Sample records for intermolecular dipole-dipole interactions

  1. 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.

  2. 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

  3. 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.

  4. Geometrical Simplification of the Dipole-Dipole Interaction Formula

    ERIC Educational Resources Information Center

    Kocbach, Ladislav; Lubbad, Suhail

    2010-01-01

    Many students meet dipole-dipole potential energy quite early on when they are taught electrostatics or magnetostatics and it is also a very popular formula, featured in encyclopedias. We show that by a simple rewriting of the formula it becomes apparent that, for example, by reorienting the two dipoles, their attraction can become exactly twice…

  5. Direct summation of dipole-dipole interactions using the Wolf formalism.

    PubMed

    Stenqvist, Björn; Trulsson, Martin; Abrikosov, Alexei I; Lund, Mikael

    2015-07-01

    We present an expanded Wolf formalism for direct summation of long-range dipole-dipole interactions and rule-of-thumbs how to choose optimal spherical cutoff (Rc) and damping parameter (?). This is done by comparing liquid radial distribution functions, dipole-dipole orientation correlations, particle energies, and dielectric constants, with Ewald sums and the Reaction field method. The resulting rule states that ?? < 1 and ?Rc > 3 for reduced densities around ?(?) = 1 where ? is the particle size. Being a pair potential, the presented approach scales linearly with system size and is applicable to simulations involving point dipoles such as the Stockmayer fluid and polarizable water models. PMID:26156467

  6. Interstrand Dipole-Dipole Interactions Can Stabilize the Collagen Triple Helix*S

    E-print Network

    Raines, Ronald T.

    Interstrand Dipole-Dipole Interactions Can Stabilize the Collagen Triple Helix*S Received sequence of collagen is composed of GlyXaaYaa repeats. A prevailing paradigm maintains that stable collagen. Anomalously, an amino acid sequence in an invertebrate collagen has (2S,4R)-4-hydroxy- proline (Hyp), a C -exo

  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. Geometrical simplification of the dipole-dipole interaction formula

    NASA Astrophysics Data System (ADS)

    Kocbach, Ladislav; Lubbad, Suhail

    2010-07-01

    Many students meet dipole-dipole potential energy quite early on when they are taught electrostatics or magnetostatics and it is also a very popular formula, featured in encyclopedias. We show that by a simple rewriting of the formula it becomes apparent that, for example, by reorienting the two dipoles, their attraction can become exactly twice as large. The physical facts are naturally known, but the transformation presented seems to underline the geometrical features in a rather unexpected way. The consequence of the features discussed is the so-called magic angle which appears in many applications. The present discussion contributes to an easier introduction of this feature. We also discuss the possibility of designing educational toys and try to suggest why this formula has not been written down frequently before this work. A similar transformation is also possible for the field of a single dipole. In this case we found one such formula on the Web, but we could not find any published detailed discussion for this case either.

  9. Effect of dipole-dipole interaction on self-control magnetization oscillation in double-domain nanomagnets

    NASA Astrophysics Data System (ADS)

    Gao, Y. J.; Guo, Y. J.; Liu, J.-M.

    2012-03-01

    A double-domain model with long-range dipole-dipole interaction is proposed to investigate the self-oscillation of magnetization in nano-magnetic systems driven by self-controlled spin-polarized current. The dynamic behavior of magnetization oscillation is calculated by a modified Landau-Lifshitz-Gilbert equation in order to evaluate the effects of the long-range dipole-dipole interaction. While the self-oscillation of magnetization can be maintained substantially, several self-oscillation regions are experienced as the dipole-dipole interaction increases gradually.

  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. Dipole-dipole interaction between a quantum dot and a graphene nanodisk

    NASA Astrophysics Data System (ADS)

    Cox, Joel D.; Singh, Mahi R.; Gumbs, Godfrey; Anton, Miguel A.; Carreno, Fernando

    2012-09-01

    We study theoretically the dipole-dipole interaction and energy transfer in a hybrid system consisting of a quantum dot and graphene nanodisk embedded in a nonlinear photonic crystal. In our model, a probe laser field is applied to measure the energy transfer between the quantum dot and graphene nanodisk, while a control field manipulates the energy transfer process. These fields create excitons in the quantum dot and surface plasmon polaritons in the graphene nanodisk which interact via the dipole-dipole interaction. Here, the nonlinear photonic crystal acts as a tunable photonic reservoir for the quantum dot, and is used to control the energy transfer. We have found that the spectrum of power absorption in the quantum dot has two peaks due to the creation of two dressed excitons in the presence of the dipole-dipole interaction. The energy transfer rate spectrum of the graphene nanodisk also has two peaks due to the absorption of these two dressed excitons. Additionally, energy transfer between the quantum dot and the graphene nanodisk can be switched on and off by applying a pump laser to the photonic crystal or by adjusting the strength of the dipole-dipole interaction. We show that the intensity and frequencies of the peaks in the energy transfer rate spectra can be modified by changing the number of graphene monolayers in the nanodisk or the separation between the quantum dot and graphene. Our results agree with existing experiments on a qualitative basis. The principle of our system can be employed to fabricate nanobiosensors, optical nanoswitches, and energy transfer devices.

  12. Dipole-dipole interaction between a quantum dot and graphene nanodisk

    E-print Network

    Joel D. Cox; Mahi R. Singh; Godfrey Gumbs; Miguel. A. Antón; Fernando Carreño

    2012-10-09

    We study theoretically the dipole-dipole interaction and energy transfer in a hybrid system consisting of a quantum dot and graphene nanodisk embedded in a nonlinear photonic crystal. In our model a probe laser field is applied to measure the energy transfer between the quantum dot and graphene nanodisk while a control field manipulates the energy transfer process. These fields create excitons in the quantum dot and surface plasmon polaritons in the graphene nanodisk which interact via the dipole-dipole interaction. Here the nonlinear photonic crystal acts as a tunable photonic reservoir for the quantum dot, and is used to control the energy transfer. We have found that the spectrum of power absorption in the quantum dot has two peaks due to the creation of two dressed excitons in the presence of the dipole-dipole interaction. The energy transfer rate spectrum of the graphene nanodisk also has two peaks due to the absorption of these two dressed excitons. Additionally, energy transfer between the quantum dot and the graphene nanodisk can be switched on and off by applying a pump laser to the photonic crystal or by adjusting the strength of the dipole-dipole interaction. We show that the intensity and frequencies of the peaks in the energy transfer rate spectra can be modified by changing the number of graphene monolayers in the nanodisk or the separation between the quantum dot and graphene. Our results agree with existing experiments on a qualitative basis. The principle of our system can be employed to fabricate nano-biosensors, optical nano-switches, and energy transfer devices.

  13. 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.

  14. Symmetric-cycle pulse sequence for dynamical decoupling of local fields and dipole–dipole interactions

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    We have proposed a new pulse sequence for the dynamical decoupling of decoherence effects in the ensemble of nuclear spins. The sequence provides a symmetric cycle that offers a strong suppression of the decoherence effects caused by the dipole–dipole interactions and the inhomogeneous local magnetic fields in nuclear spin ensemble dynamics. We have discussed a potential of the proposed pulse sequence for the long-lived storage of the multi-qubit quantum states.

  15. Effects of dipole-dipole interaction between cigar-shaped BECs of cold alkali atoms: towards inverse-squared interactions

    NASA Astrophysics Data System (ADS)

    Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

    2014-07-01

    We show that the dipole-dipole coupling between Wannier modes in cigar-shaped Bose-Einstein condensates (BECs) is significantly enhanced while the short-range coupling is strongly suppressed. As a result, the dipole-dipole interaction can become the dominant interaction between ultracold alkali Bose atoms. In the long length limit of a cigar-shaped BEC, the resulting effective one-dimensional models possess an effective inverse squared interacting potential, the Calogero-Sutherland potential, which plays a fundamental role in many fields of contemporary physics; but its direct experimental realization has been a challenge for a long time. We propose to realize the Calogero-Sutherland model in ultracold alkali Bose atoms and study the effects of the dipole-dipole interaction.

  16. 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.

  17. Entanglement between two atoms in the presence of dipole-dipole interaction and atomic coherence

    NASA Astrophysics Data System (ADS)

    Bashkirov, Eugene K.; Litvinova, Darya V.

    2015-03-01

    We have investigated the influence of dipole-dipole interaction and initial atomic coherence on dynamics of two-atom systems. We have considered a model, in which only one atom is trapped in a cavity, and the other one can be spatially moved freely outside the cavity. We have shown the possibility of disappearance of the entanglement sudden death effect in the presence of the dipole interaction of atoms. We have also derived that the initial atomic coherence can be used for effective control of the degree of the atom-atom entanglement.

  18. Stability of superflow in supersolid phases of lattice bosons with dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Yamamoto, Daisuke; Danshita, Ippei

    2011-01-01

    We investigate the stability of superflow of bosons with isotropic dipole-dipole interactions in a two-dimensional optical lattice. We perform linear stability analyses for the dipolar Bose-Hubbard model in the hardcore boson limit, and show that the superflow can exist in a supersolid phase unless the velocity exceeds a certain critical value and that the critical value is remarkably smaller than that in the standard superfluid phase. Additionally, it is found that there exists a parameter range in which the SS phases are stabilized by a finite superflow. We also discuss the influence of quantum fluctuations on these results within the cluster mean-field approximation.

  19. Spatially Resolved Observation of Dipole-Dipole Interaction between Rydberg Atoms

    SciTech Connect

    Ditzhuijzen, C. S. E. van; Noordam, L. D.; Heuvell, H. B. van Linden van den [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Koenderink, A. F. [FOM-Institute for Atomic and Molecular Physics, Kruislaan 407, 1098 SJ Amsterdam (Netherlands); Hernandez, J. V.; Robicheaux, F. [Department of Physics, Auburn University, Alabama 36849-5311 (United States)

    2008-06-20

    We have observed resonant energy transfer between cold Rydberg atoms in spatially separated cylinders. Resonant 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. We have measured the production of the 49p state as a function of separation of the cylinders (0-80 {mu}m) and the interaction time (0-25 {mu}s). In addition, we measured the width of the electric field resonances. A full many-body quantum calculation reproduces the main features of the experiments.

  20. PHYSICAL REVIEW A 88, 013616 (2013) Effective dipole-dipole interactions in multilayered dipolar Bose-Einstein condensates

    E-print Network

    Bao, Weizhu

    2013-01-01

    -dipole interaction (DDI) between the underlying particles. The study of magnetic single- and multilayer films has.g., hard disks or magnetic sensors. One theoretical goal of studying multilayers is to illuminatePHYSICAL REVIEW A 88, 013616 (2013) Effective dipole-dipole interactions in multilayered dipolar

  1. Self-assembled microspheres driven by dipole-dipole interactions: UCST-type transition in water.

    PubMed

    Morimoto, Nobuyuki; Muramatsu, Kanna; Wazawa, Tetsuichi; Inoue, Yuichi; Suzuki, Makoto

    2014-01-01

    A double hydrophilic block copolymer, poly(ethylene glycol)-poly(3-dimethyl (methacryloyloxyethyl) ammonium propane sulfonate) (PEG-SB), is synthesized by reversible addition-fragmentation transfer (RAFT) polymerization using PEG methyl ether (4-cyano-4-pentanoate dodecyl trithiocarbonate) as a chain transfer agent. PEG-SB forms multi-layered microspheres with dipole-dipole interactions of the SB side chains as the driving force. The PEG-SB polymers show an upper critical solution temperature (UCST) and the UCST is controllable by the polymerization degree. The PEG-SB microspheres are dissociated above the UCST and then monodispersed microspheres (?1 ?m) are obtained when the solution temperature is decreased below the UCST again. The disassociation/association of the microspheres is also controllable using the concentration of NaCl. These multi-responsive microspheres could be a powerful tool in the field of nano-biotechnology. PMID:24307305

  2. Effect of resonance dipole-dipole interaction on spectra of adsorbed SF6 molecules.

    PubMed

    Dobrotvorskaia, Anna N; Kolomiitsova, Tatiana D; Petrov, Sergey N; Shchepkin, Dmitriy N; Smirnov, Konstantin S; Tsyganenko, Alexey A

    2015-09-01

    Adsorption of SF6 on zinc oxide and on silicalite-1 was investigated by a combination of IR spectroscopy with the calculations of spectra by means of a modernized model, developed previously for liquids. Comparison of the experimental spectra and the results of modeling shows that the complex band shapes in spectra of adsorbed molecules with extremely high absorbance are due to the strong resonance dipole-dipole interaction (RDDI) rather that the surface heterogeneity or the presence of specific surface sites. Perfect agreement between calculated and observed spectra was found for ZnO, while some dissimilarity in band intensities for silicalite-1 was attributed to complicated geometry of molecular arrangement in the channels. PMID:25897721

  3. 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

  4. 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.

  5. Variational Calculations for the Effects of Magnetic Dipole-Dipole Interaction in Bose-Einstein Condensates

    NASA Astrophysics Data System (ADS)

    Olson, Abraham; Chen, Yong P.

    2010-03-01

    Employing previously developed variational calculation techniques [1, 2], we explore various possibilities for observing effects of magnetic dipole-dipole interaction (MDDI) in Bose-Einstein condensates (BECs). The effects of MDDI on both in-trap and time-of-flight expansion dynamics are investigated, as well as effects on condensate stability. The variational calculation has been verified to agree well with experimental data in Cr^52[3] and Li^7[4]. Using current knowledge of Feshbach resonances, we determine the experimental accessibility of observing MDDI effects for the bosonic alkalis and find most favorable results for Li^7, K^39, and Cs^133. We also present calculations for Dy and Er, motivated by advances in cooling such high magnetic moment species. These results would be useful to experimentalists working on dipolar quantum gases. [4pt] [1] S. Yi and L. You, Phys. Rev. A, 63, 053607 (2001)[0pt] [2] T. Koch et al. Nature Physcis 4, 218-222 (2008)[0pt] [3] T. Lahaye et al. Nature 448, 672-675 (2007)[0pt] [4] S.E. Pollack et al. Phys. Rev. Lett. 102, 090402 (2009).

  6. Dipole-Dipole Interactions of High-spin Paramagnetic Centers in Disordered Systems

    SciTech Connect

    Maryasov, Alexander G.; Bowman, Michael K.; Tsvetkov, Yuri D.

    2007-09-13

    Dipole-dipole interactions between distant paramagnetic centers (PCs) where at least one PC has spin S>1/2 are examined. The results provide a basis for the application of pulsed DEER or PELDOR methods to the measurement of distances between PC involving high-spin species. A projection operator technique based on spectral decomposition of the secular Hamiltonian is used to calculate EPR line splitting caused by the dipole coupling. This allows calculation of operators projecting arbitrary wavefunction onto high PC eigenstates when the eigenvectors of the Hamiltonian are not known. The effective spin vectors-that is, the expectation values for vector spin operators in the PC eigenstates-are calculated. The dependence of these effective spin vectors on the external magnetic field is calculated. There is a qualitative difference between pairs having at least one integer spin (non Karmers PC) and pairs of two half-integer (Kramers PC) spins. With the help of these effective spin vectors, the dipolar lineshape of EPR lines is calculated. Analytical relations are obtained for PCs with spin S=1/2 and 1. The dependence of Pake patterns on variations of zero field splitting, Zeeman energy, temperature and dipolar coupling are illustrated.

  7. Role of dipole-dipole interaction on enhancing Brownian coagulation of charge-neutral nanoparticles in the free molecular regime.

    PubMed

    Zhang, Yiyang; Li, Shuiqing; Yan, Wen; Yao, Qiang; Tse, Stephen D

    2011-02-28

    In contrast to van der Waals (vdW) forces, Coulombic dipolar forces may play a significant role in the coagulation of nanoparticles (NPs) but has received little or no attention. In this work, the effect of dipole-dipole interaction on the enhancement of the coagulation of two spherically shaped charge-neutral TiO(2) NPs, in the free molecular regime, is studied using classical molecular dynamics (MD) simulation. The enhancement factor is evaluated by determining the critical capture radius of two approaching NPs for different cases of initial dipole direction with respect to path (parallel?perpendicular) and orientation with respect to each other (co-orientated?counterorientated). As particle diameter decreases, the enhancement of coagulation is augmented as the ratio of dipole-dipole force to vdW force becomes larger. For 2-nm TiO(2) NPs at 273 K, the MD simulation predicts an average enhancement factor of about 8.59, which is much greater than the value of 3.78 when only the vdW force is considered. Nevertheless, as temperature increases, the enhancement factor due to dipole-dipole interaction drops quickly because the time-averaged dipole moment becomes small due to increased thermal fluctuations (in both magnitude and direction) of the instantaneous dipole moment. PMID:21361545

  8. Role of dipole-dipole interaction on enhancing Brownian coagulation of charge-neutral nanoparticles in the free molecular regime

    NASA Astrophysics Data System (ADS)

    Zhang, Yiyang; Li, Shuiqing; Yan, Wen; Yao, Qiang; Tse, Stephen D.

    2011-02-01

    In contrast to van der Waals (vdW) forces, Coulombic dipolar forces may play a significant role in the coagulation of nanoparticles (NPs) but has received little or no attention. In this work, the effect of dipole-dipole interaction on the enhancement of the coagulation of two spherically shaped charge-neutral TiO2 NPs, in the free molecular regime, is studied using classical molecular dynamics (MD) simulation. The enhancement factor is evaluated by determining the critical capture radius of two approaching NPs for different cases of initial dipole direction with respect to path (parallel/perpendicular) and orientation with respect to each other (co-orientated/counterorientated). As particle diameter decreases, the enhancement of coagulation is augmented as the ratio of dipole-dipole force to vdW force becomes larger. For 2-nm TiO2 NPs at 273 K, the MD simulation predicts an average enhancement factor of about 8.59, which is much greater than the value of 3.78 when only the vdW force is considered. Nevertheless, as temperature increases, the enhancement factor due to dipole-dipole interaction drops quickly because the time-averaged dipole moment becomes small due to increased thermal fluctuations (in both magnitude and direction) of the instantaneous dipole moment.

  9. 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.

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

    E-print Network

    Sang Jae Yun; Jaewan Kim; Chang Hee Nam

    2015-03-30

    In quantum information processing, one of the most useful interaction 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, controlled-Z gate time will be 8.5 ms. We suggest diverse search and study to achieve optimal implementation of this scheme.

  11. 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.

  12. Bright solitons in the one-dimensional discrete Gross-Pitaevskii equation with dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Gligori?, Goran; Maluckov, Aleksandra; Hadžievski, Ljup?o; Malomed, Boris A.

    2008-12-01

    A model of the Bose-Einstein condensate of dipolar atoms, confined in a combination of a cigar-shaped trap and deep optical lattice acting in the axial direction, is introduced, taking into regard the dipole-dipole (DD) and contact interactions. The model is based on the discrete nonlinear Schrödinger equation with an additional nonlocal term accounting for the DD interactions. The existence and stability of fundamental unstaggered solitons are studied for attractive and repulsive signs of both the local and nonlocal interactions. The DD forces strongly affect the shape and stability of on-site and intersite discrete solitons. The corresponding existence and stability regions in the parametric space are summarized in the form of diagrams, which feature a multiple stability exchange between the on-site and intersite families; in the limit of the dominating DD attraction, the on-site solitons are stable, while their intersite counterparts are not. We also demonstrate that the DD interactions reduce the Peierls-Nabarro barrier and enhance the mobility of the discrete solitons.

  13. The influence of dipole-dipole interaction on entanglement in nondegenerate two-photon Tavis-Cummings model with atomic coherence

    E-print Network

    E. K. Bashkirov; M. S. Mastuygin

    2012-10-13

    The entanglement of two dipole-coupled atoms with nondegenerate two-photon transitions interacting with two-mode field in lossless cavity has been investigated. It shows that the entanglement is dependent on the initial atomic states. The possibility of considerable growth of atomic entanglement due atomic coherence and dipole-dipole interaction is shown in the case of great mean values of thermal photons.

  14. Creation of entanglement in a scalable spin quantum computer with long-range dipole-dipole interaction between qubits

    E-print Network

    D. I. Kamenev; G. P. Berman; V. I. Tsifrinovich

    2006-03-24

    Creation of entanglement is considered theoretically and numerically in an ensemble of spin chains with dipole-dipole interaction between the spins. The unwanted effect of the long-range dipole interaction is compensated by the optimal choice of the parameters of radio-frequency pulses implementing the protocol. The errors caused by (i) the influence of the environment,(ii) non-selective excitations, (iii) influence of different spin chains on each other, (iv) displacements of qubits from their perfect locations, and (v) fluctuations of the external magnetic field are estimated analytically and calculated numerically. For the perfectly entangled state the z component, M, of the magnetization of the whole system is equal to zero. The errors lead to a finite value of M. If the number of qubits in the system is large, M can be detected experimentally. Using the fact that M depends differently on the parameters of the system for each kind of error, varying these parameters would allow one to experimentally determine the most significant source of errors and to optimize correspondingly the quantum computer design in order to decrease the errors and M. Using our approach one can benchmark the quantum computer, decrease the errors, and prepare the quantum computer for implementation of more complex quantum algorithms.

  15. 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).

  16. Dipole-dipole interaction and anisotropy effects in the itinerant oscillator model

    NASA Astrophysics Data System (ADS)

    Coffey, W. T.

    1997-10-01

    The itinerant oscillator model whereby a typical molecule of a polar fluid may exhibit librational motion under the influence of the field of its large cage of neighboring dipoles is examined when the restriction of rotation about a common fixed axis is removed, both cage and tagged molecule now being free to rotate about a common fixed point of themselves. It is shown that the equations of motion of the system cannot, in general, be decomposed into the equations of motion of the tagged molecule relative to the cage and that of the cage alone on account of the Coriolis torques. If, however, one can make the assumption that the cage is much more massive than the tagged molecule so that in a short time (essentially a time less than the Debye relaxation time of the cage so that the cage represents a slowly relaxing local structure) after the removal of an external uniform field the cage remains virtually at rest relative to the tagged molecule, then the dipole autocorrelation function of the tagged molecule is approximately the product of the autocorrelation function of the cage and the autocorrelation functions of the motion of the tagged molecule relative to the cage. The behavior of the model, with a cage-dipole interaction potential including both the permanent and induced dipole terms in the noninertial limit is discussed using the above assumption. It is shown that the inclusion of the induced dipole term essentially creates an asymmetric bistable interaction potential in which a relaxation process indicative of a slow overbarrier (activation) process coexists with the relatively fast relaxation modes in the wells of the potentials [as predicted by Polemino and Freed, Adv. Chem. Phys. 83, 89 (1993) in their numerical analysis of the model]. The conditions under which the fast relaxation processes may come to dominate the overall relaxation behavior are discussed by analogy with superparamagnetic relaxation [cf. Coffey, Crothers, and Kalmykov, Phys. Rev. E 55, 4812 (1997)].

