short-range forces) isotropic attractive long-range interaction at the "characteristic" distance of a pore diameter is employed, and its effect carefully studied. This interaction is crucial for a formation of closed porous ordered systems, pin-wheel hexagons in particular. If each side of a pin-wheel hexagon is formed of n parallel molecules, the distance of this characteristic interaction is a?{3n^2+1}. The phase diagrams including different pin-wheel hexagon phases and a variety of other ordered structures are obtained. By changing the distance of characteristic interaction, different ordering routes into the experimental pin-wheel honeycomb phase are explored. The results obtained imply that classical explanation of the origin of the pin-wheel honeycomb phase in terms of some balance of attractive and repulsive forces cannot be totally discounted yet.

  18. Pin-wheel hexagons: a model for anthraquinone ordering on Cu(111).

    PubMed

    Simenas, M; Tornau, E E

    2013-10-21

    The 4-state model of anthraquinone molecules ordering in a pin-wheel large-pore honeycomb phase on Cu(111) is proposed and solved by Monte Carlo simulation. The model is defined on a rescaled triangular lattice with the lattice constant a being equal to intermolecular distance in the honeycomb phase. The pin-wheel triangle formations are obtained taking into account the elongated shape of the molecules and anisotropic interactions for main two attractive short range (double and single dimeric) H-bond interactions. The long-range intermolecular interactions, corresponding to repulsive dipole-dipole forces, are assumed to be isotropic. Also, a very small (compared to short-range forces) isotropic attractive long-range interaction at the "characteristic" distance of a pore diameter is employed, and its effect carefully studied. This interaction is crucial for a formation of closed porous ordered systems, pin-wheel hexagons in particular. If each side of a pin-wheel hexagon is formed of n parallel molecules, the distance of this characteristic interaction is a?(3n(2)+1). The phase diagrams including different pin-wheel hexagon phases and a variety of other ordered structures are obtained. By changing the distance of characteristic interaction, different ordering routes into the experimental pin-wheel honeycomb phase are explored. The results obtained imply that classical explanation of the origin of the pin-wheel honeycomb phase in terms of some balance of attractive and repulsive forces cannot be totally discounted yet. PMID:24160537

  19. Control of the spatial arrangements of supramolecular networks based on saddle-distorted porphyrins by intermolecular hydrogen bonding.

    PubMed

    Ishizuka, Tomoya; Sankar, Muniappan; Kojima, Takahiko

    2013-12-01

    Supramolecular integration of a saddle-distorted zinc(II) porphyrin complex, which has hydroxyl groups at the para-position of the four meso-aryl groups, has been demonstrated on the basis of hydrogen bonding among the peripheral hydroxyl groups. The hydrogen-bonding patterns were controlled by the recrystallization solvents and additives, and particularly, addition of a bifunctional ligand such as 4,4'-bipyridine (bpy). The coordination of bpy to form dinuclear Zn(II)-porphyrin complexes causes a conformational difference: the dimeric complex with four hydroxyl groups is in an eclipsed form, however, a derivative without hydroxyl groups is in a staggered form due to the presence or absence of the intermolecular hydrogen bonding. In addition, the dimerization by the bpy coordination resulted in the expansion of the intermolecular space formed in the porphyrin networks, suggesting the potential to be applied for inclusion of guest molecules. PMID:23969510

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  1. Highly Convergent Total Synthesis of (+)-Lithospermic Acid via a Late-Stage Intermolecular C–H Olefination

    PubMed Central

    Wang, Dong-Hui; Yu, Jin-Quan

    2011-01-01

    The total synthesis of (+)-lithospermic acid is reported, which exploits two successive C–H activation reactions as the key steps. Rh-catalyzed carbene C–H insertion reaction using Davies’ catalyst built the dihydrobenzofuran core, and a late-stage intermolecular C–H olefination coupled the olefin unit with the dihydrobenzofuran core to construct the molecule in a highly convergent manner. PMID:21443224

  2. Highly regio- and enantioselective synthesis of N-substituted 2-pyridones: iridium-catalyzed intermolecular asymmetric allylic amination.

    PubMed

    Zhang, Xiao; Yang, Ze-Peng; Huang, Lin; You, Shu-Li

    2015-02-01

    The first iridium-catalyzed intermolecular asymmetric allylic amination reaction with 2-hydroxypyridines has been developed, thus providing a highly efficient synthesis of enantioenriched N-substituted 2-pyridone derivatives from readily available starting materials. This protocol features a good tolerance of functional groups in both the allylic carbonates and 2-hydroxypyridines, thereby delivering multifunctionalized heterocyclic products with up to 98?% yield and 99?%?ee. PMID:25504907

  3. Convergent approach to the tetracyclic core of the apparicine class of indole alkaloids via a key intermolecular nitrosoalkene conjugate addition.

    PubMed

    Chauhan, Pradeep S; Weinreb, Steven M

    2014-07-01

    Readily available methyl 3-formylindol-2-ylacetate and N-tosyl-4-chloro-3-piperidone oxime have been used to construct the tetracyclic skeleton of the apparicine class of monoterpene indole alkaloids in only four steps in 80% overall yield. Key transformations in this convergent approach involve use of an intermolecular ester enolate/nitrosoalkene conjugate addition to form the C-15/16 bond, followed by a reductive cyclization to construct the C-ring of the tetracycle. PMID:24927230

  4. One-pot stereoselective synthesis of ?,?-differentiated diamino esters via the sequence of aminochlorination, aziridination and intermolecular SN2 reaction

    PubMed Central

    Xiong, Yiwen; Qian, Ping; Cao, Chenhui; Mei, Haibo; Li, Guigen

    2014-01-01

    Summary We report here an efficient one-pot method for the synthesis of ?,?-differentiated diamino esters directly from cinnamate esters using N,N-dichloro-p-toluenesulfonamide and benzylamine as nitrogen sources. The key transformations include a Cu-catalyzed aminohalogenation and aziridination, followed by an intermolecular SN2 nucleophilic ring opening by benzylamine. The reactions feature a wide scope of substrates and proceed with excellent stereo- and regioselectivity (anti:syn >99:1) . PMID:25161740

  5. Regioselective rhodium-catalyzed intermolecular [2+2+2] cycloaddition of alkynes and isocyanates to form pyridones

    PubMed Central

    Oberg, Kevin M.; Lee, Ernest E.; Rovis, Tomislav

    2011-01-01

    A highly regioselective rhodium-catalyzed intermolecular [2+2+2] cycloaddition of terminal alkynes with a variety of isocyanates to provide 2- and 4-pyridones has been developed. This reaction proceeds in good to excellent yields and overcomes the problem of dimerization and trimerization through the use of phosphoramidite ligands. A CO migration in the metallacycle is proposed to account for the formation of 4-pyridone. PMID:21927511

  6. Organic Compounds Capable to Form Intermolecular Hydrogen Bonds for Nanostructures Created on Solid Surface, Aimed to Sensor Design

    Microsoft Academic Search

    O. Neilands

    \\u000a Redox-active organic compounds capable of forming intermolecular complementary hydrogen bonds during recent years have received\\u000a much attention due to the recognition and detection possibility of nucleic acids and their components. Bäuerle [1, 2] has investigated conducting polythiophenes functionalized with uracil or adenine derivatives. As was demonstrated in voltammetric\\u000a and spectroelectrochemical experiments, succsessive addition of complementary bases to polymers leads to

  7. Time-resolved IR spectroscopy in liquid rare gases: Direct rate measurement of an intermolecular alkane CH oxidative addition reaction

    Microsoft Academic Search

    B. H. Weiller; E. P. Wasserman; R. G. Bergman; C. B. Moore; G. C. Pimentel

    1989-01-01

    Since the first demonstration of the intermolecular oxidative addition of alkane C-H bonds to transition-metal centers, there have been many studies of the mechanism of this reaction. While these studies have illuminated many aspects of the C-H activation process, they do not provide direct information about the reactive intermediates or the potential energy surface for the elementary insertion reaction. Flash

  8. Molecular Interactions and Hydrogen Bond Tunneling Dynamics: Some New Perspectives

    NASA Astrophysics Data System (ADS)

    Saykally, Richard J.; Blake, Geoffrey A.

    1993-03-01

    The recent development of tunable far-infrared lasers and other high-resolution spectroscopic probes of weakly bound clusters is having a significant impact on our understanding of intermolecular forces and on the complex quantum tunneling dynamics that occur in hydrogen-bonded systems. Far-infrared studies of a variety of interactions are discussed, including several prototypical water-hydrophobe complexes, the water trimer, and the ammonia dimer. Particular attention is paid to the inversion of spectroscopic data to yield detailed intermolecular potential energy surfaces. Investigations of nonpairwise additivity are also described.

  9. Inter-Molecular Spin-Orbital Coupling Effects on Magnetoresistance and Spin-Dependent Excited Processes in Organic Semiconductors

    NASA Astrophysics Data System (ADS)

    Yan, Liang; Hu, Bin

    2009-03-01

    A low magnetic field can change electrical current and electroluminescence in organic semiconductors, leading to magnetoresistance and magnetic field effects due to magnetic field-dependent singlet/triplet ratio involved in charge transport and excited states. In general, an external magnetic field can change singlet and triplet ratios through two major pathways: spin-dependent electron-hole pairing and field-dependent intersystem crossing. We found that tuning inter-molecular spin-orbital coupling leads to a significant change in magnetoresistance, electro-fluorescence, and electro-phosphorescence. These experimental findings indicate that (i) inter-molecular and intra-molecular electron-hole pairs account for magnetoresistance and magnetic field effects, respectively, (ii) spin mixing occurs in inter-molecular excited states, and (iii) spin-mixing is a function of both spin-orbital coupling and singlet-triplet energy difference. This presentation will discuss the effects of magnetic field on both spin-dependent electron-hole pairing and spin mixing in magnetoresistance and magnetic field effects in organic semiconductors.

  10. Site-specific intermolecular valence-band dispersion in ?-phase crystalline films of cobalt phthalocyanine studied by angle-resolved photoemission spectroscopy.