  17. Two-dimensional array of particles originating from dipole-dipole interaction as evidenced by potential curve measurements at vertical oil/water interfaces.

    PubMed

    Sakka, Tetsuo; Kozawa, Daichi; Tsuchiya, Kiyoto; Sugiman, Nao; Øye, Gisle; Fukami, Kazuhiro; Nishi, Naoya; Ogata, Yukio H

    2014-08-28

    We propose a new method to evaluate the interaction potential energy between the particles adsorbed at an oil/water interface as a function of interparticle distance. The method is based on the measurement of the interparticle distance at a vertical oil/water interface, at which the gravitational force is naturally applied to compress the particle monolayer in the in-plane direction. We verified the method by examining whether we obtained the same potential curve upon varying the gravitational acceleration by tilting the interface. The present method is applicable in the force range from ?0.1 to ?100 pN, determined by the effective weight of the particles at the interface. The method gives a rather simple procedure to estimate a long range interaction among the particles adsorbed at oil/water interfaces. We applied this method to polystyrene particles at the decane/aqueous surfactant solution interface, and obtained the interparticle potential curves. All the potential curves obtained by the present method indicated that the interparticle repulsion is due to the electrical dipole-dipole interaction based on the negative charge of the particles. The mechanism of the dipole-dipole interaction is further discussed on the basis of the effects of surfactants. PMID:25005863

  18. 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 October 2005; published 5 June 2006 Laser-cooled 85 Rb atoms were optically excited to 46d5/2 Rydberg states. A microwave pulse transferred a fraction of the atoms to the 47p3/2 Rydberg state. The resonant

  19. Application of analytical and numerical methods to simulation of systems with orientation interactions

    NASA Astrophysics Data System (ADS)

    Petrova, T. O.; Maksimova, O. G.; Gerasimov, R. A.; Maksimov, A. V.

    2012-05-01

    The effect of temperature and intermolecular interaction constants on the short-range orientational order in two-dimensional films with a dipole-dipole potential has been investigated using the variational method and the Monte Carlo method. The parameters of the long-range order in three-dimensional systems with dipole-dipole and quadrupole potentials have been computed.

  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. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. Intermolecular interaction from biorthogonal orbitals: new developments

    NASA Astrophysics Data System (ADS)

    Weck, Gaétan; Kochanski, Elise; Gouyet, Jean-François

    New developments to compute the intermolecular interaction between two subsystems are proposed. They are based on biorthogonal orbitals and second quantization techniques. Test calculations have been performed on some geometrical configurations of a water dimer and on the strongly H-bonded OH-(H2O) system. All second-order intermolecular and mixed (inter-intra) terms are included. The results are compared with previously published SAPT calculations and with MP2 supermolecule treatment. They are all generally in good agreement. However, the description of the repulsive wall is sensitive to the quality of the basis set. The choice of a suitable basis set for the strongly H-bonded system is especially delicate.

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

    NASA Astrophysics Data System (ADS)

    Berezovsky, Igor N.

    2011-06-01

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

  9. 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

    . 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

  10. Interactions Between Thermal Ground or Excited Atoms in the Vapor Phase: Many-Body Dipole–Dipole Effects, Molecular Dissociation, and Photoassociation Probed By Laser Spectroscopy

    Microsoft Academic Search

    J. G. Eden; B. J. Ricconi; Y. Xiao; F. Shen; A. A. Senin

    2008-01-01

    Atom–atom and atom–molecule interactions in the absence or presence of an optical radiation field are among the fundamental processes in atomic, molecular, and optical physics. This review addresses recent advances that provide insight into the dynamics of many-body fipole–dipole interactions between excited atoms at long range, and the production of a transient molecule from a pair of thermal, ground state

  11. Intermolecular Forces (Netorials)

    NSDL National Science Digital Library

    Intermolecular Forces: this is a resource in the collection "Netorials". In this resource there is a review of Lewis structures, molecular geometry, electronegativity, or molecular polarity. After that, you can learn about the forces of attraction that exist between molecules. This module explores London forces and dipole-dipole forces (including hydrogen bonds). The Netorials cover selected topics in first-year chemistry including: Chemical Reactions, Stoichiometry, Thermodynamics, Intermolecular Forces, Acids & Bases, Biomolecules, and Electrochemistry.

  12. Spatiotemporal Dynamics of Quantum Computing Solid Dipole-Dipole Block Systems

    Microsoft Academic Search

    Hideaki Matsueda

    1998-01-01

    This paper enstimates the stability of dipole-dipole interaction in quantum dot array, and proposes a novel solid state quantum\\u000a CCN (controlled controlled not) gate having a block structure, which is effective to maintain quantum mechanical coherence\\u000a and reduce both the bit error and the phase error. The spatiotemporal dynamics of quantum computation process involving the\\u000a quantum entangled pure states is

  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. 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.

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

    SciTech Connect

    Chang, D.E.; Lukin, M.D. [Department of Physics, Harvard University, Cambridge, Massachusetts, 02138 (United States); Ye Jun [JILA, National Institute of Standards and Technology and University of Colorado, Boulder, Colorado 80309-0440 (United States)

    2004-02-01

    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 resonancelike 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. Dipole-Dipole Correlations for the sine-Gordon Model

    E-print Network

    Guowei Zhao

    2011-08-16

    We consider the dipole-dipole correlations for the two-dimensional Coulomb gas/sine-Gordon model for $\\beta> 8\\pi$ by a renormalization group method. First we re-establish the renormalization group analysis for the partition function using finite range decomposition of the covariance. Then we extend the analysis to the correlation functions. Finally, we show a power-law decay characteristic of the dipole gas.

  18. Influence of dipole-dipole correlations on the stability of the biaxial nematic phase in the model bent-core liquid crystal.

    PubMed

    Osipov, Mikhail A; Paj?k, Grzegorz

    2012-04-11

    A molecular theory of biaxial nematic ordering in the system of bent-core molecules has been developed in the two-particle cluster approximation which enables one to take into account short-range polar correlations determined by both electrostatic dipole-dipole interaction and polar molecular shape. All orientational order parameters and short-range correlation functions are calculated numerically as functions of temperature in the uniaxial and in the biaxial nematic phases, and the results are compared with the ones obtained in the mean-field approximation and in the cluster approximation but without taking into consideration the dipole-dipole interaction. It is shown that short-range polar correlations and, in particular, the dipole-dipole correlations dramatically increase the temperature of the transition into the biaxial nematic phase and enhancing its stability range. The results are also very sensitive to the value of the opening angle of a model bent-core molecule. PMID:22388661

  19. Probing Intermolecular Interactions with Picosecond Photon Echo Experiments

    E-print Network

    Fayer, Michael D.

    as vibrations of the lattice, i.e., acoustic and optical phonons.2 Acoustic phonons Probing Intermolecular Interactions with Picosecond Photon Echo Experiments CECILIAA. WALSH. In the picosecond photon echo experiments presented below, the samples are mixed molecular crystals or organic

  20. Intermolecular interactions in electrospun collagen–chitosan complex nanofibers

    Microsoft Academic Search

    Zonggang Chen; Xiumei Mo; Chuanglong He; Hongsheng Wang

    2008-01-01

    The collagen–chitosan complex nanofibers have been prepared here by electrospinning. Intermolecular interactions in electrospun collagen–chitosan complex fibers have been studied by Fourier transform infrared spectroscopy (FT-IR), differential scanning calorimetry (DSC) and the mechanical measurements of single ultrafine fiber. It was found that the –OH group, the –NH2 group and the amide I, II and III characteristic absorption bands in FT-IR

  1. A charge density study of ?-delocalization and intermolecular interactions.

    PubMed

    Wu, L-C; Chung, W-C; Wang, C-C; Lee, G-H; Lu, S-I; Wang, Y

    2015-06-01

    The compound trans-4,4'-azo-1,2,4-triazole (atrz) is a planar molecule with two planar triazole rings bridged by an azo group. The molecule is a good donor ligand and has an interesting ?-delocalized character. In addition, intermolecular interactions in the crystalline state through ?-? stacking are found between triazole rings with a very short inter-planar distance of 3.17 Å. The electron density distribution is obtained from both high resolution X-ray diffraction data at 100 K and density functional theory (DFT) calculations using the ?B97X-D functional. Bond characterization is performed in terms of the charge density distribution and the associated topological properties. The Laplacian distribution around each atom reveals the shape of the valence-shell charge concentration and demonstrates a sp(2) hybrid orbital shape for each atom in the molecule. The ?-delocalization of the planar molecule is further illustrated by the Fermi-hole distribution. The weak intermolecular ?-? interactions and hydrogen bonds are further illustrated by the Hirshfeld surface. The energies of weak intermolecular ?-? interactions and hydrogen bonds have been calculated using ?B97X-D/6-311++G(3df,2p) at experimental geometry. PMID:25959566

  2. 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

  3. Intermolecular interactions and the thermodynamic properties of supercritical fluids

    NASA Astrophysics Data System (ADS)

    Yigzawe, Tesfaye M.; Sadus, Richard J.

    2013-05-01

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

  4. Modulation of intermolecular interactions in single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Heroux, Katie Jeanne

    Polynuclear manganese clusters exhibiting interesting magnetic and quantum properties have been an area of intense research since the discovery of the first single-molecule magnet (SMM) in 1993. These molecules, below their blocking temperature, function as single-domain magnetic particles which exhibit classical macroscale magnetic properties as well as quantum mechanical phenomena such as quantum tunnelling of magnetization (QTM) and quantum phase interference. The union of classical and quantum behavior in these nanomaterials makes SMMs ideal candidates for high-density information storage and quantum computing. However, environmental coupling factors (nuclear spins, phonons, neighboring molecules) must be minimized if such applications are ever to be fully realized. The focus of this work is making small structural changes in well-known manganese SMMs in order to drastically enhance the overall magnetic and quantum properties of the system. Well-isolated molecules of high crystalline quality should lead to well-defined energetic and spectral properties as well. An advantage of SMMs over bulk magnetic materials is that they can be chemically altered from a "bottom-up" approach providing a synthetic tool for tuning magnetic properties. This systematic approach is utilized in the work presented herein by incorporating bulky ligands and/or counterions to "isolate" the magnetic core of [Mn4] dicubane SMMs. Reducing intermolecular interactions in the crystal lattice (neighboring molecules, solvate molecules, dipolar interactions) is an important step toward developing viable quantum computing devices. Detailed bulk magnetic studies as well as single crystal magnetization hysteresis and high-frequency EPR studies on these sterically-isolated complexes show enhanced, and sometimes even unexpected, quantum dynamics. The importance of intra- and intermolecular interactions remains a common theme throughout this work, extending to other SMMs of various topology including large wheel-shaped complexes, hexanuclear rods, and even small dinuclear species.

  5. Very strong metal ligand aromatic cation-? interactions in transition metal complexes: intermolecular interaction in tetraphenylborate salts

    Microsoft Academic Search

    Miloš K. Mil?i?; Zoran D. Tomi?; Snežana D. Zari?

    2004-01-01

    Strong intermolecular interactions between ligands in cationic metal complexes and aromatic rings of tetraphenylborate anion, so-called metal ligand aromatic cation-? (MLAC?) interactions, were found by screening Cambridge Structural Database. Distances between phenyl ring and ligand are shorter in these structures than in previously reported MLAC? interactions by 0.2 Å.

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

    E-print Network

    2013-07-10

    Jul 10, 2013 ... Assuming Gaussian layer width, we also derive closed forms of the effective 2D ... We note that it is possible to modify the DDI strength cdd by means of a rotating .... and drops exponentially for short wavelengths. It has been.

  8. Supplemental Data Interstrand DipoleDipole Interactions Can Stabilize

    E-print Network

    Raines, Ronald T.

    Cl) refer to saturated aqueous solutions. Flash chromatography was performed with columns of silica gel 60 of Chemistry. Representative Procedure for the Synthesis of Boc-Yaa-OBn--A solution of Cs2CO3 (5.4 mmol) in water (31 ml) at 0 °C was added to a solution of Boc-Yaa-OH (10.7 mmol) in MeOH (41 ml) at 0 °C

  9. 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…

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

    SciTech Connect

    Castner, E.W. Jr.; Chang, Y.J. [Brookhaven National Lab., Upton, NY (United States); Melinger, J.S.; McMorrow, D. [Naval Research Lab., Washington, DC (US)

    1993-07-01

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

  11. Identification and measurement of intermolecular interaction in polyester/polystyrene blends by FTIR-photoacoustic spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fourier transform infrared photoacoustic spectrometry was used to reveal and identify n-p type intermolecular interaction formed in plastic comprising binary blends of polystyrene and a biodegradable polymer, either polylactic acid, polycaprolactone or poly(tetramethyleneadipate-co-terephthalate)....

  12. Influence of intermolecular interactions on spectroscopic characteristics of metal nanoparticles and their composites.

    PubMed

    Shaganov, Igor I; Perova, Tatiana S; Mukhina, Maria V; Martynenko, Irina V; Baranov, Alexander V; Fedorov, Anatoly V; Gerard, Valerie; Gun'ko, Yuri K

    2014-11-28

    In this paper we investigate the possibility to apply the concepts of non-specific intermolecular interactions and dispersive local field effect approach for study of the influence of interactions of metal nanoparticles with matrix molecules on the spectral characteristics of composites. The effect of intermolecular (interparticle) interactions and the influence of the dielectric environment on the peak position of the plasmon resonance band of colloidal solutions and thin films formed from noble metal nanostructures is determined. Simulated and experimental absorption spectra obtained for a colloidal solution of silver and gold nanoparticles, of various shapes and sizes in water and glycerol, are in good agreement. PMID:25310112

  13. Communication: Density functional theory overcomes the failure of predicting intermolecular interaction energies

    SciTech Connect

    Podeszwa, Rafal [Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice (Poland); Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716 (United States); Szalewicz, Krzysztof [Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice (Poland)

    2012-04-28

    Density-functional theory (DFT) revolutionized the ability of computational quantum mechanics to describe properties of matter and is by far the most often used method. However, all the standard variants of DFT fail to predict intermolecular interaction energies. In recent years, a number of ways to go around this problem has been proposed. We show that some of these approaches can reproduce interaction energies with median errors of only about 5% in the complete range of intermolecular configurations. Such errors are comparable to typical uncertainties of wave-function-based methods in practical applications. Thus, these DFT methods are expected to find broad applications in modelling of condensed phases and of biomolecules.

  14. Silicone\\/polypropylene oxide-polyethylene oxide copolymer\\/clay composites (i) - curing behavior, intermolecular interaction and thermomechanical properties

    Microsoft Academic Search

    Hsien-Tang Chiu; Jyh-Horng Wu

    2005-01-01

    This research explores the dispersion pattern, curing behavior and intermolecular interaction of liquid silicone, polypropylene oxide-polyethylene oxide copolymer and clay composites. It analyzes the curing behavior of each component composite by means of the rigid-body pendulum rheometer, and then it is followed by the exploration of the intermolecular interaction with the dynamic mechanical analysis. Results show that the polymer chains

  15. Molecular Structure and Intermolecular Interactions of N1'-Methoxycarbonylbiotin Methyl Ester: A Model for Carboxybiotin

    Microsoft Academic Search

    William C. Stallings; C. T. Monti; George T. Detitta

    1980-01-01

    The crystal structure of N1'-methoxycarbonylbiotin methyl ester, a model for N1'-carboxybiotin, has been determined. The ureido carbonyl bond has more double bond (keto) character than does the corresponding bond in free biotin, which has single bond (enolate) character. In addition, there is an interesting intermolecular interaction between the ureido carbonyl oxygen and a methyl group. Comparison of the molecular structure

  16. Intermolecular interactions of the malate synthase of Paracoccidioides spp

    PubMed Central

    2013-01-01

    Background The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell. PMID:23672539

  17. Assessing intermolecular RNA:RNA interactions within a ribonucleoprotein complex using heavy metal cleavage mapping.

    PubMed

    Gagnon, Keith T; Maxwell, E Stuart

    2015-01-01

    Heavy metal cleavage mapping analysis of both assembling and fully mature ribonucleoprotein (RNP) complexes are informative techniques for assessing the intermolecular base pairing between small non-coding RNAs and their interacting target RNAs. Lead cleavage of the RNA in partially or fully assembled RNPs in the absence or presence of the interacting RNA can determine both the accessibility of the base pairing sequence within the RNP itself as well as its interaction with the target RNA. In this chapter, we detail how this technique was used to map the intermolecular RNA:RNA base pairing of a box C/D RNA with its target RNA within the assembling archaeal RNP complex. PMID:25352141

  18. 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.

  19. 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.

  20. Intermolecular interactions between cucurbit[7]uril and pilocarpine.

    PubMed

    Saleh, Na'il; Al-Handawi, Marieh B; Al-Kaabi, Leena; Ali, Liaquat; Salman Ashraf, S; Thiemann, Thies; Al-Hindawi, Bassam; Meetani, Mohammed

    2014-01-01

    The interactions between cucurbit[7]uril (CB7) macrocycles and pilocarpine (PIL) were investigated in aqueous solution by using (1)H NMR and circular dichroism (CD) spectroscopic techniques. The characterizations of the freeze-drying solid complex were conducted by electrospray ionization mass spectroscopy (ESI-MS), Fourier transform-infrared spectroscopy (FT-IR), thermogravimetry, and differential scanning calorimetry (DSC) techniques. The DSC and thermogravimetry confirmed the production of a thermally stable solid complex. The NMR, CD and ESI-MS measurements confirmed asymmetric induction during the complexation reaction, in which the ?-lactone ring of PIL (not the imidazole nucleus) has been fully encapsulated within the cavity of CB7. The stability of the drug has significantly enhanced as evidenced by the high-performance liquid chromatographic (HPLC) method. The results are discussed in the context of utilizing non-conventional supramolecular host-guest approaches to enhance the chemical stability in aqueous media of hydrophilic PIL drugs as model compounds. The non-classical stereospecific interactions between CB7 and PIL drugs are also highlighted. PMID:24239578

  1. 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.

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

    PubMed

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

    2015-07-01

    The study highlights the balance of the intermolecular forces governing the interaction between drugs and mucin. The interaction strength is expressed as a retention factor k (data retrieved from the literature (Gargano et al., 2014)) obtained by a new bio-affinity chromatographic method in which the stationary phase is based on covalently immobilized mucin (porcine gastric mucin, PGM). A quantitative structure-property relationship (QSPR) between logk and 82 VolSurf+ descriptors was established and mechanistically interpreted. Results evidence that all blocks contribute similarly to the model; moreover, hydrogen bonding donor (HBD) properties of solutes favor the interaction with mucin; and thus, support their detrimental role on drug permeability. PMID:25907510

  3. Intermolecular interactions between a Ru complex and organic dyes in cosensitized solar cells: a computational study.

    PubMed

    Kusama, Hitoshi; Funaki, Takashi; Koumura, Nagatoshi; Sayama, Kazuhiro

    2014-08-14

    Intermolecular interactions in cyclometalated Ru complex dye (FT89) dimers, carbazole organic dye (MK-45 and MK-111) dimers, FT89-MK-45 complexes, and FT89-MK-111 complexes were investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) to elucidate the improvement mechanism of dye-sensitized solar cell (DSSC) performance due to cosensitization with FT89 and MK dyes. All of the dimers and complexes form intermolecular cyclic hydrogen bonds via the carboxyl groups. The FT89 dimer and complexes with the TiO2Na model system promote intermolecular interactions with I2via the NCS ligand of the FT89 monomer. The computational results verify that MK-111 behaves not only as a sensitizer but also inhibits FT89 aggregation by effectively serving as a coadsorbent similar to deoxycholic acid (DCA) in the dye solution, suppressing recombination of the injected electrons in TiO2 with I2, improving DSSC performance. PMID:24968132

  4. 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.

  5. Intermolecular interactions of IgG1 monoclonal antibodies at high concentrations characterized by light scattering.

    PubMed

    Scherer, Thomas M; Liu, Jun; Shire, Steven J; Minton, Allen P

    2010-10-14

    Light scattering intensity measurements of solutions of two purified monoclonal antibodies were performed over a wide range of concentrations (0.5-275 mg/mL) and ionic strengths (0.02 to 0.6 M). Despite extensive sequence homology between these mAbs, alteration of ?20 amino acids in the complementarity determining regions resulted in different net intermolecular interactions and responses to solution ionic strength. The concentration dependence of scattering was analyzed by comparison with the predictions of three models, allowing for intermolecular interaction of various types. In order of increasing complexity, the three models account for: (1) steric repulsions (simple hard-sphere model), (2) steric repulsion with short-ranged attractive interactions of varying magnitude (adhesive hard-sphere model), and (3) steric and nonsteric repulsive interactions between several species whose relative concentrations may change as a function of total protein concentration as dictated by equilibrium self-association (effective hard-sphere mixture model). Simple scattering models of noninteracting and adhesive hard-sphere species permitted qualitative interpretation of contributions from excluded volume, electrostatic, and van der Waals interactions on net mAb interactions at high concentration as a function of ionic strength. mAb2 electrostatic interactions were repulsive, whereas mAb1 interactions were net attractive at low ionic strengths, attributed to an anisotropic distribution of molecular charge. The effective hard-sphere mixture model can account quantitatively for the dependence of scattering for both antibodies over the entire concentration range and at salt concentrations exceeding 40 mM. This analysis showed that at high ionic strength both mAbs self-associate weakly to form dimer with an affinity that varies little with salt concentration at concentrations exceeding 75 mM. In addition, mAb1 appears to self-associate further to form oligomers with stoichiometry of 4-6 and an affinity that declines substantially with increasing ionic strength. All three models lead to the conclusion that at high concentrations repulsive interactions are predominantly due to excluded volume, whereas additional features are salt-dependent and reflect a substantial electrostatic contribution to intermolecular interactions of both mAbs. PMID:20849134

  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. Effect of Nonadditive Repulsive Intermolecular Interactions on the Light Scattering of Concentrated Protein–Osmolyte Mixtures

    PubMed Central

    Fernández, Cristina; Minton, Allen P.