    PubMed

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2014-12-14

    The valence band structure of ?-phase crystalline films of cobalt phthalocyanine (CoPc) grown on Au(111) is investigated by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The photo-induced change in the ARPES peaks is noticed in shape and energy of the highest occupied molecular orbital (HOMO, C 2p) and HOMO-1 (Co 3d) of CoPc, and is misleading the interpretation of the electronic properties of CoPc films. From the damage-free normal-emission ARPES measurement, the clear valence-band dispersion has been first observed, showing that orbital-specific behaviors are attributable to the interplay of the intermolecular ?-? and ?-d interactions. The HOMO band dispersion of 0.1 eV gives the lower limit of the hole mobility for ?-CoPc of 28.9 cm(2) V(-1) s(-1) at 15 K. The non-dispersive character of the split HOMO-1 bands indicates that the localization of the spin state is a possible origin of the antiferromagnetism. PMID:25494764

  11. Site-specific intermolecular valence-band dispersion in ?-phase crystalline films of cobalt phthalocyanine studied by angle-resolved photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2014-12-01

    The valence band structure of ?-phase crystalline films of cobalt phthalocyanine (CoPc) grown on Au(111) is investigated by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The photo-induced change in the ARPES peaks is noticed in shape and energy of the highest occupied molecular orbital (HOMO, C 2p) and HOMO-1 (Co 3d) of CoPc, and is misleading the interpretation of the electronic properties of CoPc films. From the damage-free normal-emission ARPES measurement, the clear valence-band dispersion has been first observed, showing that orbital-specific behaviors are attributable to the interplay of the intermolecular ?-? and ?-d interactions. The HOMO band dispersion of 0.1 eV gives the lower limit of the hole mobility for ?-CoPc of 28.9 cm2 V-1 s-1 at 15 K. The non-dispersive character of the split HOMO-1 bands indicates that the localization of the spin state is a possible origin of the antiferromagnetism.

  12. T cell receptor (TCR) recognition of MHC class I variants: intermolecular second-site reversion provides evidence for peptide/MHC conformational variation

    PubMed Central

    1996-01-01

    We investigated mechanistic differences in antigen presentation between murine MHC class I variants H-2K(b) and H-2K(bm)8. H-2K(bm)8 differs from H-2K(b) by four residues at the floor of the peptide-binding site, affecting its B pocket which interacts with the second (P2) residue of the peptide. The rest of the molecule, including the T cell receptor (TCR)-contacting residues, is identical to H-2K(b). Due to this variation, CTLs that recognize the ovalbumin 257-264 and HSV gB 498-505 peptides on H-2K(b) cannot recognize them on H-2K(bm)8. This could be due to impaired peptide binding or an altered peptide: K(bm)8 conformation. Peptide binding studies ruled out the first explanation. Molecular modeling indicated that the most obvious consequence of amino acid variation between peptide/H-2K(b) and peptide/H-2K(bm)8 complexes would be a loss of the conserved hydrogen bond network in the B pocket of the latter. This could cause conformational variation of bound peptides. Intermolecular second-site reversion was used to test this hypothesis: P2-substituted OVA and HSV peptides, engineered to restore the hydrogen bond network of the B pocket, were the only ones which restored CTL recognition. These results provide a molecular understanding of peptide/MHC conformational variation. PMID:8691139

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

    PubMed Central

    Krylov, Igor B; Vil’, Vera A

    2015-01-01

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

  14. On the role of electrodynamic interactions in long-distance biomolecular recognition

    E-print Network

    Boyer, Edmond

    place between them. At this stage, molecular motions are mainly governed by chemical forces of short-range nature (hydrophilic/hydrophobic interactions, van der Waals forces, covalent bonds, etc.) besides a point of view of the dynamics, intermolecular electrostatic interactions might a priori play a role

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  16. 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

  17. Study of intermolecular contacts in proteins and oligomer interfaces and preliminary investigations into the design and production of nanomaterials from proteins

    NASA Astrophysics Data System (ADS)

    Iyer, Ganesh Hariharan

    The first part of this research involved a study of the nature and extent of nonbonded interactions at crystal and oligomer interfaces. A survey was compiled of several characteristics of intersubunit contacts in 58 different oligomeric proteins, and of the intermolecular contacts in 223 protein crystal structures. Routines written in "S" language were utilized for the generation of the observed and expected contacts. The information in the Protein Data Bank (PDB) was extracted using the database management system, Protein Knowledge Base (PKB). Potentials of mean force for atom-atom contacts and residue-residue contacts were derived by comparison of the number of observed interactions with the number expected by mass action. Preference association matrices and log-linear analyses were applied to determine the different factors that could contribute to the overall interactions at the interfaces of oligomers and crystals. Surface patches at oligomer and crystal interfaces were also studied to further investigate the origin of the differences in their stabilities. Total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acid prominent in oligomer interfaces. Contact potentials indicate that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. The second part involved the development of a new class of biomaterials from two-dimensional arrays of ordered proteins. Point mutations were planned to introduce cysteine residues at appropriate locations to enable cross-linking at the molecular interface within given crystallographic planes. Crystallization and subsequent cross-linking of the modified protein would lead to the formation of arrays on subsequent dissociation of the crystal. Novel protein architectures can be generated from these cross-linked nanostructures. Experiments with model protein, maltose-binding protein (MBP) were performed to develop purification, cross-linking and crystallization techniques. The long-term goal of this project is to apply the experience gained with MBP to the fabrication of nanomaterials from other, application-specific proteins for ultrafiltration and microelectronic devices.

  18. Hydration-dependent dynamical transition in protein: protein interactions at approximately 240 K.

    PubMed

    Kurkal-Siebert, Vandana; Agarwal, Ritesh; Smith, Jeremy C

    2008-04-01

    Interprotein motions in low and fully hydrated carboxymyoglobin crystals are investigated using molecular dynamics simulation. Below approximately 240 K, the calculated dynamic structure factor exhibits a peak arising from interprotein vibration. Above approximately 240 K, the intermolecular fluctuations of the fully hydrated crystal increase drastically, whereas the low-hydration model exhibits no transition. Autocorrelation function analysis shows the transition to be dominated by the activation of diffusive intermolecular motion. The potential of mean force for the interaction remains quasiharmonic. The results indicate useful experimental avenues on protein:protein interactions to be explored using next-generation neutron sources. PMID:18518001

  19. Tuning of intermolecular electron transfer reaction by modulating the microenvironment inside copolymer-surfactant supramolecular assemblies.

    PubMed

    Kumbhakar, Manoj; Dey, Swayandipta; Singh, Prabhat Kumar; Nath, Sukhendu; Satpati, Ashis Kumar; Gangully, Rajib; Aswal, Vinod Kumar; Pal, Haridas

    2011-02-24

    Photoinduced intermolecular electron transfer (ET) dynamics between various 7-aminocoumarin acceptors and N,N-dimethylaniline (DMAN) donor has been studied in copolymer-surfactant supramolecular assemblies prepared in aqueous 1% P123 triblock copolymer micellar solution with varying concentration of surfactants (sodium dodecyl sulfate (SDS), cetyl trimethyl ammonium chloride (CTAC), and triton-X-100 (TX100)). The aim of the present study is to modulate the reaction environment, especially the degree of micellar hydration inside the P123 micelle by the addition of the surfactants, which can modulate the ET reaction through the changes in the ET rates and the reaction exergonicity. Within the limited surfactant to copolymer molar ratios (n) used in the present study, fluorescence spectroscopy, dynamic light scattering (DLS), and small-angle neutron scattering (SANS) investigations indicate that the copolymer-surfactant supramolecular assemblies retain their micellar structure, although the micellar size gradually decreases with n. The redox potentials of the electron donor and acceptors are also found to change with n, although the extent of the effect is different for SDS, CTAC, and TX100 cosurfactants. In the presence of CTAC, the estimated exergonicity (-?G(0)) of the ET reaction is found to increase with an increase in n compared with that in pure P123, whereas it decreases marginally with SDS and remains almost the same for TX100. Substantial quenching of coumarin fluorescence is observed in the presence of DMAN in all copolymer-surfactant micellar aggregates because of ET reaction. The ET rate is seen to increase gradually with an increase in SDS and CTAC concentration in the supramolecular assembly, although it remains unaffected on the addition of TX100. The increased ionic strength in the Corona region of the copolymer-surfactant supramolecular aggregates due to the addition of the ionic surfactants has been envisaged for the increase in the ET rates. A correlation of the quenching rate constants with the free-energy changes (?G(0)) of the ET reactions shows the typical bell-shaped curve as predicted by Marcus outersphere ET theory. A substantial shift along the exergonicity axis (~0.3 eV) for the appearance of the Marcus correlation is observed in some cases, although the extent of such shift depends on both the nature of the cosurfactant and the amount of cosurfactant used in the copolymer-surfactant supramolecular assembly. Therefore, these preliminary results suggest a possibility of not only modulating the ET rates but also tuning the appearance of Marcus inversion along the exergonicity scale by suitably tuning the reaction environment inside the copolymer-surfactant supramolecular assemblies with a relatively more hydrophilic cosurfactant. PMID:21271727

  20. 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 ?-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 ?-insertive pathway that involves fast and reversible migratory C=C bond insertion into the polar Ae-N pyrrolido ? 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 (Ca

  1. 1H-NMR as a structural and analytical tool of intra- and intermolecular hydrogen bonds of phenol-containing natural products and model compounds.