    2012-01-01

    The static light scattering of three globular proteins, bovine serum albumin, ovalbumin, and ovomucoid, and binary mixtures of each protein and trimethylamine oxide (TMAO) containing between 10 and 70% protein, were measured as a function of total weight per volume concentration up to 100 g/L. The observed dependence of scattering upon concentration may be accounted for quantitatively by an effective hard sphere model incorporating an extension that takes into account the nonadditive nature of the repulsive intermolecular interaction between protein and TMAO. PMID:21175126

  8. Effect of nonadditive repulsive intermolecular interactions on the light scattering of concentrated protein-osmolyte mixtures.

    PubMed

    Fernández, Cristina; Minton, Allen P

    2011-02-10

    The static light scattering of three globular proteins, bovine serum albumin, ovalbumin, and ovomucoid, and binary mixtures of each protein and trimethylamine oxide (TMAO) containing between 10 and 70% protein, were measured as a function of total weight per volume concentration up to 100 g/L. The observed dependence of scattering upon concentration may be accounted for quantitatively by an effective hard sphere model incorporating an extension that takes into account the nonadditive nature of the repulsive intermolecular interaction between protein and TMAO. PMID:21175126

  9. Empirical intermolecular potential from depolarized interaction-induced light scattering spectra for tetrafluoromethane

    NASA Astrophysics Data System (ADS)

    Kader, Mohamed Sayed Abdel

    2002-07-01

    Depolarized interaction-induced light scattering spectra of tetrafluoromethane in the frequency range 2-150 cm-1 at 294.5 K and 0.91 mol/l with the interaction pressure virial coefficient and viscosity have been used for deriving the empirical multiparameter Morse-Morse-Morse-Spline-van der Waals (M3SV), Lennard-Jones, Kihara, and exp-6 intermolecular potentials. The line shape at relatively low frequencies is determined largely by the effect of bound and free transitions. At intermediate frequencies it is sensitive to both the attractive part of the potential and the short-range part of the polarizability anisotropy. The high frequency wings are discussed in terms of the collision-induced rotational Raman effect and estimates for the dipole-quadrupole and dipole-octopole polarizabilities A and E, respectively, are obtained. Absolute zeroth and second moments have been measured and compared with theoretical calculations using these models of the intermolecular potentials. The results show that M3SV is the most accurate potential yet reported for this system.

  10. Remote Pummerer Reaction via Intermolecular Through-Space Interaction between Sulfonium and Sulfenyl Sulfur Atoms.

    PubMed

    Kobayashi, Kenji; Koyama, Emiko; Namatame, Kazuhiko; Kitaura, Toyokazu; Kono, Chihiro; Goto, Mariko; Obinata, Takanobu; Furukawa, Naomichi

    1999-04-30

    The remote Pummerer reaction of the mono-sulfoxide of p-bis(methylthio)-aromatic 1 is described. The reaction of 1 with (CF(3)CO)(2)O in CH(2)Cl(2) gave a mixture of the corresponding mono-Pummerer product 2, the bis-Pummerer product 3, and the bis-sulfide 4 in an n:1:1 ratio (n >/= 2). The 1:1 formation of 3 and 4 indicates an intermolecular interaction between sulfur atoms. The reaction with the deuterium-labeled 1-d(3)() showed that the formation of 2 occurs at the sulfenyl as well as sulfinyl groups in 1a-d(3)()-1d-d(3)(), in which the product ratio of 2-d(3)():2-d(2)() is in the range of 3.5-10. On the other hand, the Pummerer reaction of 1e-d(3)() occurred preferably at the sulfinyl group in a usual manner. The reaction of a 1:1 mixture of the bis-sulfide 4 and the bis-sulfoxide 5 with (CF(3)CO)(2)O also gave 2, 3, and 4 in a ratio similar to that for the reaction of 1. The mechanism in the present remote Pummerer reactions is discussed in light of an intermolecular through-space interaction between the sulfonium and sulfenyl sulfur atoms, and a dithia dication dimer B and/or a bis(dithia dication) cyclic dimer C are proposed as intermediates. PMID:11674420

  11. 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

  12. Dipole Interactions In Nanosystems

    E-print Network

    Philip B. Allen

    2003-09-16

    The dipole-dipole interaction influences nanoscopic matter by fixing the patterns of permanent, displacive, and induced dipole moments, subject to constraints of molecular size and other short range interactions. Prediction of these arrangements is a challenging problem. The eigenvector of maximum eigenvalue of the dipole-dipole interaction matrix can provide insights and sometimes a complete solution. As an example, the octahedral tilt instabilities of perovskite-type crystals is shown to optimize dipolar interactions. Therefore this instability can be designated as antiferroelectric, because dipole-dipole interactions are a dominant driving force.

  13. The size of the intermolecular energy funnel in protein-protein interactions.

    PubMed

    Hunjan, Jagtar; Tovchigrechko, Andrey; Gao, Ying; Vakser, Ilya A

    2008-07-01

    Revealing the fundamental principles of protein interactions is essential for the basic knowledge of molecular processes and designing better predictive tools. Protein docking procedures allow systematic sampling of intermolecular energy landscapes, revealing the distribution of energy basins and their characteristics. A systematic search docking procedure GRAMM-X was applied to a comprehensive nonredundant database of nonobligate protein-protein complexes to determine the size of the intermolecular energy funnel. The unbound structures were simulated using rotamer library. The procedure generated grid-based matches, based on a smoothed Lennard-Jones potential, and minimized them off the grid with the same potential. The minimization generated a distribution of distances, based on a variety of metrics, between the grid-based and the minimized matches. The metric selected for the analysis, ligand interface RMSD, provided three independent estimates of the funnel size: based on the distribution amplitude for the near-native matches, deviation from random, and correlation with the energy values. The three methods converge to similar estimates of approximately 6-8 A ligand interface RMSD. The results indicated dependence of the funnel size on the type of the complex (smaller for antigen-antibody, medium for enzyme-inhibitor, and larger for the rest of the complexes) and the funnel size correlation with the size of the interface. Guidelines for the optimal sampling of docking coordinates, based on the funnel size estimates, were explored. PMID:18214966

  14. High-energy hadron-hadron (dipole-dipole) scattering from lattice QCD

    SciTech Connect

    Giordano, Matteo; Meggiolaro, Enrico [Dipartimento di Fisica, Universita di Pisa, and INFN, Sezione di Pisa, Largo Pontecorvo 3, I-56127 Pisa (Italy)

    2008-10-01

    In this paper the problem of high-energy hadron-hadron (dipole-dipole) scattering is approached (for the first time) from the point of view of lattice QCD, by means of Monte Carlo numerical simulations. In the first part, we give a brief review of how high-energy scattering amplitudes can be reconstructed, using a functional-integral approach, in terms of certain correlation functions of two Wilson loops, and we also briefly recall some relevant analyticity and crossing-symmetry properties of these loop-loop correlation functions, when going from Euclidean to Minkowskian theory. In the second part, we shall see how these (Euclidean) loop-loop correlation functions can be evaluated in lattice QCD, and we shall compare our numerical results with some nonperturbative analytical estimates that appeared in the literature, discussing, in particular, the question of the analytic continuation from Euclidean to Minkowskian theory and its relation to the still unsolved problem of the asymptotic s dependence of the hadron-hadron total cross sections.

  15. Fourier-transform Raman spectroscopy of biological molecules: weak intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Zhbankov, R. G.; Firsov, S. P.; Kolosova, T. E.; Prihodchenko, L. K.; Grinshpan, D. D.; Baran, J.; Marchewka, M. K.; Ratajczak, H.

    2003-08-01

    The low-frequency (50-150 cm-1) FT Raman spectra of the carbohydrate and protein series have been systematized for the first time. The spectra were measured with a Bruker IFS-88 spectrometer equipped with a FRA-106 Raman accessory. The excited light was the 1064 nm line of the Nd:YAG laser and laser power was 150 mW. In the spectra of compounds containing carboxyl, carbonyl, nitrate, acetate, sulfate, and other groups containing double bonds, for some kinds of regenerated cellulose and amide fibers, we have revealed strong bands assigned to inductive-type weak intermolecular interactions. The position and intensity of these bands depend on the structure of the compound being analyzed.

  16. Intermolecular interaction between a branching ribozyme and associated homing endonuclease mRNA.

    PubMed

    Birgisdottir, Ása B; Nielsen, Henrik; Beckert, Bertrand; Masquida, Benoît; Johansen, Steinar D

    2011-04-01

    RNA tertiary interactions involving docking of GNRA (N; any base; R; purine) hairpin loops into helical stem structures on other regions of the same RNA are one of the most common RNA tertiary interactions. In this study, we investigated a tertiary association between a GAAA hairpin tetraloop in a small branching ribozyme (DiGIR1) and a receptor motif (HEG P1 motif) present in a hairpin structure on a separate mRNA molecule. DiGIR1 generates a 2', 5' lariat cap at the 5' end of its downstream homing endonuclease mRNA by catalysing a self-cleavage branching reaction at an internal processing site. Upon release, the 5' end of the mRNA forms a distinct hairpin structure termed HEG P1. Our biochemical data, in concert with molecular 3D modelling, provide experimental support for an intermolecular tetraloop receptor interaction between the L9 GAAA in DiGIR1 and a GNRA tetraloop receptor-like motif (UCUAAG-CAAGA) found within the HEG P1. The biological role of this interaction appears to be linked to the homing endonuclease expression by promoting post-cleavage release of the lariat capped mRNA. These findings add to our understanding of how protein-coding genes embedded in nuclear ribosomal DNA are expressed in eukaryotes and controlled by ribozymes. PMID:21495911

  17. Intra- and intermolecular electrostatic interactions and their significance for the structure, acidity, and tautomerization behavior of trinitromethane.

    PubMed

    Murray, Jane S; Lane, Pat; Göbel, Michael; Klapötke, Thomas M; Politzer, Peter

    2009-03-14

    We have addressed several interesting issues related to trinitromethane: the propellerlike arrangement of its nitro groups, its lower-than-predicted (although still high) acidity, its aci tautomerization, and the absence of expected very short C-HO intermolecular bridges in the crystal. A combination of crystallographic and computed data was used in our analysis. The structural features mentioned and the anomalous acidity can be attributed to intra- and/or intermolecular electrostatic interactions. Decomposition via C-NO(2) bond scission may occur before aci tautomerization can take place. PMID:19292531

  18. Intra- and intermolecular electrostatic interactions and their significance for the structure, acidity, and tautomerization behavior of trinitromethane

    NASA Astrophysics Data System (ADS)

    Murray, Jane S.; Lane, Pat; Göbel, Michael; Klapötke, Thomas M.; Politzer, Peter

    2009-03-01

    We have addressed several interesting issues related to trinitromethane: the propellerlike arrangement of its nitro groups, its lower-than-predicted (although still high) acidity, its aci tautomerization, and the absence of expected very short C-H•••O intermolecular bridges in the crystal. A combination of crystallographic and computed data was used in our analysis. The structural features mentioned and the anomalous acidity can be attributed to intra- and/or intermolecular electrostatic interactions. Decomposition via C-NO2 bond scission may occur before aci tautomerization can take place.

  19. Coordination compounds of tetravalent silicon, germanium and tin: the structure, chemical bonding and intermolecular interactions in them

    NASA Astrophysics Data System (ADS)

    Korlyukov, A. A.

    2015-04-01

    The review is devoted to analysis and generalization of the results of (i) quantum chemical studies on the structure, chemical bonding and intermolecular interactions in coordination compounds of tetravalent silicon, germanium and tin in crystals, in solutions and in the gas phase and (ii) experimental investigations of the electron density distribution in these systems. The bibliography includes 147 references.

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

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian [Peter Gruenberg Institut (PGI-3), Forschungszentrum Juelich, 52425 Juelich (Germany); Juelich-Aachen Research Alliance (JARA) - Fundamentals of Future Information Technology, 52425 Juelich (Germany)

    2011-12-21

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

  1. Intermolecular interactions and substrate effects for an adamantane monolayer on a Au(111) surface

    NASA Astrophysics Data System (ADS)

    Sakai, Yuki; Nguyen, Giang D.; Capaz, Rodrigo B.; Coh, Sinisa; Pechenezhskiy, Ivan V.; Hong, Xiaoping; Wang, Feng; Crommie, Michael F.; Saito, Susumu; Louie, Steven G.; Cohen, Marvin L.

    2013-12-01

    We study theoretically and experimentally the infrared (IR) spectrum of an adamantane monolayer on a Au(111) surface. Using a STM-based IR spectroscopy technique (IRSTM) we are able to measure both the nanoscale structure of an adamantane monolayer on Au(111) as well as its infrared spectrum, while DFT-based ab initio calculations allow us to interpret the microscopic vibrational dynamics revealed by our measurements. We find that the IR spectrum of an adamantane monolayer on Au(111) is substantially modified with respect to the gas-phase IR spectrum. The first modification is caused by the adamantane-adamantane interaction due to monolayer packing, and it reduces the IR intensity of the 2912 cm-1 peak (gas phase) by a factor of 3.5. The second modification originates from the adamantane-gold interaction, and it increases the IR intensity of the 2938 cm-1 peak (gas phase) by a factor of 2.6 and reduces its frequency by 276 cm-1. We expect that the techniques described here can be used for an independent estimate of substrate effects and intermolecular interactions in other diamondoid molecules and for other metallic substrates.

  2. 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

  3. 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.

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

    PubMed Central

    Yogesha, SD; Sharff, A; Bricogne, G; Izard, T

    2011-01-01

    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 ?-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 Å resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 ?-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle. PMID:21648001

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

    PubMed

    Yogesha, S D; Sharff, A; Bricogne, G; Izard, T

    2011-08-01

    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 ?-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 Å resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 ?-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle. PMID:21648001

  6. 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

  7. RecN is a cohesin-like protein that stimulates intermolecular DNA interactions in vitro.

    PubMed

    Reyes, Emigdio D; Patidar, Praveen L; Uranga, Lee A; Bortoletto, Angelina S; Lusetti, Shelley L

    2010-05-28

    The bacterial RecN protein is involved in the recombinational repair of DNA double-stranded breaks, and recN mutants are sensitive to DNA-damaging agents. Little is known about the biochemical function of RecN. Protein sequence analysis suggests that RecN is related to the SMC (structural maintenance of chromosomes) family of proteins, predicting globular N- and C-terminal domains connected by an extensive coil-coiled domain. The N- and C-domains contain the nucleotide-binding sequences Walker A and Walker B, respectively. We have purified the RecN protein from Deinococcus radiodurans and characterized its DNA-dependent and DNA-independent ATPase activity. The RecN protein hydrolyzes ATP with a k(cat) of 24 min(-1), and this rate is stimulated 4-fold by duplex DNA but not by single-stranded DNA. This DNA-dependent ATP turnover rate exhibits a dependence on the concentration of RecN protein, suggesting that RecN-RecN interactions are required for efficient ATP hydrolysis, and those interactions are stabilized only by duplex DNA. Finally, we show that RecN stimulates the intermolecular ligation of linear DNA molecules in the presence of DNA ligase. This DNA bridging activity is strikingly similar to that of the cohesin complex, an SMC family member, to which RecN is related. PMID:20360008

  8. RecN Is a Cohesin-like Protein That Stimulates Intermolecular DNA Interactions in Vitro*

    PubMed Central

    Reyes, Emigdio D.; Patidar, Praveen L.; Uranga, Lee A.; Bortoletto, Angelina S.; Lusetti, Shelley L.

    2010-01-01

    The bacterial RecN protein is involved in the recombinational repair of DNA double-stranded breaks, and recN mutants are sensitive to DNA-damaging agents. Little is known about the biochemical function of RecN. Protein sequence analysis suggests that RecN is related to the SMC (structural maintenance of chromosomes) family of proteins, predicting globular N- and C-terminal domains connected by an extensive coil-coiled domain. The N- and C-domains contain the nucleotide-binding sequences Walker A and Walker B, respectively. We have purified the RecN protein from Deinococcus radiodurans and characterized its DNA-dependent and DNA-independent ATPase activity. The RecN protein hydrolyzes ATP with a kcat of 24 min?1, and this rate is stimulated 4-fold by duplex DNA but not by single-stranded DNA. This DNA-dependent ATP turnover rate exhibits a dependence on the concentration of RecN protein, suggesting that RecN-RecN interactions are required for efficient ATP hydrolysis, and those interactions are stabilized only by duplex DNA. Finally, we show that RecN stimulates the intermolecular ligation of linear DNA molecules in the presence of DNA ligase. This DNA bridging activity is strikingly similar to that of the cohesin complex, an SMC family member, to which RecN is related. PMID:20360008

  9. Effects of strong hydrogen bonds and weak intermolecular interactions on supramolecular assemblies of 4-fluorobenzylamine

    NASA Astrophysics Data System (ADS)

    Wang, Shi; Ding, Xue-Hua; Li, Yong-Hua; Huang, Wei

    2015-07-01

    A series of supramolecular salts have been obtained by the self-assembly of 4-fluorobenzylamine and halide ions or metal chloride with 18-crown-6 as the host in the hydrochloric acid medium, i.e. (C7H9FN)+?X- (X = Cl-, 1; Br-, 2), [(C7H9FN)2?(18-crown-6)2]2+?(MCl4)2- (M = Mn, 3; Co, 5; Zn, 7; Cd, 8), [(C7H9FN)?(18-crown-6)]+?(FeCl4)- (4) and [(C7H9FN)?(18-crown-6)]+?1/2(CuCl4)2- (6). Structural analyses indicate that 1-2 crystallize in the triclinic space group P-1, 4 in orthorhombic space group Pnma and 3, 5, 6-8 in the monoclinic space group P21/c or C2/c. In these compounds, extensive intermolecular interactions have been utilized for the self-assembly of diverse supramolecular architectures, ranging from strong N-H⋯X (X = O, Cl, Br) hydrogen bonds to weak C-H⋯Y (Y = F, Cl, ?) interactions. N-H⋯Cl/Br hydrogen bonds offer the major driving force in the crystal packing of salts 1-2 while N-H⋯O hydrogen bonds are found in salts 3-8.

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

    SciTech Connect

    Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw [Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan (China)

    2013-11-21

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

  11. Molecular structure and intermolecular interactions of N1'-methoxycarbonylbiotin methyl ester: a model for carboxybiotin.

    PubMed

    Stallings, W C; Monti, C T; Lane, M D; DeTitta, G T

    1980-03-01

    The crystal structure of N1'-methoxycarbonylbiotin methyl ester, a model for N1'-carboxybiotin, has been determined. The ureido carbonyl bond has more double bond (keto) character than does the corresponding bound in free biotin, which has single bond (enolate) character. In addition, there is an interesting intermolecular interaction between the ureido carbonyl oxygen and a methyl group. Comparison of the molecular structure and crystal packing with those of free biotin suggests that the coenzyme may have evolved with the incorporation of the ureido moiety because the electronic configuration of this region of the molecule is sensitive to N1' carboxylation. On decarboxylation, the ureido carbonyl bond becomes more polarized (C-O-), thereby facilitating the deprotonation of N1' and increasing its nucleophilicity. As a result, carboxylation can occur readily. On carboxylation, the carbonyl bond is depolarized (C = O), allowing the carboxylated coenzyme to interact with nonpolar groups and carboxylate them. Thus, the carboxylation and decarboxylation of biotin appear to act as a mechanistic switch, turning off and on the polarization of the ureido carbonyl bond as well as modulating the nucleophilicity of N1'. PMID:6929481

  12. Do intermolecular interactions control crystallization abilities of glass-forming liquids?

    PubMed

    Kaminski, K; Adrjanowicz, K; Wojnarowska, Z; Dulski, M; Wrzalik, R; Paluch, M; Kaminska, E; Kasprzycka, A

    2011-10-13

    Broadband dielectric spectroscopy was used to investigate molecular dynamics of three very similar systems: D-glucose, ?-pentaacetylglucose, and ?-pentaacetylglucose in a wide range of temperatures. We found out that two latter systems (differing only in location of the acetyl group attached to the first carbon in the sugar ring) reveal completely opposite tendencies to crystallization. Therefore, the aim of this Article was to investigate in detail molecular dynamics of both pentaacetylglucoses to assess what are the underlying of different crystallization abilities of so closely related carbohydrates. To analyze the kinetics of crystallization, we used Avrami and Avramov approaches. Interestingly, we found out that both ?-and ?-pentaacetylglucose exhibit completely different crystallization mechanisms. In the first case, the value of Avrami exponent was estimated to be n = 2, whereas for the second carbohydrate this exponent was equaled to n = 5.5. Additionally, we have carried out isothermal time-dependent dielectric measurements on D-glucose to demonstrate that this saccharide is more stable than its acetyl derivatives. Results presented in this Article indicate that besides molecular mobility, the character of the intermolecular interactions might also be another important factor governing crystallization process. Surprisingly, this issue is not often addressed during studies on crystallization abilities of different glass-formers. Finally, additional optical measurements were carried out to get more detailed information about nucleation density, activation barrier for a crystal growth, and morphology of crystallization structures. PMID:21877734

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

    NASA Astrophysics Data System (ADS)

    Azar, Richard Julian; Head-Gordon, Martin

    2015-05-01

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

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

    PubMed

    Azar, Richard Julian; Head-Gordon, Martin

    2015-05-28

    Your correspondents develop and apply fully nonorthogonal, local-reference perturbation theories describing non-covalent interactions. Our formulations are based on a Löwdin partitioning of the similarity-transformed Hamiltonian into a zeroth-order intramonomer piece (taking local CCSD solutions as its zeroth-order eigenfunction) plus a first-order piece coupling the fragments. If considerations are limited to a single molecule, the proposed intermolecular similarity-transformed perturbation theory represents a frozen-orbital variant of the "(2)"-type theories shown to be competitive with CCSD(T) and of similar cost if all terms are retained. Different restrictions on the zeroth- and first-order amplitudes are explored in the context of large-computation tractability and elucidation of non-local effects in the space of singles and doubles. To accurately approximate CCSD intermolecular interaction energies, a quadratically growing number of variables must be included at zeroth-order. PMID:26026428

  15. High-resolution NMR spectra in inhomogeneous fields via IDEAL (intermolecular dipolar-interaction enhanced all lines) method.

    PubMed

    Chen, Zhong; Chen, Zhiwei; Zhong, Jianhui

    2004-01-21

    Intermolecular double-quantum technique is used to yield high-resolution NMR spectra in inhomogeneous magnetic fields. The method exploits the distant dipolar interactions between the solvent and solute nuclear spins. Chemical shifts, J couplings, multiplicity patterns, and relative areas are retained with the method. Except for a 1.5-fold change in the scale factor of J couplings, other parameters are consistent with those extracted from one-dimensional spectra obtained in a homogeneous field. PMID:14719924

  16. Transport properties in a hydrogen-bonded chain model including dipole-dipole interactions

    Microsoft Academic Search

    I. Chochliouros; J. Pouget

    1995-01-01

    The proton mobility and transport of energy in hydrogen-bonded chains is an interesting problem because they play a crucial role in the interpretation of certain biological processes. We propose a physical model which consists basically of two one-dimensional harmonically coupled sublattices corresponding to the oxygens and protons, respectively. Our study starts with an improved form of the Antonchenko-Davydov-Zolotaryuk (ADZ) model

  17. Dead-time free measurement of dipole-dipole interactions between electron spins

    NASA Astrophysics Data System (ADS)

    Pannier, M.; Veit, S.; Godt, A.; Jeschke, G.; Spiess, H. W.

    2011-12-01

    A four-pulse version of the pulse double electron-electron resonance (DEER) experiment is presented, which is designed for the determination of interradical distances on a nanoscopic lengthscale. With the new pulse sequence electron-electron couplings can be studied without dead-time artifacts, so that even broad distributions of electron-electron distances can be characterized. A version of the experiment that uses a pulse train in the detection period exhibits improved signal-to-noise ratio. Tests on two nitroxide biradicals with known length indicate that the accessible range of distances extends from about 1.5 to 8 nm. The four-pulse DEER spectra of an ionic spin probe in an ionomer exhibit features due to probe molecules situated both on the same and on different ion clusters. The former feature provides information on the cluster size and is inaccessible with previous methods.

  18. Many particle magnetic dipole–dipole and hydrodynamic interactions in magnetizable stent assisted magnetic drug targeting

    Microsoft Academic Search

    P. J. Cregg; Kieran Murphy; Adil Mardinoglu; Adriele Prina-Mello

    2010-01-01

    The implant assisted magnetic targeted drug delivery system of Avilés, Ebner and Ritter is considered both experimentally (in vitro) and theoretically. The results of a 2D mathematical model are compared with 3D experimental results for a magnetizable wire stent. In this experiment a ferromagnetic, coiled wire stent is implanted to aid collection of particles which consist of single domain magnetic

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

    PubMed

    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. PMID:25296807

  20. Relativistic effects in the intermolecular interaction-induced nuclear magnetic resonance parameters of xenon dimer

    NASA Astrophysics Data System (ADS)

    Hanni, Matti; Lantto, Perttu; Iliaš, Miroslav; Jensen, Hans Jørgen Aagaard; Vaara, Juha

    2007-10-01

    Relativistic effects on the Xe129 nuclear magnetic resonance shielding and Xe131 nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe2 system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift ?, the anisotropy of the shielding tensor ??, and the NQC constant along the internuclear axis ? ? are calculated as a function of the internuclear distance. DHF shielding calculations are carried out using gauge-including atomic orbitals. For comparison, the full leading-order one-electron Breit-Pauli perturbation theory (BPPT) is applied using a common gauge origin. Electron correlation effects are studied at the nonrelativistic (NR) coupled-cluster singles and doubles with perturbational triples [CCSD(T)] level of theory. The fully relativistic second-order Møller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for ? and ?? by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for ? and ?? in Xe2. For these properties, the currently most complete theoretical description is obtained by a piecewise approximation where the uncorrelated relativistic DHF results obtained close to the basis-set limit are corrected, on the one hand, for NR correlation effects and, on the other hand, for the BPPT-based cross coupling of relativity and correlation. For ? ?, the fully relativistic DMP2 results obtain a correction for NR correlation effects beyond MP2. The computed temperature dependence of the second virial coefficient of the Xe129 nuclear shielding is compared to experiment in Xe gas. Our best results, obtained with the piecewise approximation for the binary chemical shift combined with the previously published state of the art theoretical potential energy curve for Xe2, are in excellent agreement with the experiment for the first time.

  1. Structural elucidation and contribution of intermolecular interactions in O-hydroxy acyl aromatics: Insights from X-ray and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Seth, Saikat Kumar

    2014-05-01

    An O-hydroxy acyl aromatics, namely 1,1?,1?-(2,4,6-trihydroxybenzene-1,3,5-triyl) triethanone (1) was synthesized and characterized by spectroscopic and single crystal X-ray structural studies with a detailed scrutiny of visualizing and exploring intermolecular interactions in molecular crystals through Hirshfeld surface. The crystal packing of (1) exhibits intermolecular ?-? stacking interactions to generate a one-dimensional parallel stacked ribbon propagating along (0 0 1) direction. Hirshfeld surface analysis for visually analyzing intermolecular interactions in crystal structures employing molecular surface contours and 2D fingerprint plots have been used to scrutinize molecular shapes. Crystal structure analysis supported with the Hirshfeld surface and fingerprint plots enabled the identification of the significant intermolecular interactions.

  2. Studies on intermolecular interactions of metal chelate complexes. Part X. Interactions of metal chelates with ozone

    Microsoft Academic Search

    Nicola D. Yordanov; Yulian Karadzhov

    1985-01-01

    The interactions of more than forty metal chelate complexes, dithiocarbamates, dithiophosphates and acetylacetonates, with ozone are studied in homogeneous phase and the stoichiometry and the rate constants of the reactions estimated. Most powerful ozone deactivators are nickel(II) and copper(II) dithiocarbamate and dithiophosphate complexes interacting with 6.5 moles ozone per mole of the ligand with rate constant >06m · I-1 ·

  3. 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

  4. 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...

  5. 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

  6. Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: probing inter-molecular interactions using PFG NMR.

    PubMed

    D'Agostino, Carmine; Gladden, Lynn F; Mantle, Mick D; Abbott, Andrew P; Ahmed, Essa I; Al-Murshedi, Azhar Y M; Harris, Robert C

    2015-06-01

    Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter-molecular interactions between the different species in the mixtures, namely the Ch(+) cation and hydrogen bond donor (HBD). The results reveal an interesting and complex behaviour of such mixtures at a molecular level. In general, it is observed that the hydroxyl protons ((1)H) of Ch(+) and the hydrogen bond donor have diffusion coefficients significantly different from those measured for their parent molecules when water is added. This indicates a clear and significant change in inter-molecular interactions. In aqueous Ethaline, the hydroxyl species of Ch(+) and HBD show a stronger interaction with water as water is added to the system. In the case of Glyceline, water has little effect on both hydroxyl proton diffusion of Ch(+) and HBD. In Reline, it is likely that water allows the formation of small amounts of ammonium hydroxide. The most surprising observation is from the self-diffusion of water, which is considerably higher that expected from a homogeneous liquid. This leads to the conclusion that Reline and Glyceline form mixtures that are inhomogeneous at a microscopic level despite the hydrophilicity of the salt and HBD. This work shows that PFG NMR is a powerful tool to elucidate both molecular dynamics and inter-molecular interactions in complex liquid mixtures, such as the aqueous DES mixtures. PMID:25994171

  7. Intermolecular Interactions in Dry and Rehydrated Pure and Mixed Bilayers of Phosphatidylcholine and Digalactosyldiacylglycerol: A Fourier Transform Infrared Spectroscopy Study

    PubMed Central

    Popova, Antoaneta V.; Hincha, Dirk K.

    2003-01-01

    Glycolipids are an important part of almost all biological membranes. Their effects on membrane structure and their interactions with phospholipids, however, have not been extensively studied so far. We have investigated the phase behavior and intermolecular interactions in dry and rehydrated bilayers made from the phospholipid egg phosphatidylcholine (EPC) and the plant chloroplast glycolipid digalactosyldiacylglycerol (DGDG), or from a mixture (1:1) of these lipids, using Fourier transform infrared spectroscopy. We show that there are extensive interactions between EPC and DGDG in mixed membranes, and also between DGDG molecules in pure DGDG membranes, involving sugar OH groups and C=O, P=O, and choline moieties in dry membranes. These interactions persist to a certain degree even after rehydration. We present evidence that these interactions influence the mixing behavior in phosphatidylcholine/DGDG membranes and also the phase behavior of both EPC/DGDG and pure DGDG membranes in the dry state. PMID:12944283

  8. Quantum effects in intermediate-temperature dipole-dipole correlation-functions in the presence of an environment.

    PubMed

    Grossmann, F

    2014-10-14

    We study thermal dipole-dipole correlation functions and their corresponding IR spectra in the presence of an intermediate temperature bath of harmonic oscillators. Whereas for a Morse oscillator without coupling to a heat bath, the quantum level structure is displayed in the spectrum, classical calculations show a broad, smeared out spectrum. In the presence of purely Ohmic dissipation already for extremely weak relaxation rate, the classical case is recovered. Using the HEOM approach of Tanimura and Wolynes [Phys. Rev. A 43, 4131 (1991)], we show that to observe some remnants of the level structure in the spectrum for moderate damping strength as well as intermediate temperatures, the dynamics has to be non-Markovian (Ohmic dissipation with cutoff). PMID:25318720

  9. Quantum effects in intermediate-temperature dipole-dipole correlation-functions in the presence of an environment

    NASA Astrophysics Data System (ADS)

    Grossmann, F.

    2014-10-01

    We study thermal dipole-dipole correlation functions and their corresponding IR spectra in the presence of an intermediate temperature bath of harmonic oscillators. Whereas for a Morse oscillator without coupling to a heat bath, the quantum level structure is displayed in the spectrum, classical calculations show a broad, smeared out spectrum. In the presence of purely Ohmic dissipation already for extremely weak relaxation rate, the classical case is recovered. Using the HEOM approach of Tanimura and Wolynes [Phys. Rev. A 43, 4131 (1991)], we show that to observe some remnants of the level structure in the spectrum for moderate damping strength as well as intermediate temperatures, the dynamics has to be non-Markovian (Ohmic dissipation with cutoff).

  10. 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

  11. Phase transitions, intermolecular interactions and electrical conductivity behavior in carbon multiwalled nanotubes/nematic liquid crystal composites

    NASA Astrophysics Data System (ADS)

    Lebovka, N.; Dadakova, T.; Lysetskiy, L.; Melezhyk, O.; Puchkovska, G.; Gavrilko, T.; Baran, J.; Drozd, M.

    2008-09-01

    The phase transitions, intermolecular interactions and electrical percolation behavior in the composites of multiwalled carbon nanotubes (MWNTs) and nematic LC ( p-ethoxybenzylidene- p'-butylaniline, EBBA) are experimentally investigated in this work. The concentration of nanotubes was between 0 and 1% (wt), and the temperature interval was 273-363 K. The experimental data of differential scanning calorimetry (DSC) and FTIR adsorption spectra evidence the presence of strong interactions inside MWNTs/EBBA nanocomposites. An increase of both isotropic-to-nematic (by 0.5-1 K) and nematic-to-crystalline (by 1.5-3 K) phase transition temperatures was observed for EBBA filled with MWNTs. The FTIR spectroscopic data evidence an enhancement of the strong binding interaction between MWNTs and EBBA with increase of the concentration of MWNTs. It was shown that intermolecular interactions affect noticeably the electrical conductivity of MWNTs/EBBA composites. The percolation transition from non-conductive to high conductive state, and the effect of positive temperature coefficient (PTC effect) were observed at MWNT concentrations exceeding 0.05-0.1 wt.% Within the nematic phase temperature range, the electrical conductivity of the composites reveals a noticeable heating-cooling hysteresis and follows Arrhenius behavior. The activation energy decreases when MWNTs concentration increases, which supports the dominating role of the junction mechanism related to the thermal motion of nanotubes. The electric field dependence of the electrical conductivity was explained by the existence of the field-enhanced charge transport through hopping junctions in the LC gaps.

  12. Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions.

    PubMed Central

    Keskin, O.; Bahar, I.; Badretdinov, A. Y.; Ptitsyn, O. B.; Jernigan, R. L.

    1998-01-01

    Whether knowledge-based intra-molecular inter-residue potentials are valid to represent inter-molecular interactions taking place at protein-protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study, the interfacial regions of protein-protein complexes are examined to extract inter-molecular inter-residue potentials, using the same statistical methods as those previously adopted for intra-molecular residue pairs. Two sets of energy parameters are derived, corresponding to solvent-mediation and "average residue" mediation. The former set is shown to be highly correlated (correlation coefficient 0.89) with that previously obtained for inter-residue interactions within single chain monomers, while the latter exhibits a weaker correlation (0.69) with its intra-molecular counterpart. In addition to the close similarity of intra- and inter-molecular solvent-mediated potentials, they are shown to be significantly more residue-specific and thereby discriminative compared to the residue-mediated ones, indicating that solvent-mediation plays a major role in controlling the effective inter-residue interactions, either at interfaces, or within single monomers. Based on this observation, a reduced set of energy parameters comprising 20 one-body and 3 two-body terms is proposed (as opposed to the 20 x 20 tables of inter-residue potentials), which reproduces the conventional 20 x 20 tables with a correlation coefficient of 0.99. PMID:9865952

  13. 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.

  14. Influence of intermolecular N-H...pi interactions on molecular packing and field-effect performance of organic semiconductors.

    PubMed

    Zhao, Huaping; Jiang, Lang; Dong, Huanli; Li, Hongxiang; Hu, Wenping; Ong, Beng S

    2009-09-14

    Charge transport in organic semiconductors is strongly dependent on their molecular packing modes in the solid state. Therefore, understanding the relationship between molecular packing and charge transport is imperative, both experimentally and theoretically. However, so far, the fundamental effects of solid-state packing and molecular interactions (e.g. N-H...pi) on charge transport need further elucidation. Herein, indolo[3,2-b]carbazole (ICZ) and a derivative thereof are used as examples to approach this scientific target. An interesting insight obtained thereby is that N-H...pi interactions among ICZ molecules facilitate charge transport for higher mobility. Subtle changes in the of N-H...pi interactions can significantly influence both the molecular packing and the charge-transport properties. Therefore, a method for exploiting intermolecular N-H...pi interactions would yield novel molecular systems with designable characteristics. PMID:19618418

  15. Effect of dipolar interactions on the magnetization of a cubic array of nanomagnets

    NASA Astrophysics Data System (ADS)

    Alcantara Ortigoza, Marisol; Rahman, Talat S.; Klemm, Richard A.

    2006-03-01

    We investigated the effect of intermolecular dipolar interactions on an ensemble of 100 3D-systems of 5x5x4 nanomagnets, each with spin S = 5, arranged in a cubic lattice. We employed the Landau-Lifshitz-Gilbert equation to solve for the magnetization curves for several values of the damping constant, the induction sweep rate, the lattice constant, the temperature, and the magnetic anisotropy. The dependencies of the magnetic hysteresis curves on these parameters will be presented. We also reproduce and test a previously reported magnetization curve for a 2D-system [M. Kayali and W. Saslow, Phys. Rev. B 70, 174404 (2004)]. Although in 3D systems, dipole-dipole interactions generally diminish the hysteresis, in two- dimensional systems, they strongly enhance it. For both square two- dimensional and rectangular three-dimensional lattices with B||(x+y), dipole-dipole interactions can cause large jumps in the magnetization. New results including the low-temperature quantum effects appropriate for single molecule magnets will be presented.

  16. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    PubMed Central

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4?-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  17. 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

  18. The Experimental Charge-Density Approach in the Evaluation of Intermolecular Interactions. Application of a New Module of the XD Programming Package to Several Solids Including a Pentapeptide

    SciTech Connect

    Abramov, Yu A.; Volkov, Anatoliy; Wu, G; Coppens, P

    2000-11-01

    A new module interfaced to the XD programming package has been used in the evaluation of intermolecular interactions and lattice energies of the crystals of p-nitroaniline, l-asparagine monohydrate and the pentapeptide Boc-Gln- d-Iva-Hyp-Ala-Phol (Boc = butoxycarbonyl, Iva = isovaline = ethylalanine, Phol = phenylalaninol).

  19. A biosensor in the time domain based on the diffusion coefficient measurement: intermolecular interaction of an intermediate of photoactive yellow protein.

    PubMed

    Khan, Javaid Shahbaz; Imamoto, Yasushi; Yamazaki, Yoichi; Kataoka, Mikio; Tokunaga, Fumio; Terazima, Masahide

    2005-10-15

    A new type of biosensor is presented for the first time. This method is based on the diffusion measurement in the time domain by the transient grating method. As the first demonstration of this new method, various intermolecular interactions with a reaction intermediate of photoactive yellow protein, such as the protein-protein interaction, protein-DNA interaction, and protein-small molecule binding are detected. The characteristic advantages and limitations are summarized. PMID:16223249

  20. Chemical force spectroscopy in heterogeneous systems: intermolecular interactions involving epoxy polymer, mixed monolayers, and polar solvents.

    PubMed

    Vezenov, Dmitri V; Zhuk, Andrew V; Whitesides, George M; Lieber, Charles M

    2002-09-01

    We used chemical force microscopy (CFM) to study adhesive forces between surfaces of epoxy resin and self-assembled monolayers (SAMs) capable of hydrogen bonding to different extents. The influence of the liquid medium in which the experiments were carried out was also examined systematically. The molecular character of the tip, polymer, and liquid all influenced the adhesion. Complementary macroscopic contact angle measurements were used to assist in the quantitative interpretation of the CFM data. A direct correlation between surface free energy and adhesion forces was observed in mixed alcohol-water solvents. An increase in surface energy from 2 to 50 mJ/m(2) resulted in an increase in adhesion from 4-8 nN to 150-300 nN for tips with radii of 50-150 nm. The interfacial surface energy for identical nonpolar surface groups of SAMs was found not to exceed 2 mJ/m(2). An analysis of adhesion data suggests that the solvent was fully excluded from the zone of contact between functional groups on the tip and sample. With a nonpolar SAM, the force of adhesion increased monotonically in mixed solvents of higher water content; whereas, with a polar SAM (one having a hydrogen bonding component), higher water content led to decreased adhesion. The intermolecular force components theory was used for the interpretation of adhesion force measurements in polar solvents. Competition between hydrogen bonding within the solvent and hydrogen bonding of surface groups and the solvent was shown to provide the main contribution to adhesion forces. We demonstrate how the trends in the magnitude of the adhesion forces for chemically heterogeneous systems (solvents and surfaces) measured with CFM can be quantitatively rationalized using the surface tension components approach. For epoxy polymer, inelastic deformations also contributed heavily to measured adhesion forces. PMID:12197760

  1. 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

  2. Investigation of ethanol-peptide and water-peptide interactions through intermolecular nuclear overhauser effects and molecular dynamics simulations.

    PubMed

    Gerig, J T

    2013-05-01

    Molecular dynamics simulations have been used to explore solvent-solute intermolecular nuclear Overhauser effects (NOEs) on NMR (nuclear magnetic resonance) signals of [val5]angiotensin dissolved in 35% ethanol-water (v/v). Consideration of chemical shift, coupling constant and intramolecular NOE data suggest that conformations of the peptide are adequately sampled by simulations of up to 0.6 ?s duration. Calculated cross relaxation terms at 0 and 25 °C are compared to experimental values and to terms predicted using a particulate model of the solvent. Many calculated solvent NOEs are in agreement with experimental results; disagreements are particularly striking for hydrogens of the Phe8 residue of the peptide. Calculations show that individual molecules of either solvent component can spend many ns in association with the peptide but dipolar interactions within such a complex account for only a few percent of an observed cross relaxation rate. Most parts of the peptide interact selectively with ethanol. Diffusion of both solvent components is slowed when they are close to the peptide. Solvent-solute cross relaxation terms for acetic acid in the same solvent obtained from simulations agree with experiment. Preferential interactions of solvent molecules with acetic acid are largely absent, as are effects of this solute on solvent diffusion rates. PMID:23477637

  3. 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.

  4. An anomalous dipole-dipole arrangement of water molecules encapsulated into C60 dimer

    NASA Astrophysics Data System (ADS)

    Nomura, Kazuya; Okada, Susumu

    2014-07-01

    Based on first-principles total energy calculations, we demonstrate that two water molecules encapsulated in the C60 dimer form a peculiar tail-to-tail dipole arrangement that is energetically unfavorable in classical electrodynamics. This arrangement is ascribed to charge depression at the wall of C60 associated with [2 + 2] cycloaddition in the dimer structure resulting in a decrease of the energy cost of Coulomb repulsive interaction in the arrangement. First-principles molecular dynamics simulations also show that the water molecules retain the peculiar arrangement up to the temperature of about 10 K.

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

    PubMed Central

    Paßens, Michael; Waser, Rainer

    2015-01-01

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

  6. The Nature of the C–H· · ·X Intermolecular Interactions in Molecular Crystals. A Theoretical Perspective

    Microsoft Academic Search

    JUAN J. NOVOA; Fernando Mota; Emiliana D'Oria

    The different C-H ??? X interactions are analyzed in this chapter. They are compared with the other types of hydrogen bonds, especially O-H ??? O ones. Theoretical tools are presented, among them the ''atoms in molecules'' theory (AIM). The H-bond motifs existing in crystals are presented. The evidences that C-H ??? X interactions may be often classified as H-bonds are

  7. 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

  8. Computational studies of intermolecular interactions in aqueous solutions of poly(vinylmethylether).

    PubMed

    Saramak, J; Halagan, K; Kozanecki, M; Polanowski, P

    2014-12-01

    Thermo-responsive materials, such as poly(vinylmethylether) (PVME), attract a common attention because of their unique physical properties resulted from metastable equilibrium between various types of interactions. In this work Monte Carlo (MC) and quantum-mechanical (QM) methods were used to study excluded volume and electrostatic interactions respectively. The graining procedure of PVME-water system was proposed. Its implementation to MC calculations allowed to distinguish how two water fractions differ on dynamics. The QM calculations showed that the formation of cyclic clusters leads to the lengthening of the hydrogen bonds and consequently to higher energies in comparison to linear forms, which is crucial looking at an application of QM results to MC calculation considering thermal interactions. PMID:25420704

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database

    Microsoft Academic Search

    Laszlo Fusti Molnar; Xiao He; Bing Wang; Kenneth M. Merz

    2009-01-01

    Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set

  11. Investigating Intermolecular Interactions via Scanning Tunneling Microscopy: An Experiment for the Physical Chemistry Laboratory

    ERIC Educational Resources Information Center

    Pullman, David; Peterson, Karen I.

    2004-01-01

    A scanning tunneling microscope (STM) project designed as a module for the undergraduate physical chemistry laboratory is described. The effects of van der Waals interactions on the condensed-phase structure are examined by the analysis of the pattern of the monolayer structures.

  12. Opalescence in monoclonal antibody solutions and its correlation with intermolecular interactions in dilute and concentrated solutions.