    PubMed

    Charisiadis, Pantelis; Kontogianni, Vassiliki G; Tsiafoulis, Constantinos G; Tzakos, Andreas G; Siskos, Michael; Gerothanassis, Ioannis P

    2014-01-01

    Experimental parameters that influence the resolution of 1H-NMR phenol OH signals are critically evaluated with emphasis on the effects of pH, temperature and nature of the solvents. Extremely sharp peaks (??1/2?2 Hz) can be obtained under optimized experimental conditions which allow the application of 1H-13C HMBC-NMR experiments to reveal long range coupling constants of hydroxyl protons and, thus, to provide unequivocal assignment of the OH signals even in cases of complex polyphenol natural products. Intramolecular and intermolecular hydrogen bonds have a very significant effect on 1H OH chemical shifts which cover a region from 4.5 up to 19 ppm. Solvent effects on -OH proton chemical shifts, temperature coefficients (??/?T), OH diffusion coefficients, and nJ(13C, O1H) coupling constants are evaluated as indicators of hydrogen bonding and solvation state of phenol -OH groups. Accurate 1H chemical shifts of the OH groups can be calculated using a combination of DFT and discrete solute-solvent hydrogen bond interaction at relatively inexpensive levels of theory, namely, DFT/B3LYP/6-311++G (2d,p). Excellent correlations between experimental 1H chemical shifts and those calculated at the ab initio level can provide a method of primary interest in order to obtain structural and conformational description of solute-solvent interactions at a molecular level. The use of the high resolution phenol hydroxyl group 1H-NMR spectral region provides a general method for the analysis of complex plant extracts without the need for the isolation of the individual components. PMID:25185070

  2. Vibrational lifetimes of cyanide ion in aqueous solution from molecular dynamics simulations: intermolecular vs intramolecular accepting modes.

    PubMed

    Talapatra, Surma; Geva, Eitan

    2014-07-01

    The lifetimes of the first vibrational state of (12)C(14)N(-) and (13)C(15)N(-) dissolved in H2O or D2O were calculated. The calculations were based on the Landau-Teller formula that puts the vibrational lifetimes in terms of the autocorrelation function of the force exerted on the C-N stretch by the remaining degrees of freedom. The force autocorrelation functions were calculated from classical molecular dynamics simulations of the four cyanide/water isotopomer combinations ((12)C(14)N(-)/H2O, (12)C(14)N(-)/D2O, (13)C(15)N(-)/H2O, (13)C(15)N(-)/D2O). The cyanide ion was described by a polarizable force field, and the water was described by either the rigid SPC/E model or the flexible SPC/Fw model, in order to compare two different types of accepting modes, namely, (1) intermolecular (translational and rotational) solvent accepting modes (rigid SPC/E water) and (2) intramolecular (vibrational) solvent accepting modes (flexible SPC/Fw water). Since quantum effects are expected to increase in size with increasing frequency mismatch between relaxing and accepting modes, different quantum correction factors were employed depending on the identity of the accepting modes, more specifically, the harmonic/Schofield quantum correction factor in the case of intermolecular accepting modes and the standard quantum correction factor in the case of intramolecular accepting modes. The lifetimes with either the rigid SPC/E or flexible SPC/Fw water models were found to be in good quantitative agreement with the experimentally measured values for all isotopomer combinations. Our results suggest that taking into account quantum effects on the vibrational energy relaxation of cyanide in aqueous solution can make the intermolecular pathway at least as likely as the intramolecular pathway. PMID:24927159

  3. Supramolecular solar cells

    NASA Astrophysics Data System (ADS)

    Subbaiyan, Navaneetha Krishnan

    Supramolecular chemistry - chemistry of non-covalent bonds including different type of intermolecular interactions viz., ion-pairing, ion-dipole, dipole-dipole, hydrogen bonding, cation-pi and Van der Waals forces. Applications based on supramolecular concepts for developing catalysts, molecular wires, rectifiers, photochemical sensors have been evolved during recent years. Mimicking natural photosynthesis to build energy harvesting devices has become important for generating energy and solar fuels that could be stored for future use. In this dissertation, supramolecular chemistry is being explored for creating light energy harvesting devices. Photosensitization of semiconductor metal oxide nanoparticles, such as titanium dioxide (TiO2) and tin oxide (SnO2,), via host-guest binding approach has been explored. In the first part, self-assembly of different porphyrin macrocyclic compounds on TiO2 layer using axial coordination approach is explored. Supramolecular dye sensitized solar cells built based on this approach exhibited Incident Photon Conversion Efficiency (IPCE) of 36% for a porphyrin-ferrocene dyad. In the second part, surface modification of SnO2 with water soluble porphyrins and phthalocyanine resulted in successful self-assembly of dimers on SnO2 surface. IPCE more than 50% from 400 - 700 nm is achieved for the supramolecular self-assembled heterodimer photocells is achieved. In summary, the axial ligation and ion-pairing method used as supramolecular tools to build photocells, exhibited highest quantum efficiency of light energy conversion with panchromatic spectral coverage. The reported findings could be applied to create interacting molecular systems for next generation of efficient solar energy harvesting devices.

  4. The polarization approximation and the Amos-Musher intermolecular perturbation theories compared to infinite order at finite separations

    NASA Astrophysics Data System (ADS)

    Adams, William H.

    1994-11-01

    We argue that the most common form of intermolecular perturbation theory, the polarization approximation (PA), gives at finite separations, for nearly all systems, no usable, exact relationship between the lowest unperturbed energy and the physical ground state energy. This would be true even if the PA energy expansion converged. In contrast, the Amos-Musher (AM) theory does give an exact relationship between the lowest unperturbed energy and the physical ground state energy. We find no theoretical justification for using the PA theory beyond second order in the energy, but the AM theory may be extended to arbitrarily high order.

  5. Charge Carrier Mobilities in Amorphous Triphenylamine-Fluorene Copolymers: Role of Triphenylamine Unit in Intra- and Intermolecular Charge Transport

    NASA Astrophysics Data System (ADS)

    Fukumatsu, Takahiro; Saeki, Akinori; Seki, Shu

    2012-06-01

    We investigated the effect of the triphenylamine (TPA) content of TPA-fluorene copolymers on their charge carrier mobilities. Intramolecular mobilities were measured by flash-photolysis time-resolved microwave conductivity (TRMC), while intermolecular hole mobilities were determined on the basis of space-charge limited current (SCLC) and field-effect transistor (FET). TRMC and SCLC except for FET showed an analogous dependence on the TPA content. The results are discussed from the viewpoints of delocalization of singly-occupied molecular orbital of radical cation, conformation of polymer chain, and trap effect. This study highlights the importance of optimizing the TPA content in the polyfluorene backbone for electronic device application.

  6. Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride

    NASA Astrophysics Data System (ADS)

    Koskelo, J.; Juurinen, I.; Ruotsalainen, K. O.; McGrath, M. J.; Kuo, I.-F.; Lehtola, S.; Galambosi, S.; Hämäläinen, K.; Huotari, S.; Hakala, M.

    2014-12-01

    We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting future experiments.

  7. Intra- and intermolecular effects on the Compton profile of the ionic liquid 1,3-dimethylimidazolium chloride.

    PubMed

    Koskelo, J; Juurinen, I; Ruotsalainen, K O; McGrath, M J; Kuo, I-F; Lehtola, S; Galambosi, S; Hämäläinen, K; Huotari, S; Hakala, M

    2014-12-28

    We present a comprehensive simulation study on the solid-liquid phase transition of the ionic liquid 1,3-dimethylimidazolium chloride in terms of the changes in the atomic structure and their effect on the Compton profile. The structures were obtained by using ab initio molecular dynamics simulations. Chosen radial distribution functions of the liquid structure are presented and found generally to be in good agreement with previous ab initio molecular dynamics and neutron scattering studies. The main contributions to the predicted difference Compton profile are found to arise from intermolecular changes in the phase transition. This prediction can be used for interpreting future experiments. PMID:25554165

  8. Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

    SciTech Connect

    Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.; Ross, Nancy L.; Cox, David F.; Rosso, Kevin M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and ?-AsS and the distorted hexagonal close-packed arrays adopted by ?- and ?-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  9. Thioarsenides: a case for long-range Lewis acid-base-directed van der Waals interactions

    NASA Astrophysics Data System (ADS)

    Gibbs, G. V.; Wallace, A. F.; Downs, R. T.; Ross, N. L.; Cox, D. F.; Rosso, K. M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local-energy density properties have been calculated for a number of As4S n ( n = 3, 4 and 5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions, and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals (vdW) bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis-base regions) with aligned regions of locally depleted electron density (Lewis-acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long-range Lewis acid-base-directed vdW interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and ?-AsS and the distorted hexagonal close-packed arrays adopted by ?- and ?-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long-range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  10. 2004 Atomic and Molecular Interactions Gordon Research Conference

    SciTech Connect

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  11. 1H NMR relaxation in glycerol solutions of nitroxide radicals: effects of translational and rotational dynamics.

    PubMed

    Kruk, D; Korpala, A; Rössler, E; Earle, K A; Medycki, W; Moscicki, J

    2012-03-21

    (1)H spin-lattice relaxation rates in glycerol solutions of selected nitroxide radicals at temperatures between 200 K and 400 K were measured at 15 MHz and 25 MHz. The frequency and temperature conditions were chosen in such a way that the relaxation rates go through their maximum values and are affected by neither the electron spin relaxation nor the electron-nitrogen nucleus hyperfine coupling, so that the focus could be put on the mechanisms of motion. By comparison with (1)H spin-lattice relaxation results for pure glycerol, it has been demonstrated that the inter-molecular electron spin-proton spin dipole-dipole interactions are affected not only by relative translational motion of the solvent and solute molecules, but also by their rotational dynamics as the interacting spins are displaced from the molecular centers; the eccentricity effects are usually not taken into account. The (1)H relaxation data have been decomposed into translational and rotational contributions and their relative importance as a function of frequency and temperature discussed in detail. It has been demonstrated that neglecting the rotational effects on the inter-molecular interactions leads to non-realistic conclusions regarding the translational dynamics of the paramagnetic molecules. PMID:22443774

  12. Intermolecular disulfide bonds are not required for the expression of the dimeric state and functional activity of the transferrin receptor.