    PubMed

    Raut, Ashlesha S; Kalonia, Devendra S

    2015-04-01

    Opalescence indicates physical instability of a formulation because of the presence of aggregates or liquid-liquid phase separation in solution and has been reported for monoclonal antibody (mAb) formulations. Increased solution opalescence can be attributed to attractive protein-protein interactions (PPIs). Techniques including light scattering, AUC, or membrane osmometry are routinely employed to measure PPIs in dilute solutions, whereas opalescence is seen at relatively higher concentrations, where both long- and short-range forces contribute to overall PPIs. The mAb molecule studied here shows a unique property of high opalescence because of liquid-liquid phase separation. In this study, opalescence measurements are correlated to PPIs measured in diluted and concentrated solutions using light scattering (kD ) and high-frequency rheology (G'), respectively. Charges on the molecules were calculated using zeta potential measurements. Results indicate that high opalescence and phase separation are a result of the attractive interactions in solution; however, the presence of attractive interactions do not always imply phase separation. Temperature dependence of opalescence suggests that thermodynamic contribution to opalescence is significant and Tcloud can be utilized as a potential tool to assess attractive interactions in solution. PMID:25556561

  13. 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.

  14. Further analysis and comparative study of intermolecular interactions using dimers from the S22 database.

    PubMed

    Molnar, Laszlo Fusti; He, Xiao; Wang, Bing; Merz, Kenneth M

    2009-08-14

    Accurate MP2 and CCSD(T) complete basis set (CBS) interaction energy curves (14 points for each curve) have been obtained for 20 of the dimers reported in the S22 set and analytical Morse curves have been fitted that can be used in developing updated density functional theory (DFT) and force field models. The magnitude and the effect of the basis set superposition error (BSSE) were carefully investigated. We found that going up to aug-cc-pVDZ and aug-cc-pVTZ basis sets is enough to obtain accurate CBS MP2 energies when BSSE corrected values are used but aug-cc-pVTZ and aug-cc-pVQZ basis sets are needed when the BSSE uncorrected total energies are used in CBS extrapolations. MP2 interaction energies with smaller basis sets such as 6-31G* are found to have very little dispersion energy and that the true source of dispersion attributed attractive interactions is almost entirely due to BSSE. MP2 and CCSD(T) CBS interaction energies are found to be very close to one another if aromatic systems are not involved. Comparative analyses have been performed with semiempirical and ab initio methods utilizing the moderate in size but affordable 6-31G* basis set both of which can be readily applied to macromolecular systems. The new M06-2X and M06-L DFT functionals were found to be more accurate than all methods tested herein. Interaction energy curves using the SG1 grid showed discontinuities for several of the dimer systems but this problem disappeared when finer DFT numerical grids were used. PMID:19691412

  15. Anisotropic intermolecular interactions in van der Waals and hydrogen-bonded complexes: What can we get from density functional calculations?

    NASA Astrophysics Data System (ADS)

    Milet, Anne; Korona, Tatiana; Moszynski, Robert; Kochanski, Elise

    1999-11-01

    The applicability of various density functional theory (DFT) methods to describe the anisotropy of the intermolecular potential energy surfaces of hydrogen-bonded [OH--H2O, (H2O)2] and van der Waals [CO-H2O, He-CO2] complexes has been tested by comparison with supermolecule CCSD(T) (coupled-cluster method restricted to single, double, and noniterative triple excitations) and perturbational SAPT (symmetry-adapted perturbation theory) results computed for the same geometries and with the same basis sets. It is shown that for strongly bound ionic hydrogen-bonded complexes, like OH--H2O, hybrid approaches provide accurate results. For other systems, including the water dimer, the DFT calculations fail to reproduce the correct angular dependence of the potential surfaces. It is also shown that a hybrid functional adjusted to reproduce the CCSD(T) value of the binding energy for the water dimer produces results worse than the standard hybrid functionals for OH--H2O, and fails to describe the correct anisotropy of the CO-H2O interaction.

  16. Structural Change in FtsZ Induced by Intermolecular Interactions between Bound GTP and the T7 Loop*

    PubMed Central

    Matsui, Takashi; Han, Xuerong; Yu, Jian; Yao, Min; Tanaka, Isao

    2014-01-01

    FtsZ is a prokaryotic homolog of tubulin and is a key molecule in bacterial cell division. FtsZ with bound GTP polymerizes into tubulin-like protofilaments. Upon polymerization, the T7 loop of one subunit is inserted into the nucleotide-binding pocket of the second subunit, which results in GTP hydrolysis. Thus, the T7 loop is important for both polymerization and hydrolysis in the tubulin/FtsZ family. Although x-ray crystallography revealed both straight and curved conformations of tubulin, only a curved structure was known for FtsZ. Recently, however, FtsZ from Staphylococcus aureus has been shown to have a very different conformation from the canonical FtsZ structure. The present study was performed to investigate the structure of FtsZ from Staphylococcus aureus by mutagenesis experiments; the effects of amino acid changes in the T7 loop on the structure as well as on GTPase activity were studied. These analyses indicated that FtsZ changes its conformation suitable for polymerization and GTP hydrolysis by movement between N- and C-subdomains via intermolecular interactions between bound nucleotide and residues in the T7 loop. PMID:24347164

  17. Intermolecular interaction between Cry2Aa and Cyt1Aa and its effect on larvicidal activity against Culex quinquefasciatus.

    PubMed

    Bideshi, Dennis K; Waldrop, Greer; Fernandez-Luna, Maria Teresa; Diaz-Mendoza, Mercedes; Wirth, Margaret C; Johnson, Jeffrey J; Park, Hyun-Woo; Federici, Brian A

    2013-08-01

    The Cyt1Aa protein of Bacillus thuringiensis susbp. israelensis elaborates demonstrable toxicity to mosquito larvae, but more importantly, it enhances the larvicidal activity of this species Cry proteins (Cry11Aa, Cry4Aa, and Cry4Ba) and delays the phenotypic expression of resistance to these that has evolved in Culex quinquefasciatus. It is also known that Cyt1Aa, which is highly lipophilic, synergizes Cry11Aa by functioning as a surrogate membrane-bound receptor for the latter protein. Little is known, however, about whether Cyt1Aa can interact similarly with other Cry proteins not primarily mosquitocidal; for example, Cry2Aa, which is active against lepidopteran larvae, but essentially inactive or has very low toxicity to mosquito larvae. Here we demonstrate by ligand binding and enzyme-linked immunosorbent assays that Cyt1Aa and Cry2Aa form intermolecular complexes in vitro, and in addition show that Cyt1Aa facilitates binding of Cry2Aa throughout the midgut of C. quinquefasciatus larvae. As Cry2Aa and Cry11Aa share structural similarity in domain II, the interaction between Cyt1Aa and Cry2Aa could be a result of a similar mechanism previously proposed for Cry11Aa and Cyt1Aa. Finally, despite the observed interaction between Cry2Aa and Cyt1Aa, only a 2-fold enhancement in toxicity resulted against C. quinquefasciatus. Regardless, our results suggest that Cry2Aa could be a useful component of mosquitocidal endotoxin complements being developed for recombinant strains of B. thuringiensis subsp. israelensis and B. sphaericus aimed at improving the efficacy of commercial products and avoiding resistance. PMID:23727800

  18. 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.

  19. 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

  20. The structural basis of androgen receptor activation: Intramolecular and intermolecular amino-carboxy interactions

    Microsoft Academic Search

    Fred Schaufele; Xavier Carbonell; Martin Guerbadot; Sabine Borngraeber; Mark S. Chapman; Aye Aye K. Ma; Jeffrey N. Miner; Marc I. Diamond

    2005-01-01

    Nuclear receptors (NRs) are ligand-regulated transcription factors important in human physiology and disease. In certain NRs, including the androgen receptor (AR), ligand binding to the carboxy-terminal domain (LBD) regulates transcriptional activation functions in the LBD and amino-terminal domain (NTD). The basis for NTD-LBD communication is unknown but may involve NTD-LBD interactions either within a single receptor or between different members

  1. 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

  2. Rebek imide platforms as model systems for the investigation of weak intermolecular interactions.

    PubMed

    Harder, Michael; Carnero Corrales, Marjorie A; Trapp, Nils; Kuhn, Bernd; Diederich, François

    2015-06-01

    A Rebek imide receptor with an acetylene-linked phenyl ring complexes 2,6-di(isobutyramido)pyridine in (CDCl2 )2 via triple H-bonding and ?-?-stacking interactions, and the influence of para-substituents on both rings was investigated by (1) H?NMR binding titrations. When the phenyl ring was extended to biphenyl and the C(4)-pyridine substituent varied, interaction energies increased in the order CH3 CH2 ???phenylinteraction with bound 2,6-di(isobutyramido)pyridine was investigated. Theoretical predictions that the mere introduction of a substituent has a stabilizing effect on ?-? stacking, regardless of its electronic nature, were experimentally confirmed. PMID:25944543

  3. Tuning intermolecular interactions to enhance solid-state nanopore force spectroscopy

    NASA Astrophysics Data System (ADS)

    Foun, Elaine

    Nanopores, nanometer sized holes in membranes, have recently come into prominence as tools for single molecule sensing. A technique called nanopore force spectroscopy uses the nanopore to probe energy landscapes between molecules. With the development of this technique, it will be possible for molecular recognition in complex fluids, such as blood. However, before that can be possible, solid-state nanopores, commonly fabricated in silicon nitride membranes, and having very confined sizes and charged surfaces, need to be optimized to minimize unwanted interactions between solution-phase molecules and the surface. DNA, for example, a crucial part of nanopore force spectroscopy, frequently sticks to the nanopore surface. Surface functionalization techniques, both on the nanopore and molecular surface, were attempted in this thesis work. These surface functionalization methods aimed to reduce surface charge or alter molecular properties in order to minimize the unwanted surface interactions, and they include silane modification, fluid lipid bilayer coating, and surfactant self-assembly on the DNA phosphate backbone. Results from some of these methods yield insights to improve nanopore force spectroscopy performance that will minimize the unwanted surface interactions and deliver on the promise of nanopore sensing.

  4. On the interactions between molecules in an off-resonant laser beam: Evaluating the response to energy migration and optically induced pair forces.

    PubMed

    Andrews, David L; Leeder, Jamie M

    2009-01-21

    Electronically excited molecules interact with their neighbors differently from their ground-state counterparts. Any migration of the excitation between molecules can modify intermolecular forces, reflecting changes to a local potential energy landscape. It emerges that throughput off-resonant radiation can also produce significant additional effects. The context for the present analysis of the mechanisms is a range of chemical and physical processes that fundamentally depend on intermolecular interactions resulting from second and fourth-order electric-dipole couplings. The most familiar are static dipole-dipole interactions, resonance energy transfer (both second-order interactions), and dispersion forces (fourth order). For neighboring molecules subjected to off-resonant light, additional forms of intermolecular interaction arise in the fourth order, including radiation-induced energy transfer and optical binding. Here, in a quantum electrodynamical formulation, these phenomena are cast in a unified description that establishes their inter-relationship and connectivity at a fundamental level. Theory is then developed for systems in which the interplay of these forms of interaction can be readily identified and analyzed in terms of dynamical behavior. The results are potentially significant in Forster measurements of conformational change and in the operation of microelectromechanical and nanoelectromechanical devices. PMID:19173528

  5. Macrocyclic beta-sheet peptides that mimic protein quaternary structure through intermolecular beta-sheet interactions.

    PubMed

    Khakshoor, Omid; Demeler, Borries; Nowick, James S

    2007-05-01

    This paper reports the design, synthesis, and characterization of a family of cyclic peptides that mimic protein quaternary structure through beta-sheet interactions. These peptides are 54-membered-ring macrocycles comprising an extended heptapeptide beta-strand, two Hao beta-strand mimics [JACS 2000, 122, 7654] joined by one additional alpha-amino acid, and two delta-linked ornithine beta-turn mimics [JACS 2003, 125, 876]. Peptide 3a, as the representative of these cyclic peptides, contains a heptapeptide sequence (TSFTYTS) adapted from the dimerization interface of protein NuG2 [PDB ID: 1mio]. 1H NMR studies of aqueous solutions of peptide 3a show a partially folded monomer in slow exchange with a strongly folded oligomer. NOE studies clearly show that the peptide self-associates through edge-to-edge beta-sheet dimerization. Pulsed-field gradient (PFG) NMR diffusion coefficient measurements and analytical ultracentrifugation (AUC) studies establish that the oligomer is a tetramer. Collectively, these experiments suggest a model in which cyclic peptide 3a oligomerizes to form a dimer of beta-sheet dimers. In this tetrameric beta-sheet sandwich, the macrocyclic peptide 3a is folded to form a beta-sheet, the beta-sheet is dimerized through edge-to-edge interactions, and this dimer is further dimerized through hydrophobic face-to-face interactions involving the Phe and Tyr groups. Further studies of peptides 3b-3n, which are homologues of peptide 3a with 1-6 variations in the heptapeptide sequence, elucidate the importance of the heptapeptide sequence in the folding and oligomerization of this family of cyclic peptides. Studies of peptides 3b-3g show that aromatic residues across from Hao improve folding of the peptide, while studies of peptides 3h-3n indicate that hydrophobic residues at positions R3 and R5 of the heptapeptide sequence are important in oligomerization. PMID:17419629

  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. Intermolecular Interactions of Sprouty Proteins and Their Implications in Development and Disease

    PubMed Central

    Edwin, Francis; Anderson, Kimberly; Ying, Chunyi

    2009-01-01

    Receptor tyrosine kinase (RTK) signaling is spatially and temporally regulated by a number of positive and negative regulatory mechanisms. These regulatory mechanisms control the amplitude and duration of the signals initiated at the cell surface to have a normal or aberrant biological outcome in development and disease, respectively. In the past decade, the Sprouty (Spry) family of proteins has been identified as modulators of RTK signaling in normal development and disease. This review summarizes recent advances concerning the biological activities modulated by Spry family proteins, their interactions with signaling proteins, and their involvement in cardiovascular diseases and cancer. The diversity of mechanisms in the regulation of Spry expression and activity in cell systems emphasizes the crucial role of Spry proteins in development and growth across the animal kingdom. PMID:19570949

  8. Carbon dioxide clathrate hydrates: selective role of intermolecular interactions and action of the SDS catalyst.

    PubMed

    Albertí, M; Pirani, F; Laganà, A

    2013-08-15

    The ability of a single sodium dodecyl sulfate (SDS) molecule to promote the formation of CO2 clathrate hydrates in water (as it does for methane) has been investigated at the microscopic level. For this purpose, the components of the related force field were carefully formulated and assembled following the procedure previously adopted for methane. The properties of the whole system (as well as those of its components) were analyzed by carrying out extended molecular dynamics calculations. Contrary to what happens for methane, the calculations singled out the propensity of CO2 (pure) water clusters to form clathrate hydrate-like structures and the disappearance of such propensity when a single SDS molecule is added to the clusters. This feature was found to be due to the strong interaction of carbon dioxide with the additive that makes the SDS molecule lose its shape together with its ability to drive water molecules to form a suitable cage. PMID:23635031

  9. Intermolecular interactions between molecules in various conformational states: the dimer of oxalic acid.

    PubMed

    Keolopile, Zibo G; Ryder, Matthew R; Gutowski, Maciej

    2014-09-01

    We considered stability of the dimer of oxalic acid. The global minimum energy structure identified by us is stabilized by two inter- and four intramolecular hydrogen bonds, whereas the most stable structure identified in previous studies is supported by two inter- and three intramolecular hydrogen bonds. The latter structure proves to be less stable by 25 meV than the former. The global minimum stability results from a balancing act between a moderately attractive two-body interaction energy and small repulsive one-body terms. We have analyzed zero-point vibrational corrections to the stability of various conformers of oxalic acid and their dimers. We have found that minimum energy structures with the most stabilizing sets of hydrogen bonds have the largest zero-point vibrational energy, contrary to a naive anticipation based on red shifts of OH stretching modes involved in hydrogen bonds. PMID:24923870

  10. Several aspects of intermolecular interactions between the carbonyl and imine groups in the crystals of compounds containing six-membered heterocycles

    Microsoft Academic Search

    N. I. Golovina; G. N. Nechiporenko; I. N. Zyuzin; D. B. Lempert; G. G. Nemtsev; G. V. Shilov; A. N. Utenyshev; K. V. Bozhenko

    2008-01-01

    Three modifier compounds that stabilize the phase state of ammonium nitrate over a wide range of temperatures, 1,3,5-trihydroxyisocyanuric\\u000a acid dihydrate (1), 4-aminouracil (2), and 4-aminouracil monohydrate (3) were studied by X-ray diffraction. Strong donor-acceptor intermolecular interactions were found for structures 2 and 3. The electronic parameters of the molecules were calculated by quantum-chemical methods, and it was found that additional

  11. 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.

  12. Isomerization and intermolecular solute-solvent interactions of ethyl isocyanate: Ultrafast infrared vibrational echoes and linear vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Levinger, Nancy E.; Davis, Paul H.; Behera, Pradipta Kumar; Myers, D. J.; Stromberg, Christopher; Fayer, M. D.

    2003-01-01

    Thermally induced gauche-trans isomerization and direct solute-solvent interactions of the solute, ethyl isocyanate (EIC), in the solvent, 2-methylpentane (2MP), are investigated using ultrafast infrared vibrational echo experiments and linear vibrational absorption spectroscopy of the isocyanate (N=C=O) antisymmetric stretching mode (2278 cm-1). Both the EIC vibrational echo measured pure vibrational dephasing and the absorption spectra show complex behavior as a function of temperature from room temperature to 8 K. The EIC data are compared to absorption experiments on the same mode of isocyanic acid (HNCO), which cannot undergo isomerization. To describe the observations, a model is presented that involves both intramolecular dynamics and intermolecular dynamical interactions. At room temperature, gauche-trans isomerization is very fast, and the isomerization dynamics contribution to the vibrational echo decay and the absorption line shape is small because it is motionally narrowed. The dominant contribution to both the vibrational echo decay and the absorption spectrum is from direct dynamical interactions of the solute with the solvent. As the temperature is lowered, the direct contribution to vibrational dephasing decreases rapidly, but the contribution from isomerization increases because the extent of motional narrowing diminishes. The combined effect is a very gradual decrease of the rate of pure dephasing as the temperature is initially lowered from room temperature. At very low temperature, below the 2MP glass transition, isomerization cannot occur. The absorption spectrum displays two peaks, interpreted as the distinct gauche and trans absorption bands. Even at 8 K, the pure dephasing is surprisingly fast. The direct solvent-induced dephasing is negligible. The dephasing is caused by motions of the ethyl group without isomerization occuring. At intermediate temperatures (150 K>T>100 K), isomerization takes place, but its contribution to the pure dephasing is not motionally narrowed. The absorption spectral shapes are complex. Dephasing arising from direct interaction with the solvent is small. Both isomerization and fluctuations on the gauche-trans surface contribute to the absorption line shape. The model that is used to describe the results involves a NMR type exchange calculation with additional contributions from the direct solvent interactions that are obtained from the temperature-dependent HNCO IR spectra. From the temperature dependence of the isomerization "jump" rate, the barrier height for the isomerization is found to be ˜400 cm-1.

  13. 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

  14. Asynchronous orthogonal sample design scheme for two-dimensional correlation spectroscopy (2D-COS) and its application in probing intermolecular interactions from overlapping infrared (IR) bands.

    PubMed

    Li, Xiaopei; Pan, Qinghua; Chen, Jing; Liu, Shaoxuan; He, Anqi; Liu, Cuige; Wei, Yongju; Huang, Kun; Yang, Limin; Feng, Juan; Zhao, Ying; Xu, Yizhuang; Ozaki, Yukihiro; Noda, Isao; Wu, Jinguang

    2011-08-01

    This paper introduces a new approach to analysis of spectra called asynchronous orthogonal sample design (AOSD). Specifically designed concentration series are selected according to mathematical analysis of orthogonal vectors. Based on the AOSD approach, the interfering portion of the spectra arising strictly from the concentration effect can be completely removed from the asynchronous spectra. Thus, two-dimensional (2D) asynchronous spectra can be used as an effective tool to characterize intermolecular interactions that lead to apparent deviations from the Beer-Lambert law, even if the characteristic peaks of two compounds are substantially overlapped. A model solution with two solutes is used to investigate the behavior of the 2D asynchronous spectra under different extents of overlap of the characteristic peaks. Simulation results demonstrate that the resulting spectral patterns can reflect subtle spectral variations in bandwidths, peak positions, and absorptivities brought about by intermolecular interaction, which are barely visualized in the conventional one-dimensional (1D) spectra. Intermolecular interactions between butanone and dimethyl formamide (DMF) in CCl(4) solutions were investigated using the proposed AOSD approach to prove the applicability of the AOSD method in real chemical systems. PMID:21819780

  15. Exploring the inter-molecular interactions in amyloid-? protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations

    NASA Astrophysics Data System (ADS)

    Liu, Fu-Feng; Liu, Zhen; Bai, Shu; Dong, Xiao-Yan; Sun, Yan

    2012-04-01

    Aggregation of amyloid-? (A?) peptides correlates with the pathology of Alzheimer's disease. However, the inter-molecular interactions between A? protofibril remain elusive. Herein, molecular mechanics Poisson-Boltzmann surface area analysis based on all-atom molecular dynamics simulations was performed to study the inter-molecular interactions in A?17-42 protofibril. It is found that the nonpolar interactions are the important forces to stabilize the A?17-42 protofibril, while electrostatic interactions play a minor role. Through free energy decomposition, 18 residues of the A?17-42 are identified to provide interaction energy lower than -2.5 kcal/mol. The nonpolar interactions are mainly provided by the main chain of the peptide and the side chains of nine hydrophobic residues (Leu17, Phe19, Phe20, Leu32, Leu34, Met35, Val36, Val40, and Ile41). However, the electrostatic interactions are mainly supplied by the main chains of six hydrophobic residues (Phe19, Phe20, Val24, Met35, Val36, and Val40) and the side chains of the charged residues (Glu22, Asp23, and Lys28). In the electrostatic interactions, the overwhelming majority of hydrogen bonds involve the main chains of A? as well as the guanidinium group of the charged side chain of Lys28. The work has thus elucidated the molecular mechanism of the inter-molecular interactions between A? monomers in A?17-42 protofibril, and the findings are considered critical for exploring effective agents for the inhibition of A? aggregation.

  16. PHYSICAL REVIEW A 88, 012716 (2013) Breakup of Rydberg-blockaded atom clouds via dipole-dipole interactions

    E-print Network

    Eisfeld, Alexander

    2013-01-01

    the clouds. The dynamics is akin to an ensemble average over systems where only one atom per cloudPHYSICAL REVIEW A 88, 012716 (2013) Breakup of Rydberg-blockaded atom clouds via dipole Rydberg-blockaded atom clouds where each cloud carries initially a coherently shared single excitation. We

  17. Optical Control of Excitons in a Pair of Quantum Dots Coupled by the Dipole-Dipole Interaction Thomas Unold,1

    E-print Network

    Peinke, Joachim

    proposed for implementing novel quantum function in man-made nanostructures such as semiconductor quantum nanosystems on ultrashort time scales. We study dipolar couplings between two individual semiconductor quantum of a 5.1 nm (100) GaAs quantum well (QW) grown by mo- lecular beam epitaxy between two Al

  18. PHYSICAL REVIEW B 85, 224303 (2012) Mixed-space approach for calculation of vibration-induced dipole-dipole interactions

    E-print Network

    Chen, Long-Qing

    2012-01-01

    . INTRODUCTION The phonon approach1,2 is currently the most efficient method for predicting thermodynamic properties of a solid at finite temperatures. It has been implemented under the frame- work of first. Lyddane et al.8 first accurately formulated the polar vibrations of cubic alkali halides in the long wave

  19. 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

  20. 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

  1. Intermolecular Forces for Polyatomic Molecules

    Microsoft Academic Search

    Taro Kihara

    1967-01-01

    Part I is a review of papers dealing with the convex-core potential (sometimes called the Kihara potential) of intermolecular forces, which is a useful mathematical model for the interaction between polyatomic molecules in gases. For molecular crystals electric multipoles of the molecules often play a decisive role in the crystal structures. This fact is demonstrated in Part II by use

  2. 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.

  3. 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

  4. In-vitro anti-proliferative and anti-oxidant activity of galangin, fisetin and quercetin: role of localization and intermolecular interaction in model membrane.

    PubMed

    Sinha, Ragini; Srivastava, Sudha; Joshi, Akshada; Joshi, Urmila J; Govil, Girjesh

    2014-05-22

    Flavonols are an important class of naturally occurring molecules and are known for their pharmacological activity. The activity is associated with the ability of flavonols to influence membrane-dependent processes. We have investigated the in-vitro anti-proliferative and anti-oxidant activity of galangin (GLN), fisetin (FTN) and quercetin (QTN), which possess variable number of phenolic hydroxyl groups. An attempt has been made to correlate the biological activity of these molecules with their interaction and localization in dipalmitoyl phosphatidyl choline (DPPC) bilayers, using differential dcanning calorimetry (DSC) and nuclear magnetic resonance (NMR) methods. Results indicate that GLN interacts to the alkyl chains of the lipid bilayer involving hydrophobic interactions. FTN and QTN interact with head region and sn-1-glycero region involving hydrogen bonding. Ring current induced chemical shifts of lipid protons, due to intermolecular interaction indicate that GLN acquires a parallel orientation with respect to the bilayer normal whereas FTN and QTN resume a mixed orientation. The membrane binding constants of these molecules are in the order GLN > QTN > FTN. It has been shown that the number and position of hydroxyl groups in these molecules play an important role in membrane binding and thereby in biological activity. PMID:24727463

  5. Intermolecular interactions in weak donor-acceptor complexes from symmetry-adapted perturbation and coupled-cluster theory: tetracyanoethylene-benzene and tetracyanoethylene-p-xylene.

    PubMed

    Kuchenbecker, Dennis; Jansen, Georg

    2012-08-01

    The interactions in the complexes of tetracyanothylene (TCNE) with benzene and p-xylene, often classified as weak electron donor-acceptor (EDA) complexes, are investigated by a range of quantum chemical methods including intermolecular perturbation theory at the DFT-SAPT (symmetry-adapted perturbation theory combined with density functional theory) level and explicitly correlated coupled-cluster theory at the CCSD(T)-F12 level. The DFT-SAPT interaction energies for TCNE-benzene and TCNE-p-xylene are estimated to be -35.7 and -44.9 kJ?mol(-1), respectively, at the complete basis set limit. The best estimates for the CCSD(T) interaction energy are -37.5 and -46.0 kJ?mol(-1), respectively. It is shown that the second-order dispersion term provides the most important attractive contribution to the interaction energy, followed by the first-order electrostatic term. The sum of second- and higher-order induction and exchange-induction energies is found to provide nearly 40?% of the total interaction energy. After addition of vibrational, rigid-rotor, and translational contributions, the computed internal energy changes on complex formation approach results from gas-phase spectrophotometry at elevated temperatures within experimental uncertainties, while the corresponding entropy changes differ substantially. PMID:22696390

  6. Separation of Anisotropy and Exchange Broadening Using 15N CSA- 15N- 1H Dipole-Dipole Relaxation Cross-Correlation Experiments

    NASA Astrophysics Data System (ADS)

    Renner, Christian; Holak, Tad A.

    2000-08-01

    Based on the measurement of cross-correlation rates between 15N CSA and 15N-1H dipole-dipole relaxation we propose a procedure for separating exchange contributions to transverse relaxation rates (R2 = 1/T2) from effects caused by anisotropic rotational diffusion of the protein molecule. This approach determines the influence of anisotropy and chemical exchange processes independently and therefore circumvents difficulties associated with the currently standard use of T1/T2 ratios to determine the rotational diffusion tensor. We find from computer simulations that, in the presence of even small amounts of internal flexibility, fitting T1/T2 ratios tends to underestimate the anisotropy of overall tumbling. An additional problem exists when the N-H bond vector directions are not distributed homogeneously over the surface of a unit sphere, such as in helix bundles or ?-sheets. Such a case was found in segment 4 of the gelation factor (ABP 120), an F-actin cross-linking protein, in which the diffusion tensor cannot be calculated from T1/T2 ratios. The 15N CSA tensor of the residues for this ?-sheet protein was found to vary even within secondary structure elements. The use of a common value for the whole protein molecule therefore might be an oversimplification. Using our approach it is immediately apparent that no exchange broadening exists for segment 4 although strongly reduced T2 relaxation times for several residues could be mistaken as indications for exchange processes.

  7. 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

  8. Observation of intermolecular interactions in large protein complexes by 2D-double difference nuclear Overhauser enhancement spectroscopy: application to the 44 kDa interferon-receptor complex.

    PubMed

    Nudelman, Ilona; Akabayov, Sabine R; Scherf, Tali; Anglister, Jacob

    2011-09-21

    NMR detection of intermolecular interactions between protons in large protein complexes is very challenging because it is difficult to distinguish between weak NOEs from intermolecular interactions and the much larger number of strong intramolecular NOEs. This challenging task is exacerbated by the decrease in signal-to-noise ratio in the often used isotope-edited and isotope-filtered experiments as a result of enhanced T(2) relaxation. Here, we calculate a double difference spectrum that shows exclusively intermolecular NOEs and manifests the good signal-to-noise ratio in 2D homonuclear NOESY spectra even for large proteins. The method is straightforward and results in a complete picture of all intermolecular interactions involving non exchangeable protons. Ninety-seven such (1)H-(1)H NOEs were assigned for the 44 KDa interferon-?2/IFNAR2 complex and used for docking these two proteins. The symmetry of the difference spectrum, its superb resolution, and unprecedented signal-to-noise ratio in this large protein/receptor complex suggest that this method is generally applicable to study large biopolymeric complexes. PMID:21819146

  9. Intermolecular bonding in conjugated polymers

    NASA Astrophysics Data System (ADS)

    Schmit, Jeremy D.; Levine, Alex J.

    2005-03-01

    Soluble conjugated polymers may enable the development of fast sensitive biosensors. However, the tendency of these molecules to aggregate even at low concentrations has a profound effect on the fluorescence signal that these sensors rely on. We propose that the aggregation of doped conjugated polymers occurs due to the formation of weak interpolymeric bonds resulting from intermolecular electron tunneling at crossing points of the chains. Although these bonds are essentially covalent in character, they are significantly weaker (˜2 kBT) due to poor the intermolecular overlap of the electron wavefunctions as well as the delocalization of the pi-electrons along the polymer backbone. We show that the aggregates resulting from these bonds form either loosely bound braids or tight bundles of parallel chains depending on the strength of the electrostatic repulsion between the polymers. Surprisingly, we find that undoped polymers are unable to form parallel bundles. We also explore the interaction of SSH solitons on the chains with these intermolecular binding sites and demonstrate a roughly a four-fold enhancement of the binding strength when each chain has a soliton at the binding site.

  10. 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

  11. Weak Chemical Interaction and van der Waals Forces: A Combined Density Functional and Intermolecular Perturbation Theory - Application to Graphite and Graphitic Systems

    NASA Astrophysics Data System (ADS)

    Dappe, Y. J.; Ortega, J.; Flores, F.

    In this contribution we address the theoretical underst anding of weak chemical interactions and of the van der Waals forces, in conjunction with the last developments in this area and selected applications to nanostructures. In the first section, we highlight the importance of these interactions, in physics and chemistry and also in biology, and we recall early treatments of these issues, as those by van der Waals and London. After a brief review of the existing methods to treat such interactions, we present a model based on DFT (for each van der Waals-interacting independent system) and an intermolecular perturbation theory that uses a localized orbitals basis set. We will first detail a weak overlap expansion (LCAO-S 2) as a perturbation treatment to determine the weak chemical interaction. Then we will show how to implement the van der Waals interaction in the DFT solution, from the dipolar approximation in a perturbation theory. We apply this model to a reference system for weak interactions, i.e., the interaction between two planes of graphene. In the framework of a minimal basis set that describes each independent system and the weak chemical repulsion, we show that it is necessary to take into account atomic dipole transitions involving high excited states like 3d orbitals to properly describe the van der Waals interaction. We demonstrate how the delicate balance between chemical repulsion and van der Waals attractive interaction gives the equilibrium geometry and the binding energy of the system. Moreover, as an extension of this work, we obtain the adsorption energy of a carbon nanotube on graphene, the adsorption energy of a C60 molecule on a carbon nanotube, and the energy of a C60 molecule encapsulated in a carbon nanotube. This gives us the opportunity to discuss incommensurable systems. A complete study of C60 dimers is also presented with future perspective for the study of C60 molecular crystals. We will conclude with an overview of this work, discussing interaction and transport at metal-organics interfaces from the point of view of applications in the field of molecular electronics.

  12. Relationship between molecular weight of poly(ethylene)glycol and intermolecular interaction of Taka-amylase A monomers

    NASA Astrophysics Data System (ADS)

    Onuma, Kazuo; Furubayashi, Naoki; Shibata, Fujiko; Kobayashi, Yoshiko; Kaito, Sachiko; Ohnishi, Yuki; Inaka, Koji

    2010-04-01

    Dynamic and static light scattering investigations of Taka-amylase A (TAA) protein monomers were done using solutions containing poly(ethylene)glycol (PEG) with molecular weights of 1500, 4000, 8000, and 20 000. The anomalies observed in a previous study using a weight of 8000, in which the hydrodynamic TAA monomer radius at a zero protein concentration and the molecular weight of the monomers decreased when the PEG concentration was increased, were observed for all four weights. These anomalies became more pronounced as the PEG molecular weight was increased. The overall interaction parameter did not move further in the direction of the attractive force despite an increase in the PEG concentration from 6% to 12.5% for the PEG 8000 and 20 000 solutions. This was due to the change in the relative contributions of the static structure factor (direct interaction) and the hydrodynamic interaction factor (indirect interaction) against the overall interaction parameter. For the PEG 1500 and 4000 solutions, the change in the overall interaction parameter with an increase in the PEG concentration was controlled by changing the static structure factor. For the PEG 8000 and 20 000 solutions, a change in the hydrodynamic interaction factor with an increase in the PEG concentration offset the change in the static structure factor, unexpectedly resulting in the overall interaction parameter being independent of the PEG concentration. This suggests that the scale and density of a PEG network structure, which are thought to be the origin of the observed anomalies, change nonlinearly with the PEG molecular weight.

  13. Calculation of intermolecular interactions in the benzene dimer using coupled-cluster and local electron correlation methods

    Microsoft Academic Search

    J. Grant Hill; James A. Platts; Hans-Joachim Werner

    2006-01-01

    Potential energy surfaces for the parallel-displaced, T-shaped and sandwich structures of the benzene dimer are computed with density tted local second-order Mller-Plesset pertur- bation theory (DF-LMP2) as well as with the spin-component scaled (SCS) variant of DF- LMP2. While DF-LMP2 strongly overestimates the dispersion interaction, in common with canonical MP2, the DF-SCS-LMP2 interaction energies are in excellent agreement with the

  14. Molecular characterization and intermolecular interaction of coat protein of Prunus necrotic ringspot virus: implications for virus assembly.

    PubMed

    Kulshrestha, Saurabh; Hallan, Vipin; Sharma, Anshul; Seth, Chandrika Attri; Chauhan, Anjali; Zaidi, Aijaz Asghar

    2013-09-01

    Coat protein (CP) and RNA3 from Prunus necrotic ringspot virus (PNRSV-rose), the most prevalent virus infecting rose in India, were characterized and regions in the coat protein important for self-interaction, during dimer formation were identified. The sequence analysis of CP and partial RNA 3 revealed that the rose isolate of PNRSV in India belongs to PV-32 group of PNRSV isolates. Apart from the already established group specific features of PV-32 group member's additional group-specific and host specific features were also identified. Presence of methionine at position 90 in the amino acid sequence alignment of PNRSV CP gene (belonging to PV-32 group) was identified as the specific conserved feature for the rose isolates of PNRSV. As protein-protein interaction plays a vital role in the infection process, an attempt was made to identify the portions of PNRSV CP responsible for self-interaction using yeast two-hybrid system. It was found (after analysis of the deletion clones) that the C-terminal region of PNRSV CP (amino acids 153-226) plays a vital role in this interaction during dimer formation. N-terminal of PNRSV CP is previously known to be involved in CP-RNA interactions, but our results also suggested that N-terminal of PNRSV CP represented by amino acids 1-77 also interacts with C-terminal (amino acids 153-226) in yeast two-hybrid system, suggesting its probable involvement in the CP-CP interaction. PMID:24426281

  15. Weak intermolecular hydrogen and halogen interactions in an isomorphous halogen series of pseudoterpyridine Zn(II) complexes.

    PubMed

    Dumitru, Florina; Legrand, Yves-Marie; Barboiu, Mihail; van der Lee, Arie

    2013-02-01

    The synthesis and characterization of a series of halogen-substituted pseudoterpyridine Zn(II) homoleptic mononuclear complexes, based on ligands L(11)-L(44) [2,6-pyridinedicarboxaldehydebis(p-R-phenylimines), R = F, Cl, Br, I] are reported. Neither of the structures contain relatively strong classical hydrogen bonds (OH···O, NH···O, OH···N, NH···N) and the structure packing is thus determined by a subtle interplay of weaker interactions. Isostructurality of the four halogen analogues is very rare, and in this study -Br, -Cl and -F are found to be isostructural in different degrees, whereas -I is not. Interestingly, although it is closely isostructural to the -Cl and -Br compounds, the F analogue is shown not to form F···O bonds, while the Cl and the Br analogues do form Hal···O bonds. This raises an important question on the role of Hal···O bonds in the structuration of the crystal packing, particularly the stabilization effect. Similarly, while the CH···Hal interaction seems to give one-dimensional cohesion in the -Cl and -Br analogues, this feature is absent in the -F analogue, despite its close isostructurality. CH···O interactions appear to dominate to a first degree the cohesion between the anionic trifluoromethanesulfonate network and the cationic Zn-pyridinedicarboxaldehydebis(p-R-phenylimines) network. The analysis of these interactions is corroborated by reduced density gradient calculations based on promolecular densities. PMID:23364459

  16. Antibiotic-DNA interactions: intermolecular nuclear Overhauser effects in the netropsin-d(C-G-C-G-A-A-T-T-C-G-C-G) complex in solution.

    PubMed Central

    Patel, D J

    1982-01-01

    The proton markers located in the minor groove of the d(C-G-C-G-A-A-T-T-C-G-C-G) duplex and its netropsin complex have been assigned from measurements of intramolecular nuclear Overhauser effects (NOEs) between exchangeable imino protons and nonexchangeable base protons on the same and adjacent base pairs. Several points of contact between the concave face of the antibiotic and the minor groove d(A-A-T-T) tetranucleotide segment of the dodecanucleotide duplex have been established based on intermolecular NOE effects between the pyrrole ring and side-chain methylene protons of netropsin and the adenosine H-2 protons of dA X dT base pairs in the center of the duplex. These NOE measurements provide a powerful method for differentiating between minor and major groove contacts in ligand-DNA complexes in solution. A model for netropsin interaction at dA X dT sites on duplex DNA is proposed. Images PMID:6292900

  17. Effect of Intermolecular Hydrogen Bonding on the Nuclear Quadrupole Interaction in Imidazole and its Derivatives as Studied by ab initio Molecular Orbital Calculations

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

    Ab initio Hartree-Fock molecular orbital calculations were applied to the crystalline imidazole and its derivatives in order to examine systematically the effect of possible N-H---N type hydrogen bond-ing on the nuclear quadrupole interaction parameters in these materials. The nitrogen quadrupole coupling constant (QCC) and the asymmetry parameter (?) of the electric field gradient (EFG) were found to depend strongly on the size of the molecular clusters, from single molecule, to dimer, trimer and to the infinite molecular chain, i.e., crystalline state, implying that the intermolecular N-H -N hydrogen bond affects significantly the electronic structure of imidazole molecule. A certain correla-tion between the QCC of 14N and the N-H bond distance R was also found and interpreted on the basis of the molecular orbital theory. However, we found that the value of the calculated EFG at the hy-drogen position of the N-H group, or the corresponding QCC value of 2 H, increases drastically as R-3 when R is shorter than about 0.1 nm, due probably to the inapplicability of the Gaussian basis sets to the very short chemical bond as revealed in the actual imidazole derivatives. We suggested that the ob-served N-H distances in imidazole derivatives should be re-examined.

  18. 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.

  19. Interaction of pyrrolobenzodiazepine (PBD) ligands with parallel intermolecular G-quadruplex complex using spectroscopy and ESI-MS.

    PubMed

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

    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 hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5'GGGGTTGGGG3') designated as d(T(2)G(8)), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T(2)G(8)) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T(2)G(8))(2) and d(T(2)G(8))(4) forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T(2)G(8)) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex. PMID:22558271

  20. 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.

  1. Effect of water potential on sol-gel transition and intermolecular interaction of gelatin near the transition temperature.

    PubMed

    Miyawaki, Osato; Norimatsu, Yuko; Kumagai, Hitoshi; Irimoto, Yoshinobu; Kumagai, Hitomi; Sakurai, Hidetoshi

    2003-12-01

    The sol-gel transition of gelatin, measured by thermal analysis and viscosity measurement, was analyzed in terms of the change in hydration state of polymer molecules. A new thermodynamic model was proposed in which the effect of water potential is explicitly taken into account for the evaluation of the free energy change in the sol-gel transition process. Because of the large number of water molecules involved and the small free energy change in the transition process, the contribution of water activity, a(W), was proved to be not negligible in the sol-gel transition process in solutions containing such low-molecular cosolutes as sugars, glycerol, urea, and formamide. The gel-stabilization effect of sugars and glycerol was linear with a(W), which seemed consistent with the contribution of water potential in the proposed model. The different stabilization effect among sugars and glycerol was explained by the difference in solvent ordering, which affects hydrophobic interaction among protein molecules. The gel-destabilization effect of urea and formamide could be explained only by the direct binding of them to protein molecules through hydrogen bonding. On the contrary, the polymer-polymer interaction, measured by the viscosity analysis, in polyethyleneglycol and dextran solutions was not sensitive to the change in a(W), suggesting that no substantial change in hydration state with a(W) occurred in these polymer solutions. PMID:14648759

  2. Intermolecular protein interactions in solutions of bovine lens beta L-crystallin. Results from 1/T1 nuclear magnetic relaxation dispersion profiles.

    PubMed Central

    Koenig, S H; Brown, R D; Kenworthy, A K; Magid, A D; Ugolini, R

    1993-01-01

    We report the magnetic field dependence of 1/T1 of solvent water protons and deuterons (nuclear magnetic relaxation dispersion, or NMRD, profiles) for solutions of steer lens beta L-crystallin. Such data allow the study of intermolecular protein interactions over a wide concentration range, here 1-34% vol/vol, by providing a measure of the rotational relaxation time of solute macromolecules. We conclude that, for approximately less than 5% protein, the solute particles are noncompact, with a rotationally averaged volume approximately three times that of a compact 60-kD sphere. (Earlier results for alpha-crystallin, approximately 1,000 kD, from optical and osmotic measurements (Vérétout and Tardieu, 1989. J. Mol. Biol. 205:713-728), show a similar, approximately twofold, effect). At intermediate concentrations, to approximately 20% protein, there is evidence for limited association or oligomerization, as found for the structurally related gamma II-crystallin (Koenig et al. 1990. Biophys. J. 57:461-469), to a limiting size about two-thirds that of alpha-crystallin. The difference in NMRD behavior of the three classes of crystallins is consonant with their differing osmotic properties (Vérétout and Tardieu. J. Mol. Biol. 1989, 205:713-728; Kenworthy, McIntosh, and Magid. Biophys. J. 1992. 61:A477; Tardieu et al. 1992. Eur. Biophys. J. 21:1-12). We indicate how the unusual structures and interactions of these three classes of proteins can be combined to optimize transparency and minimize colloid osmotic difficulties in eye lens. PMID:8388267

  3. Controlling gold atom penetration through alkanethiolate self-assembled monolayers on Au{111} by adjusting terminal group intermolecular interactions.

    PubMed

    Zhu, Zihua; Daniel, Thomas A; Maitani, Masato; Cabarcos, Orlando M; Allara, David L; Winograd, Nicholas

    2006-10-25

    The penetration behavior of thermally evaporated Au on S(CH(2))(15)CH(3), S(CH(2))(15)CO(2)CH(3), S(CH(2))(15)CO(2)H, K-modified S(CH(2))(15)CO(2)CH(3), and K-modified S(CH(2))(15)CO(2)H self-assembled monolayers (SAM) on Au substrates is investigated. Gold is a particularly interesting metal since vapor-deposited Au atoms are known to pass through alkanethiolate SAMs on Au{111} substrates at room temperature. Here we show that it is possible to control Au penetration by adjusting the interactions between terminal groups. It is found that Au atoms evenly penetrate into the CH(3) and CO(2)CH(3) films, forming smooth buried layers below the organic thin films. For the CO(2)H film, although Au atoms can still penetrate through it, filaments and mushroomlike clusters form due to H-bonding between film molecules. In the case of the K-modified CO(2)CH(3) or CO(2)H films, however, most Au atoms form islands at the vacuum interface. These results suggest that van der Waals forces and H-bonds are not strong enough to block Au from going through but that ionic interactions are able to block Au penetration. The measurements were performed primarily using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). The combination of these highly complementary probes provides a very useful strategy for the study of metal atom behavior on SAMs. PMID:17044698

  4. Preparation and characterization of co-amorphous Ritonavir-Indomethacin systems by solvent evaporation technique: improved dissolution behavior and physical stability without evidence of intermolecular interactions.