    PubMed Central

    Alvarez, E; Gironès, N; Davis, R J

    1989-01-01

    The human transferrin receptor is expressed as a disulfide-linked dimer at the cell surface. The sites of intermolecular disulfide bonds are Cys-89 and Cys-98. We have examined the functional significance of the covalent dimeric structure of the transferrin receptor by substitution of Cys-89 and Cys-98 with serine residues. Wild-type and mutated transferrin receptors were expressed in Chinese hamster ovary cells (clone TF-) that lack detectable endogenous transferrin receptors. The rates of receptor endocytosis and recycling were measured and the accumulation of iron by cells incubated with [59Fe]diferric transferrin was investigated. No significant differences between these rates were observed when cells expressing wild-type and mutated receptors were compared. The structure of the mutant receptor lacking intermolecular disulfide bonds was investigated. The presence of a population of mutant receptors with a non-covalent dimeric structure was indicated by cross-linking studies using diferric [125I]transferrin and the bifunctional reagent disuccinimidyl suberimidate. However, sucrose density gradient sedimentation analysis of Triton X-100 solubilized transferrin receptors demonstrated that the mutant receptor existed as a monomer in the absence of diferric transferrin and as an apparent dimer in the presence of this receptor ligand. We conclude that the covalent dimeric structure of the transferrin receptor is not required for the expression of the dimeric state and functional activity of the receptor. Images PMID:2507316

  13. Electronic spectra of protonated benzaldehyde clusters with Ar and N2: effect of ??* excitation on the intermolecular potential.

    PubMed

    Patzer, Alexander; Zimmermann, Max; Alata, Ivan; Jouvet, Christophe; Dopfer, Otto

    2010-12-01

    Electronic spectra of the S(1)?S(0) transition of dimers of protonated benzaldehyde (BZH(+)) with Ar and N(2) are recorded by resonance-enhanced photodissociation in a tandem mass spectrometer. The S(1) origins observed are shifted to higher frequency upon complexation with Ar (?S(1) = 300 cm(-1)) and N(2) (?S(1) = 628 cm(-1)). Ab initio calculations at the CC2/aug-cc-pVDZ level suggest an assignment to H-bonded dimers of L = Ar and N(2) binding to the cis isomer of O-protonated BZH(+), yielding values of ?S(1) = 242 and 588 cm(-1) for cis-BZH(+)-L(H). Electronic ??* excitation results in a substantial increase of the proton affinity of BZH(+), which in turn destabilizes the intermolecular H-bonds to the inert ligands by 35%. The drastic effects of electronic ??* excitation on the geometric and electronic structure as well as the strength and anisotropy of the intermolecular potential (H-bonding and ?-bonding) are investigated. PMID:21069976

  14. Structure and interactions in simple solutions.

    PubMed Central

    Bowron, D T

    2004-01-01

    Neutron scattering with hydrogen/deuterium isotopic substitution techniques has been used to investigate the full range of structural interactions in a dilute 0.02 mol fraction solution of tertiary butanol in water, both in the absence and in the presence of a small amount of sodium chloride. Emphasis is given to the detailed pictures of the intermolecular interactions that have been derived using the empirical potential structure refinement technique. Analysis has been performed to the level of the spatial density distribution functions that illustrate the orientational dependence of the intermolecular interactions between all combinations of molecular and ionic components. The results show the key structural motifs involved in the interactions between the various components in a complex aqueous system. They underline the structural versatility of the water molecule in accommodating a range of different kinds of interactions while retaining its characteristic first-neighbour interaction geometry. Within this framework, the results highlight the complex interplay between the polar, non-polar and charged molecular interactions that exist in the system. PMID:15306374

  15. Crystal structure of the anti-(carcinoembryonic antigen) single-chain Fv antibody MFE-23 and a model for antigen binding based on intermolecular contacts.

    PubMed Central

    Boehm, M K; Corper, A L; Wan, T; Sohi, M K; Sutton, B J; Thornton, J D; Keep, P A; Chester, K A; Begent, R H; Perkins, S J

    2000-01-01

    MFE-23 is the first single-chain Fv antibody molecule to be used in patients and is used to target colorectal cancer through its high affinity for carcinoembryonic antigen (CEA), a cell-surface member of the immunoglobulin superfamily. MFE-23 contains an N-terminal variable heavy-chain domain joined by a (Gly(4)Ser)(3) linker to a variable light-chain (V(L)) domain (kappa chain) with an 11-residue C-terminal Myc-tag. Its crystal structure was determined at 2.4 A resolution by molecular replacement with an R(cryst) of 19.0%. Five of the six antigen-binding loops, L1, L2, L3, H1 and H2, conformed to known canonical structures. The sixth loop, H3, displayed a unique structure, with a beta-hairpin loop and a bifurcated apex characterized by a buried Thr residue. In the crystal lattice, two MFE-23 molecules were associated back-to-back in a manner not seen before. The antigen-binding site displayed a large acidic region located mainly within the H2 loop and a large hydrophobic region within the H3 loop. Even though this structure is unliganded within the crystal, there is an unusually large region of contact between the H1, H2 and H3 loops and the beta-sheet of the V(L) domain of an adjacent molecule (strands DEBA) as a result of intermolecular packing. These interactions exhibited remarkably high surface and electrostatic complementarity. Of seven MFE-23 residues predicted to make contact with antigen, five participated in these lattice contacts, and this model for antigen binding is consistent with previously reported site-specific mutagenesis of MFE-23 and its effect on CEA binding. PMID:10677374