    PubMed

    Dengale, Swapnil J; Ranjan, Om Prakash; Hussen, Syed Sajjad; Krishna, B S M; Musmade, Prashant B; Gautham Shenoy, G; Bhat, Krishnamurthy

    2014-10-01

    The aim of this study was to stabilize the amorphous form of Ritonavir (RTV) a BCS class-II drug with known amorphous stabilizing small molecule Indomethacin (IND) by co-amorphous technology. The co-amorphous samples were prepared by solvent evaporation technique in the molar ratios RTV:IND (2:1), RTV:IND (1:1), RTV:IND (1:2) and their amorphous nature was confirmed by XRPD, DSC and FT-IR. Physical stability studies were carried out at temp 25°C and 40°C for maximum up to 90 days under dry conditions. Solubility and dissolution testing were carried out to investigate the dissolution advantage of prepared co-amorphous systems. The amorphous mixtures of all tested molar ratios were found to become amorphous after solvent evaporation. The same was confirmed by detecting halo pattern in diffractograms of co-amorphous mixtures. The Tg values of all three systems were found to be more than 40°C, the highest being 51.88°C for RTV:IND (2:1) system. Theoretical Tg values were calculated by Gordon-Taylor equation. Insignificant deviation of theoretical Tg values from that of practical one, corroborated by FT-IR studies showed no evidence of intermolecular interactions between RTV and IND. Almost 3-folds increase in the solubility for both amorphous RTV and IND was found as compared to their respective crystalline counterparts. The study demonstrated significant increase in the dissolution rate as well as increase in the total amount of drug dissolved for amorphous RTV, however it failed to demonstrate any significant improvement in the dissolution behavior of IND. PMID:24878386

  5. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast 1 1 Edited by J. Karn

    Microsoft Academic Search

    Jong Park; Michael Lappe; Sarah A Teichmann

    2001-01-01

    In the postgenomic era, one of the most interesting and important challenges 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 independently. To study the large-scale patterns and evolution of

  6. THE JOURNAL OF CHEMICAL PHYSICS 134, 084501 (2011) Role of dipoledipole interaction on enhancing Brownian coagulation

    E-print Network

    Tse, Stephen D.

    2011-01-01

    Brownian coagulation of charge-neutral nanoparticles in the free molecular regime Yiyang Zhang,1 Shuiqing in the coagulation of nanoparticles (NPs) but has received little or no attention. In this work, the ef- fect of dipole­dipole interaction on the enhancement of the coagulation of two spherically shaped charge

  7. Solvation Dynamics of Dipolar Probes in Dipolar Room Temperature Ionic Liquids: Separation of Ion-Dipole and Dipole-Dipole Interaction Contributions

    E-print Network

    Biswas, Ranjit

    Solvation Dynamics of Dipolar Probes in Dipolar Room Temperature Ionic Liquids: Separation of Ion temperature ionic liquids (RTIL) have revealed large dynamic Stokes' shifts and biphasic solvation energy to the observed Stokes' shift and its dynamics. Conventional time-resolved measurements, however, cannot separate

  8. 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.

  9. Intermolecular perturbation theory

    NASA Astrophysics Data System (ADS)

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

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

  10. Competing interactions in semiconductor quantum dots

    DOE PAGESBeta

    van den Berg, R.; Brandino, G. P.; El Araby, O.; Konik, R. M.; Gritsev, V.; Caux, J. -S.

    2014-10-01

    We introduce an integrability-based method enabling the study of semiconductor quantum dot models incorporating both the full hyperfine interaction as well as a mean-field treatment of dipole-dipole interactions in the nuclear spin bath. By performing free induction decay and spin echo simulations we characterize the combined effect of both types of interactions on the decoherence of the electron spin, for external fields ranging from low to high values. We show that for spin echo simulations the hyperfine interaction is the dominant source of decoherence at short times for low fields, and competes with the dipole-dipole interactions at longer times. Onmore »the contrary, at high fields the main source of decay is due to the dipole-dipole interactions. In the latter regime an asymmetry in the echo is observed. Furthermore, the non-decaying fraction previously observed for zero field free induction decay simulations in quantum dots with only hyperfine interactions, is destroyed for longer times by the mean-field treatment of the dipolar interactions.« less

  11. Competing interactions in semiconductor quantum dots

    DOE PAGESBeta

    van den Berg, R. [Univ. of Amsterdam (Netherlands). Inst. for Theoretical Physics; Brandino, G. P. [Univ. of Amsterdam (Netherlands). Inst. for Theoretical Physics; El Araby, O. [Univ. of Amsterdam (Netherlands). Inst. for Theoretical Physics; Konik, R. M. [Brookhaven National Lab. (BNL), Upton, NY (United States); Gritsev, V. [Univ. of Amsterdam (Netherlands). Inst. for Theoretical Physics; Caux, J. -S. [Univ. of Amsterdam (Netherlands). Inst. for Theoretical Physics

    2014-10-01

    We introduce an integrability-based method enabling the study of semiconductor quantum dot models incorporating both the full hyperfine interaction as well as a mean-field treatment of dipole-dipole interactions in the nuclear spin bath. By performing free induction decay and spin echo simulations we characterize the combined effect of both types of interactions on the decoherence of the electron spin, for external fields ranging from low to high values. We show that for spin echo simulations the hyperfine interaction is the dominant source of decoherence at short times for low fields, and competes with the dipole-dipole interactions at longer times. On the contrary, at high fields the main source of decay is due to the dipole-dipole interactions. In the latter regime an asymmetry in the echo is observed. Furthermore, the non-decaying fraction previously observed for zero field free induction decay simulations in quantum dots with only hyperfine interactions, is destroyed for longer times by the mean-field treatment of the dipolar interactions.

  12. Molecular structure, spectral studies, intra and intermolecular interactions analyses in a novel ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate and its dimer: A combined DFT and AIM approach.

    PubMed

    Singh, R N; Baboo, Vikas; Rawat, Poonam; Kumar, Amit; Verma, Divya

    2012-08-01

    A newly synthesized chalcone, Ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (ECPADMPC) has been characterized by (1)H NMR, (13)C NMR, UV-Vis, FT-IR, Mass spectroscopy and elemental analysis. Quantum chemical calculations have been performed by DFT level of theory using B3LYP functional and 6-31G(d,p) as basis set. The time dependent density functional theory (TD-DFT) is used to find the various electronic transitions within molecule. A combined theoretical and experimental wavenumber analysis confirms the existence of dimer. Topological parameters-electron density (?(BCP)), Laplacian of electron density (?(2)?(BCP)), energetic parameters-kinetic electron energy density (G(BCP)), potential electron density (V(BCP)) and the total electron energy density (H(BCP)) at the bond critical points (BCP) have been analyzed by 'Atoms in molecules' AIM theory in detail. The intermolecular hydrogen bond energy of dimer is calculated as -12.3kcal/mol using AIM calculations. AIM ellipticity analysis is carried out to confirm the presence of resonance assisted intermolecular hydrogen bonds in stabilization of dimer. The analysis clearly depicts the presence of different kind of interactions in dimer. This dimer may work as model system to understand the H-bonding interaction in biomolecules. The local reactivity descriptor analysis is performed to find the reactive sites within molecule. PMID:22537939

  13. Intermolecular interactions involving C-H bonds, 3, Structure and energetics of the interaction between CH{sub 4} and CN{sup {minus}}

    SciTech Connect

    Novoa, J.J.; Whangbo, Myung-Hwan [North Carolina State Univ., Raleigh, NC (United States). Dept. of Chemistry; Williams, J.M. [Argonne National Lab., IL (United States)

    1991-12-31

    On the basis of SCF and single reference MP2 calculations, the full potential energy surface of the interaction between CH{sub 4} and CN{sup {minus}} was studied using extended basis sets of up to near Hartree-Fock limit quality. Colinear arrangements C-N{sup {minus}}{hor_ellipsis}H-CH{sub 3} and N-C{sup {minus}}{hor_ellipsis}H-CH{sub 3} are found to be the only two energy minima. The binding energies of these two structures are calculated to be 2.5 and 2.1 kcal/mol, respectively, at the MP2 level. The full vibrational analyses of two structures show a red shift of about 30 cm{sup {minus}1} for the v{sub s} C-H stretching.

  14. 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

  15. Intermolecular Forces: A Jigsaw Activity

    NSDL National Science Digital Library

    Boise State Edu.

    2011-09-20

    This jigsaw activity is designed as a cooperative learning activity used to introduce the idea of intermolecular forces. Intermolecular forces are the types of attractive forces that occur between molecules in a solid, liquid, or gas. Each force causes different physical properties of matter. Each member of the group will become an expert on one type of force and then teach the rest of the group.

  16. Interaction potential for aluminum nitride: A molecular dynamics study of mechanical and thermal properties of crystalline and amorphous aluminum nitride

    Microsoft Academic Search

    Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; José Pedro Rino

    2011-01-01

    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

  17. Bose-Einstein condensation of trapped atoms with dipole interactions

    SciTech Connect

    Nho, Kwangsik; Landau, D.P. [Center for Simulational Physics, University of Georgia, Athens, Georgia 30602 (United States)

    2005-08-15

    The path-integral Monte Carlo method is used to simulate dilute trapped Bose gases and to investigate the equilibrium properties at finite temperatures. The quantum particles have a long-range dipole-dipole interaction and a short-range s-wave interaction. Using an anisotropic pseudopotential for the long-range dipolar interaction and a hard-sphere potential for the short-range s-wave interaction, we calculate the energetics and structural properties as a function of temperature and the number of particles. Also, in order to determine the effects of dipole-dipole forces and the influence of the trapping field on the dipolar condensate, we use two cylindrically symmetric harmonic confinements (a cigar-shaped trap and a disk-shaped trap). We find that the net effect of dipole-dipole interactions is governed by the trapping geometry. For a cigar-shaped trap, the net contribution of dipolar interactions is attractive and the shrinking of the density profiles is observed. For a disk-shaped trap, the net effect of long-range dipolar forces is repulsive and the density profiles expand.

  18. 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.

  19. Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide

    Microsoft Academic Search

    Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; José Pedro Rino

    2007-01-01

    An effective interatomic interaction potential for SiC 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 Si-C-Si and C-Si-C

  20. Interaction potential for silicon carbide: A molecular dynamics study of elastic constants and vibrational density of states for crystalline and amorphous silicon carbide

    Microsoft Academic Search

    Priya Vashishta; Rajiv K. Kalia; Aiichiro Nakano; Jose´ Pedro Rino

    2007-01-01

    An effective interatomic interaction potential for SiC 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 Si–C–Si and C–Si–C

  1. Intermolecular Packing in Isotactic Polypropylene Liquids

    NASA Astrophysics Data System (ADS)

    Curro, J. G.; Rajasekaran, J. J.; Habenschuss, A.; Londono, J. D.; Honeycutt, J. D.

    1996-03-01

    Integral equation (PRISM) calculations were performed for isotactic polypropylene (i-PP) melts. The intramolecular structure functions, used as input to PRISM, were obtained from single chain Monte Carlo simulations of an i- PP molecule. Both explicit atom and united atom simulations were performed with continuous rotational potentials and local van der Waals interactions. Repulsive interactions beyond the pentane effect were intentionally set to zero to mimic the intramolecular structure in a melt. 3-site PRISM theory was used to calculate the 6 intermolecular radial distribution functions between methylene, methine and methyl group sites. The total structure factor computed from PRISM theory was compared with results from wide angle x-ray scattering measurements on i-PP melts at 200^circC. Excellent agreement between PRISM theory and scattering was found in the low wave vector regime where intermolecular packing effects are important. Although no evidence of a ``pre-peak'' is observed as in some vinyl chains, the low angle peak at k? 1 Åis considerably broadened relative to polyethylene melts.

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

    SciTech Connect

    Zhou, Y. L. [College of Science, National University of Defense Technology, Changsha, 410073 (China); Ortner, M. [Institute for Theoretical Physics, University of Innsbruck, AT-6020 Innsbruck (Austria); Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, AT-6020 Innsbruck (Austria); Rabl, P. [Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences, AT-6020 Innsbruck (Austria)

    2011-11-15

    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.

  3. 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

  4. Entanglement dynamics of three interacting two-level atoms within a common structured environment

    SciTech Connect

    An, Nguyen Ba; Kim, Jaewan; Kim, Kisik [Center for Theoretical Physics, Institute of Physics, 10 Dao Tan, Hanoi (Viet Nam) and School of Computational Sciences, Korea Institute for Advanced Study, 207-43 Cheongryangni 2-dong, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of); Department of Physics, Inha University, 253 Yonghyun-Dong, Nam-Gu, Incheon 402-751 (Korea, Republic of)

    2011-08-15

    We derive exact time evolution of three two-level atoms coupled to a common environment. The environment is structured and is modeled by a leaky cavity with Lorentzian spectral density. The atoms are initially prepared in a generalized W state and later on experience pairwise dipole-dipole interactions and couplings to the cavity. We study tripartite disentangling and entangling dynamics as well as protecting bipartite entanglement with both atom-atom interactions and atom-cavity couplings taken simultaneously into account.

  5. 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

  6. Quantum Correlations of Two Two-level Atoms Interacting with a Single Mode Vacuum Field

    NASA Astrophysics Data System (ADS)

    Zeng, Ke; Fang, Mao-Fa

    2015-04-01

    The quantum correlations (QC) of two two-level atoms interacting with a single mode vacuum field are investigated. The relationship between the quantum discord (QD) and the entanglement of formation (EOF), the influence of the atomic dipole-dipole interaction along with two-atom initial states on QC of two atoms are discussed. The results indicate that when two-atom is initially in an entangled state, QD is consistent with EOF. Compared with the quantumness of correlations, the latter is always larger than the former, and the larger the initial QE, the larger the QD. Meanwhile, there is no occurrence of sudden death phenomenon of QC throughout the temporal evolution. Moreover, QD is more robust than QE under strong dipole-dipole interaction, and then the relative stable QC resources can be achieved.

  7. Configurations of macromolecules subject to intermolecular volume exclusions

    Microsoft Academic Search

    Frederick T. Wall; John C. Chin; Frederic Mandel

    1977-01-01

    The effects of intermolecular interactions on the mean square end-to-end separations of macromolecules were studied by statistical sampling of multiple nonintersecting random walks on a square planar lattice. The ''slithering snake'' procedure was used to obtain large numbers of interacting random configurations, representing chains of 10, 20, 34, 62, and 104 links at various concentrations. The mean square end-to-end separation

  8. Configurations of macromolecules subject to intermolecular volume exclusions

    Microsoft Academic Search

    Frederick T. Wall; John C. Chin; Frederic Mandel

    1977-01-01

    The effects of intermolecular interactions on the mean square end-to-end separations of macromolecules were studied by statistical sampling of multiple nonintersecting random walks on a square planar lattice. The ’’slithering snake’’ procedure was used to obtain large numbers of interacting random configurations, representing chains of 10, 20, 34, 62, and 104 links at various concentrations. The mean square end-to-end separation

  9. Intermolecular interactions investigation of nickel(II) and zinc(II) salts of ortho-sulfobenzoic acid by X-ray diffraction and vibrational spectra

    NASA Astrophysics Data System (ADS)

    Chagas, Luciano H.; Janczak, Jan; Gomes, Fernando S.; Fernandes, Nelson G.; de Oliveira, Luiz Fernando C.; Diniz, Renata

    2008-12-01

    Two isostructural compounds consisting of hexaaquanickel(II) or hexaaquazinc(II) cations and hydrogen ortho-sulfobenzoate (HSBZ) as counter-ions have been synthesized and characterized by X-ray diffraction and vibrational spectroscopy techniques. The metal atom is located in the inversion centre and has a slightly distorted octahedral environment formed by water molecules, giving rise to ionic compounds with HSBZ. The HSBZ ions which are related by a c-glide plane interact to each other by medium to weak hydrogen bonds, developing wave-like chains parallel to the crystallographic c-axis. The [M(H 2O) 6] 2+ cation interacts with six surrounding HSB via the coordinated water molecules by hydrogen bonds. The oppositely charged units are interconnected into a 2D-polymeric superstructure parallel to (1 0 0) plane. The vibrational spectra of both salts are very similar to ortho-sulfobenzoic acid spectrum, and no significant shifts in SO and CO stretching bands were observed, suggesting the formation of ionic salts, which is in agreement with the X-ray results, thus indicating that the ortho-sulfobenzoate anion is a weaker ligand than water. Moreover, the presence of the acidic structure is very important in the definition of the supramolecular structure, since the hydrogen bonds design of the HSBZ is related to the cation size, probably due to the spatial factors involved in the crystal packing stability.

  10. Long-time joint spectra and entanglement of two photoelectrons originating in interacting auto-ionization systems

    E-print Network

    Jan Perina Jr.; A. Luks; W. Leonski

    2015-03-27

    Two auto-ionization systems in a stationary optical field mutually interacting via the dipole-dipole interaction are considered. Their evolution is analytically found. Joint spectra of two ionized electrons are analyzed in detail in the long-time limit for comparable strengths of direct and indirect ionization paths as well as the dominating indirect ionization path. Entanglement in the state of two ionized electrons is quantified using the density of quadratic negativity. Suitable conditions for obtaining highly entangled states are discussed.

  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 R(cm) 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. Intermolecular Interactions Between Formaldehyde and Dimethyl Ether and Between Formaldehyde Abd Dimethyl Sulfide in the Complex, Investigated by Fourier Transform Microwave Spectroscopy and AB Initio Calculations

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    The ground-state rotational spectra of the formaldehyde-dimethyl ether (H_2CO-DME) and the formaldehyde-dimethyl sulfide (H_2CO-DMS) complexes have been studied by Fourier transform microwave spectroscopy, and a-type and c-type transitions have been observed and assigned for the H_2CO as well as D_2CO species of both the complexes. In the case of the H_2CO-DME, doublets were observed with the splitting of a few 100 kHz, whereas no such splitting was found for the H_2CO-DMS. The observed rotational constants were analyzed to conclude a Cs geometry, where DME and DMS were bound to H_2CO by the two C-H(DME/DMS)---O(H_2CO) and the two O(DME)/S(DMS)---H-C(H_2CO) hydrogen bonds. The distances Rcm between the centers of mass of the constituents were determined to be 3.102 and 3.200 Å for the two complexes, respectively. Both the H_2CO-DME and H_2CO-DMS complexes were shown by the natural bond orbital (NBO) analysis, to have strong charge transfer interactions between the constituents, as expected from the strong electron-accepting character of the H_2CO.

  13. 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

  14. Calculation of the fluorescence spectrum of two interacting atoms in external field

    Microsoft Academic Search

    A. V. Gorokhov; V. V. Semin

    2009-01-01

    The radiation line profile for two identical dipole-dipole interacting two-level atoms in an external laser field is calculated.\\u000a The stochastic component of the laser radiation is explicitly taken into account simulating it by the optical white noise.\\u000a An explicit analytical expression for the radiation line profile is found for the case where the regular field component can\\u000a be neglected.

  15. Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies

    Microsoft Academic Search

    Paulo Sergio Branicio; José Pedro Rino; Chee Kwan Gan; Hélio Tsuzuki

    2009-01-01

    Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for

  16. Interaction potential for indium phosphide: a molecular dynamics and first-principles study of the elastic constants, generalized stacking fault and surface energies

    Microsoft Academic Search

    Paulo Sergio Branicio; José Pedro Rino; Chee Kwan Gan; Hélio Tsuzuki

    2009-01-01

    Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge–charge, charge–dipole and dipole–dipole interactions as well as covalent bond bending and stretching. Predictions are made for

  17. 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.

  18. Time displacement rotational echo double resonance: Heteronuclear dipolar recoupling with suppression of homonuclear interaction under fast magic-angle spinning

    NASA Astrophysics Data System (ADS)

    Tsai, Tim W. T.; Mou, Yun; Chan, Jerry C. C.

    2012-01-01

    We have developed a novel variant of REDOR which is applicable to multiple-spin systems without proton decoupling. The pulse sequence is constructed based on a systematic time displacement of the pi pulses of the conventional REDOR sequence. This so-called time displacement REDOR (td-REDOR) is insensitive to the effect of homonuclear dipole-dipole interaction when the higher order effects are negligible. The validity of td-REDOR has been verified experimentally by the P-31{C-13} measurements on glyphosate at a spinning frequency of 25 kHz. The experimental dephasing curve is in favorable agreement with the simulation data without considering the homonuclear dipole-dipole interactions.

  19. Characterization of amide-alkanediol intermolecular interactions.

    PubMed

    Alcalde, Rafael; García, Gregorio; Trenzado, José Luis; Atilhan, Mert; Aparicio, Santiago

    2015-04-01

    The properties of formamide + 1,2-alkanediol binary liquid systems were studied both at the macro- and microscopic levels using a combined experimental and computational methodology. Physicochemical properties, infrared spectroscopy, and solvatochromic studies together with classic molecular dynamics and quantum chemistry calculations allowed the main characteristics of these binary fluids to be inferred with regard to the variations of hydrogen bonding with formamide and 1,2-alkanediol molecular structures, mixture composition, and temperature. The complexity of these liquid systems arising from the presence of three different functional groups, which may act as hydrogen bond donors and acceptors, is analyzed, allowing a detailed picture to be inferred of the studied systems which is of relevance both for basic liquid state theory and for industrial purposes. PMID:25764128

  20. Intermolecular Interaction Studies of Winter Flounder

    E-print Network

    Nguyen, Dat H.

    freezing temperature of fish blood serum cannot be attributed to colligative effects of dissolved. Biopolymers, Vol. 75, 109­117 (2004) © 2004 Wiley Periodicals, Inc. 109 #12;water distribution in the region and entropic effects. Therefore, two nearly energetically degenerate states, an aggregated state

  1. Intermolecular interactions and viscosity of petroleum oils

    SciTech Connect

    Fuks, G.I.; Galkina, V.V.; Marcheva, E.N.