  16. Resonances in ultracold dipolar atomic and molecular gases

    E-print Network

    Bruno Schulz; Simon Sala; Alejandro Saenz

    2014-12-09

    A previously developed approach for the numerical treatment of two particles that are confined in a finite optical-lattice potential and interact via an arbitrary isotropic interaction potential has been extended to incorporate an additional anisotropic dipole-dipole interaction. The interplay of a model but realistic short-range Born-Oppenheimer potential and the dipole-dipole interaction for two confined particles is investigated. A variation of the strength of the dipole-dipole interaction leads to diverse resonance phenomena. In a harmonic confinement potential some resonances show similarities to $s$-wave scattering resonances while in an anharmonic trapping potential like the one of an optical lattice inelastic confinement-induced dipolar resonances occur. The latter are due to a coupling of the relative and center-of-mass motion caused by the anharmonicity of the external confinement.

  17. Dimer asymmetry defines ?-catenin interactions

    PubMed Central

    Rangarajan, Erumbi S.; Izard, Tina

    2013-01-01

    The F-actin binding cytoskeletal protein ?-catenin interacts with ?-catenin-cadherin complexes and stabilizes cell-cell junctions. The ?-catenin–?-catenin complex cannot bind to F-actin, whereas interactions of ?-catenin with the cytoskeletal protein vinculin appear necessary to stabilize adherens junctions. Here we report the crystal structure of nearly full-length human ?-catenin at 3.7 Å resolution. ?-Catenin forms an asymmetric dimer, where the four-helix bundle domains of each subunit engage in distinct intermolecular interactions. This results in a left handshake-like dimer, where the two subunits have remarkably different conformations. The crystal structure explains why dimeric ?-catenin has a higher affinity for F-actin than monomeric ?-catenin, why the ?-catenin–?-catenin complex does not bind to F-actin, how activated vinculin links the cadherin-catenin complex to the cytoskeleton, and why ?-catenin but not inactive vinculin can bind to F-actin. PMID:23292143

  18. On atom–atom ‘short contact’ bonding interactions in crystals1

    PubMed Central

    Lecomte, Claude; Espinosa, Enrique; Matta, Cherif F.

    2015-01-01

    Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom–atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context. PMID:25866651

  19. Nanomechanics and intermolecular forces of amyloid revealed by four-dimensional electron microscopy.

    PubMed

    Fitzpatrick, Anthony W P; Vanacore, Giovanni M; Zewail, Ahmed H

    2015-03-17

    The amyloid state of polypeptides is a stable, highly organized structural form consisting of laterally associated ?-sheet protofilaments that may be adopted as an alternative to the functional, native state. Identifying the balance of forces stabilizing amyloid is fundamental to understanding the wide accessibility of this state to peptides and proteins with unrelated primary sequences, various chain lengths, and widely differing native structures. Here, we use four-dimensional electron microscopy to demonstrate that the forces acting to stabilize amyloid at the atomic level are highly anisotropic, that an optimized interbackbone hydrogen-bonding network within ?-sheets confers 20 times more rigidity on the structure than sequence-specific sidechain interactions between sheets, and that electrostatic attraction of protofilaments is only slightly stronger than these weak amphiphilic interactions. The potential biological relevance of the deposition of such a highly anisotropic biomaterial in vivo is discussed. PMID:25733888

  20. Crossover from layering to island formation in Langmuir-Blodgett growth: Role of long-range intermolecular forces

    NASA Astrophysics Data System (ADS)

    Mukherjee, Smita; Datta, Alokmay

    2011-04-01

    Combined studies by atomic force microscopy, x-ray reflectivity, and Fourier transform infrared spectroscopy on transition-metal stearate (M-St, M = Mn, Co, Zn, and Cd) Langmuir-Blodgett films clearly indicate association of bidentate coordination of the metal-carboxylate head group to layer-by-layer growth as observed in MnSt and CoSt and partially in ZnSt. Crossover to islandlike growth, as observed in CdSt and ZnSt, is associated with the presence of unidentate coordination in the head group. Morphological evolutions as obtained from one, three, and nine monolayers (MLs) of M-St films are consistent with Frank van der Merwe, Stranski-Krastanov, and Volmer Weber growth modes for M=Mn/Co, Zn, and Cd, respectively, as previously assigned, and are found to vary with number (n) of metal atoms per head group, viz. n=1 (Mn/Co), n=0.75 (Zn), and n=0.5 (Cd). The parameter n is found to decide head-group coordination such that n=1.0 corresponds to bidentate and n=0.5 corresponds to unidentate coordination; the intermediate value in Zn corresponds to a mixture of both. The dependence of the growth mode on head-group structure is explained by the fact that in bidentate head groups, with the in-plane dipole moment being zero, intermolecular forces between adjacent molecules are absent and hence growth proceeds via layering. On the other hand, in unidentate head groups, the existence of a nonzero in-plane dipole moment results in the development of weak in-plane intermolecular forces between adjacent molecules causing in-plane clustering leading to islandlike growth.