    1983-07-01

    The temperature coefficient of viscosities of petroleum oils increases with decreasing temperature. This paper surveys attempts to explain the temperature dependence of oil viscosity, and in particular analyze the data to show that at temperatures above 150/sup 0/ oils and oil hydrocarbons follow Frenkel's equation (as specified) in the first approximation. The magnitude of the viscosity, the contribution of associates with polymeric additives to viscosity, and the concept that oils are supercooled liquids are also studied. The relationships among the parameters of association of such complex mixtures as petroleum oils have not been studied adequately.

  2. Tuning the color emission of thin film molecular organic light emitting devices by the solid state solvation effect

    Microsoft Academic Search

    V Bulovi?; R Deshpande; M. E Thompson; S. R Forrest

    1999-01-01

    We demonstrate a general method for tuning the luminescent emission spectrum of dipolar molecules by adjusting the strength of intermolecular dipole–dipole interactions using a doped guest–host molecular organic thin film system. Spectral shifting is achieved by introducing dopants that change the local electric field in the film. This `solid state solvation effect' is used to continuously tune, by up to

  3. Intermolecular coupling and dynamics through infrared nano-spectroscopic imaging

    NASA Astrophysics Data System (ADS)

    Pollard, Benjamin; Muller, Eric A.; Khatib, Omar; Raschke, Markus B.

    2015-03-01

    Intermolecular interactions and coupling on the nanoscale lead to a variety of structural phases and degrees of crystallinity in soft-matter and biological systems, producing unique functional properties. We combine multi-spectral vibrational scattering-scanning near-field optical microscopy (s-SNOM) with multimodal scanning probe imaging to investigate structure-function relationships in soft matter. Using vibrational resonances as sensitive reporters of local structure, coupling, and dynamics, we resolve spectral shifts and line broadening on the nanoscale. These spectral shifts allow us to map intermolecular electric fields across nanoscale domains through solvatochromism or transition dipole coupling. Similarly, linewidths relate directly to the spatially-varying coupling dynamics of vibrational oscillators. Comparing spectral maps of peak position and linewidth to maps of adhesion and Young's modulus, for example, provides insight into the structure-function relationship dictating nanoscale self assembly in, e.g., block copolymer thin films.

  4. Intermolecular forces between large molecules

    Microsoft Academic Search

    A. T. Amos; R. J. Crispin

    1976-01-01

    The long-range interaction between large molecules with localized electrons is written as the sum of individual interactions between localized charge distributions. Using minimal basis set ab initio Hartree-Fock wavefunctions the parameters needed to compute these interactions are obtained for water, methane and ethane. Interactions between pairs of these molecules are computed for various orientations to demonstrate the complex orientational dependence

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  6. Combined effect of small- and large-angle scattering collisions on a spectral line shape

    NASA Astrophysics Data System (ADS)

    Kochanov, V. P.

    2015-07-01

    Algebraic approximations for line profiles calculated on the basis of quantum-mechanical collision integral kernels for dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole intermolecular interaction potentials were obtained. In derivation of the profiles velocity-changing collisions of molecules with scattering on small and large angles also with the speed-dependence of collision relaxation constants have been taken into account. It was shown that the relative contribution of small-angle collisions into the frequency of elastic velocity-changing collisions is much more pronounced for long-range potentials. A sensitive criterion for analysis of a line narrowing was proposed and tested.

  7. Anisotropy in the Interaction of Ultracold Dysprosium

    E-print Network

    Kotochigova, Svetlana

    2011-01-01

    The nature of the interaction between ultracold atoms with a large orbital and spin angular momentum has attracted considerable attention. It was suggested that such interactions can lead to the realization of exotic states of highly correlated matter. Here, we report on a theoretical study of the competing anisotropic dispersion, magnetic dipole-dipole, and electric quadrupole-quadrupole forces between two dysprosium atoms. Each dysprosium atom has an orbital angular momentum L=6 and magnetic moment $\\mu=10\\mu_B$. We show that the dispersion coefficients of the ground state adiabatic potentials lie between 1865 a.u. and 1890 a.u., creating a non-negligible anisotropy with a spread of 25 a.u. and that the electric quadrupole-quadrupole interaction is weak compared to the other interactions. We also find that for interatomic separations $R< 50\\,a_0$ both the anisotropic dispersion and magnetic dipole-dipole potential are larger than the atomic Zeeman splittings for external magnetic fields of order 10 G to ...

  8. Addendum to the paper "Dead-time free measurement of dipole-dipole interactions between electron spins" by M. Pannier, S. Veit, A. Godt, G. Jeschke, and H.W. Spiess [J. Magn. Reson. 142 (2000) 331-340

    NASA Astrophysics Data System (ADS)

    Spiess, Hans Wolfgang

    2011-12-01

    The development of four-pulse DEER as described, which has been published in the Journal of Magnetic Resonance more than 10 years ago. The corresponding paper is an example where a slight advance, such as adding a refocusing pulse, which in retrospect looks so simple, can have a remarkable impact on an entire field of science. In our case it offered a simple way to exact measurements of distances between defined species in the nanometer range. The current applications are mainly in determining structures of proteins and nucleic acids.

  9. Intermolecular energy-transfer processes

    NASA Astrophysics Data System (ADS)

    Lee, E. K. C.

    1983-10-01

    Equipment used for the fluorescence excitation and emission spectroscopy are described. The following were studied: singlet electronic energy transfer, photophysics of single vibrational levels (H2CO), photophysics of single rotational levels (H2CO and SO2), rotation-vibration interaction by Coriolis perturbation, and matrix isolation photochemistry and spectroscopy (SO2, H2CO, H2C2O2).

  10. COMMUNICATIONS Femtosecond pumpprobe spectroscopy of intermolecular vibrations

    E-print Network

    Mukamel, Shaul

    COMMUNICATIONS Femtosecond pump­probe spectroscopy of intermolecular vibrations in molecular dimers spectroscopy of molecular aggregates provides a direct probe for the joint electronic and nuclear dynamics. Various systems such as the photosynthetic reac- tion center,1­4 J aggregates,5­8 and charge transfer

  11. Mapping intermolecular bonding in C60

    PubMed Central

    Sundqvist, Bertil

    2014-01-01

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

  12. Mapping intermolecular bonding in C60

    NASA Astrophysics Data System (ADS)

    Sundqvist, Bertil

    2014-08-01

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

  13. Long-range Rydberg-Rydberg interactions in calcium, strontium and ytterbium

    E-print Network

    Vaillant, C L; Potvliege, R M

    2012-01-01

    Long-range dipole-dipole and quadrupole-quadrupole interactions between pairs of Rydberg atoms are calculated perturbatively for calcium, strontium and ytterbium within the Coulomb approximation. Quantum defects, obtained by fitting existing laser spectroscopic data, are provided for all $S$, $P$, $D$ and $F$ series of strontium and for the $^3P_2$ series of calcium. The results show qualitative differences with the alkali metal atoms, including isotropically attractive interactions of the strontium $^1S_0$ states and a greater rarity of F\\"orster resonances. Only two such resonances are identified, both in triplet series of strontium. The angular dependence of the long range interaction is briefly discussed.

  14. Long-range Rydberg-Rydberg interactions in calcium, strontium and ytterbium

    E-print Network

    C. L. Vaillant; M. P. A. Jones; R. M. Potvliege

    2012-05-11

    Long-range dipole-dipole and quadrupole-quadrupole interactions between pairs of Rydberg atoms are calculated perturbatively for calcium, strontium and ytterbium within the Coulomb approximation. Quantum defects, obtained by fitting existing laser spectroscopic data, are provided for all $S$, $P$, $D$ and $F$ series of strontium and for the $^3P_2$ series of calcium. The results show qualitative differences with the alkali metal atoms, including isotropically attractive interactions of the strontium $^1S_0$ states and a greater rarity of F\\"orster resonances. Only two such resonances are identified, both in triplet series of strontium. The angular dependence of the long range interaction is briefly discussed.

  15. Dipolar interaction and size effects in powder samples of colloidal iron oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Vargas, José M.; Socolovsky, Leandro M.; Knobel, Marcelo; Zanchet, Daniela

    2005-05-01

    Dipole-dipole interactions in nanostructured materials deeply affect their magnetic properties, and detailed studies are still required to fully understand them. In this work, the dependence of magnetic properties on particle size has been evaluated in powder samples of Fe oxide nanoparticles produced by colloidal methods. Zero-field-cooled and field-cooled magnetization curves and magnetization versus applied field data have been analysed by taking into account dipolar interactions through a correction to the classical superparamagnetic model. Morphological and magnetic data were in very good agreement, which has allowed us to quantify relevant physical parameters, such as the anisotropy constant, magnetic moment, and interacting volume for our system.

  16. Direct evidence of three-body interactions in a cold {sup 85}Rb Rydberg gas

    SciTech Connect

    Han Jianing [Department of Physics, University of Virginia, Charlottesville, Virginia 22904 (United States)

    2010-11-15

    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. 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. 91, 183002 (2003); K. R. Overstreet, Arne Schwettmann, Jonathan Tallant, and James P. Shaffer, Phys. Rev. A 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.

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

    SciTech Connect

    Muenter, J.S.

    1997-04-01

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

  18. Effect of the short-range interaction on low-energy collisions of ultracold dipoles

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Jie, Jianwen

    2014-12-01

    We consider the low-energy scattering of two ultracold polarized dipoles with both a short-range interaction (SRI) and a weak dipole-dipole interaction (DDI), which is far away from shape resonances. In previous analytical studies, the scattering amplitude in this system was often calculated via the first-order Born approximation (FBA). Our results show that significant derivations from this approximation can arise in some cases. In these cases, the SRI can significantly modify the interdipole scattering amplitudes even if the scattering amplitudes for the SRI alone are much smaller than the dipolar length of the DDI. We further obtain approximate analytical expressions for these interdipole scattering amplitudes.

  19. Near-field interactions in electric inductive-capacitive resonators for metamaterials

    NASA Astrophysics Data System (ADS)

    Withayachumnankul, Withawat; Fumeaux, Christophe; Abbott, Derek

    2012-12-01

    Near-field interactions in an array of electric inductive-capacitive (ELC) resonators are investigated analytically, numerically and experimentally. The measurement and simulation results show that inter-cell coupling plays an important role in determining the response of metamaterials. A quasistatic dipole-dipole interaction model, together with a Lagrangian formalism, quantitatively explains the interplay between the electric and magnetic couplings in the resonator array. Depending on the alignment of the resonators, the couplings can cause resonance shifting and/or splitting. The knowledge obtained from this study is crucial in designing metamaterials with ELC resonators.

  20. He-, Ne-, and Ar-phosgene intermolecular potential energy surfaces.

    PubMed

    Munteanu, Cristian R; Henriksen, Christian; Felker, Peter M; Fernández, Berta

    2013-05-01

    Using the CCSD(T) model, we evaluated the intermolecular potential energy surfaces of the He-, Ne-, and Ar-phosgene complexes. We considered a representative number of intermolecular geometries for which we calculated the corresponding interaction energies with the augmented (He complex) and double augmented (Ne and Ar complexes) correlation-consistent polarized valence triple-? basis sets extended with a set of 3s3p2d1f1g midbond functions. These basis sets were selected after systematic basis set studies carried out at geometries close to those of the surface minima. The He-, Ne-, and Ar-phosgene surfaces were found to have absolute minima of -72.1, -140.4, and -326.6 cm(-1) at distances between the rare-gas atom and the phosgene center of mass of 3.184, 3.254, and 3.516 Å, respectively. The potentials were further used in the evaluation of rovibrational states and the rotational constants of the complexes, providing valuable results for future experimental investigations. Comparing our results to those previously available for other phosgene complexes, we suggest that the results for Cl2-phosgene should be revised. PMID:23617631

  1. 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 .

  2. An assay for intermolecular exchange of alpha crystallin

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

  3. Interaction of H2 with simple metal surfaces - A model based on the anisotropic effective medium theory

    NASA Technical Reports Server (NTRS)

    Karimi, M.; Ila, D.; Dalins, I.; Vidali, G.

    1990-01-01

    Calculations are presented for the interaction of H2 with surfaces of Cu, Ag, Au and Al. The repulsive part of the potential is evaluated using the results of anisotropic effective medium theory (AEMT) while the attractive part is calculated from anisotropic damped dipole-dipole and damped dipole-quadrupole interactions. The model does not have any fitting parameters and its predictions are in excellent agreement with the available experimental data. The anisotropy of H2 is included in the model but our results show that this effect is very small.

  4. Long-time joint spectra and entanglement of two photoelectrons originating in interacting auto-ionization systems

    NASA Astrophysics Data System (ADS)

    Pe?ina, Jan, Jr.; Lukš, Antonín; Leo?ski, Wieslaw

    2015-06-01

    Two auto-ionization systems in a stationary optical field that are mutually interacting via the dipole–dipole interaction are considered. Their evolution is found analytically. Joint spectra of two ionized electrons are analyzed in detail in the long-time limit for comparable strengths of direct and indirect ionization paths as well as the dominating indirect ionization path. Entanglement in the state of two ionized electrons is quantified using the density of quadratic negativity. Suitable conditions for obtaining highly entangled states are discussed.

  5. An in vitro network of intermolecular interactions between viral RNA segments of an avian H5N2 influenza A virus: comparison with a human H3N2 virus

    PubMed Central

    Gavazzi, Cyrille; Isel, Catherine; Fournier, Emilie; Moules, Vincent; Cavalier, Annie; Thomas, Daniel; Lina, Bruno; Marquet, Roland

    2013-01-01

    The genome of influenza A viruses (IAV) is split into eight viral RNAs (vRNAs) that are encapsidated as viral ribonucleoproteins. The existence of a segment-specific packaging mechanism is well established, but the molecular basis of this mechanism remains to be deciphered. Selective packaging could be mediated by direct interaction between the vRNA packaging regions, but such interactions have never been demonstrated in virions. Recently, we showed that the eight vRNAs of a human H3N2 IAV form a single interaction network in vitro that involves regions of the vRNAs known to contain packaging signals in the case of H1N1 IAV strains. Here, we show that the eight vRNAs of an avian H5N2 IAV also form a single network of interactions in vitro, but, interestingly, the interactions and the regions of the vRNAs they involve differ from those described for the human H3N2 virus. We identified the vRNA sequences involved in five of these interactions at the nucleotide level, and in two cases, we validated the existence of the interaction using compensatory mutations in the interacting sequences. Electron tomography also revealed significant differences in the interactions taking place between viral ribonucleoproteins in H5N2 and H3N2 virions, despite their canonical ‘7 + 1’ arrangement. PMID:23221636

  6. Weakly interacting two-dimensional system of dipoles: Limitations of the mean-field theory

    SciTech Connect

    Astrakharchik, G. E.; Boronat, J.; Casulleras, J.; Kurbakov, I. L.; Lozovik, Yu. E. [Departament de Fisica i Enginyeria Nuclear, Campus Nord B4-B5, Universitat Politecnica de Catalunya, E-08034 Barcelona (Spain); Institute of Spectroscopy, 142190 Troitsk, Moscow region (Russian Federation)

    2007-06-15

    We consider a homogeneous two-dimensional Bose gas with repulsive dipole-dipole interactions. The ground-state equation of state, calculated using the diffusion Monte Carlo method, shows quantitative differences from the predictions of the commonly used Gross-Pitaevskii mean-field theory. The static structure factor, pair distribution function, and condensate fraction are calculated in a wide range of the gas parameter. Differences from mean-field theory are reflected in the frequency of the lowest ''breathing'' mode for harmonically trapped systems.

  7. Ab initio and Gordon-Kim intermolecular potentials for two nitrogen molecules

    NASA Astrophysics Data System (ADS)

    Ree, Francis H.; Winter, Nicholas W.

    1980-07-01

    Both ab initio MO-LCAO-SCF and the electron-gas (or Gordon-Kim) methods have been used to compute the intermolecular potential (?) of N2 molecules for seven different N2-N2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for ??0.002 hartree or intermolecular separations less than 6.5-7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N2 molecules. The Gordon-Kim method with Rae's self-exchange correction yields ?, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon-Kim calculations. Using the ab initio data we derive an atom-atom potential of the two N2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio ? remarkably well. The spherically averaged ab initio ? is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio ? to the classical quadrupole-quadrupole interaction at large intermolecular separation is also discussed.

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

    SciTech Connect

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

    2008-08-14

    The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O{sub 2} molecules interact predominantly through the half-filled 1{pi}{sub g}* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1{pi}{sub g}* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O{sub 2} molecules at the transition to the {epsilon}-phase. The {epsilon}-phase, which consists of (O{sub 2}){sub 4} clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O{sub 2}){sub 4} clusters develop upon compression of the {epsilon}-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases.

  9. Inelastic x-ray scattering of dense solid oxygen: evidence for intermolecular bonding.

    PubMed

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

    2008-08-19

    The detailing of the intermolecular interactions in dense solid oxygen is essential for an understanding of the rich polymorphism and remarkable properties of this element at high pressure. Synchrotron inelastic x-ray scattering measurements of oxygen K-edge excitations to 38 GPa reveal changes in electronic structure and bonding on compression of the molecular solid. The measurements show that O(2) molecules interact predominantly through the half-filled 1pi(g)* orbital <10 GPa. Enhanced intermolecular interactions develop because of increasing overlap of the 1pi(g)* orbital in the low-pressure phases, leading to electron delocalization and ultimately intermolecular bonding between O(2) molecules at the transition to the epsilon-phase. The epsilon-phase, which consists of (O(2))(4) clusters, displays the bonding characteristics of a closed-shell system. Increasing interactions between (O(2))(4) clusters develop upon compression of the epsilon-phase, and provide a potential mechanism for intercluster bonding in still higher-pressure phases. PMID:18687889

  10. 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

  11. Osmotic Stress Measurements of Intermolecular Forces in Ordered Assemblies Formed by Solvated Block Copolymers

    Microsoft Academic Search

    Zhiyong Gu; Paschalis Alexandridis

    2004-01-01

    Intermolecular interactions in ordered (lyotropic liquid crystalline) assemblies formed by hydrated poly(ethylene oxide)-poly(propylene oxide) (PEO-PPO) block copolymers (Pluronics or Polox- amers) have been probed using the osmotic stress method. This method involves the equilibration, following the removal or the addition of an appropriate amount of water, of hydrated block copolymer samples with a system (aqueous polymer solution or water vapor)

  12. Intermolecular Band Dispersion for Self-Assembly Monolayers of A Polyphenyl Thiol

    Microsoft Academic Search

    D.-Q. Feng; P. A. Dowben; Ya. B. Losovyj; Y. Tai; M. Zharnikov

    2007-01-01

    We find evidence of intermolecular interactions for a self-assembled monolayer (SAM) formed from a large molecular adsorbate, [1,1?;4?,1?-terphenyl]-4,4?-dimethanethiol, from the dispersion of the molecular orbitals with changing the wave vector k. Both unoccupied and occupied molecular orbitals hybridize to electronic bands, with significant band dispersion that appears to be dependent on structure. The results demonstrate that Bloch's theorem can apply

  13. Intermolecular relaxation in glycerol as revealed by field cycling 1H NMR relaxometry dilution experiments.

    PubMed

    Meier, R; Kruk, D; Gmeiner, J; Rössler, E A

    2012-01-21

    (1)H spin-lattice relaxation rates R(1) = 1/T(1) have been measured for partly deuterated glycerol-h(5) diluted in fully deuterated glycerol-h(0) for progressively lower concentrations of glycerol-h(5). By means of the field cycling (FC) technique relaxation dispersion data, R(1)(?), have been collected for several temperatures in the frequency range of 10 kHz-20 MHz. In order to disclose the spectral shape of the intra- and intermolecular relaxation, extrapolation of the relaxation data to the zero concentration limit has been performed. The paper confirms that the low frequency excess contribution to the total relaxation rate R(1)(?) previously reported for several liquids is of intermolecular origin and reflects translational motion, whereas the high-frequency part is attributed to molecular rotation. Thus, intra- and intermolecular relaxation contributions are spectrally separated. The intermolecular relaxation itself contains also a contribution from rotational motion, which is due to non-central positions of the interacting nuclei in the molecule. This eccentricity effect is quantitatively reproduced by treating the intermolecular spectral density as a sum of translational-like (described by the free diffusion model) and rotational-like contributions (described by a Cole-Davidson function). Applying frequency-temperature superposition master curves as well as individual relaxation dispersion data, R(1)(?), are analyzed. It is demonstrated that, in spite of the rotational influence, the translational diffusion coefficients, D(T), can be extracted from the (1)H relaxation dispersion which gives (1)H NMR relaxometry the potential to become a routine technique determining the diffusion coefficient in liquids. PMID:22280768

  14. Interpreting the widespread nonlinear force spectra of intermolecular bonds

    PubMed Central

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

    2012-01-01

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

  15. Intermolecular enolate heterocoupling: scope, mechanism, and application.

    PubMed

    DeMartino, Michael P; Chen, Ke; Baran, Phil S

    2008-08-27

    This full account presents the background on, discovery of, and extensive insight that has been gained into the oxidative intermolecular coupling of two different carbonyl species. Optimization of this process has culminated in reliable and scalable protocols for the union of amides, imides, ketones, and oxindoles using soluble copper(II) or iron(III) salts as oxidants. Extensive mechanistic studies point to a metal-chelated single-electron-transfer process in the case of copper(II), while iron(III)-based couplings appear to proceed through a non-templated heterodimerization. This work presents the most in-depth findings on the mechanism of oxidative enolate coupling to date. The scope of oxidative enolate heterocoupling is extensive (40 examples) and has been shown to be efficient even on a large scale (gram-scale or greater). Finally, the method has been applied to the total synthesis of the unsymmetrical lignan lactone (-)-bursehernin and a medicinally important 2,3-disubstituted succinate derivative. PMID:18680297

  16. 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.

  17. Novel helical assembly of a Pt(ii) phenylbipyridine complex directed by metal-metal interaction and aggregation-induced circularly polarized emission.

    PubMed

    Ikeda, Toshiaki; Takayama, Midori; Kumar, Jatish; Kawai, Tsuyoshi; Haino, Takeharu

    2015-07-14

    Pt(ii) phenylbipyridine complexes possessing bis(phenylisoxazolyl)phenylacetylene ligands self-assembled to form stacked aggregates via Pt-Pt, ?-? stacking, and dipole-dipole interactions. The assembled structures were influenced by the solvent properties. Non-helical assemblies found in chloroform displayed metal-metal-to-ligand charge transfer absorption and emission, whereas helical assemblies formed in toluene showed aggregation-induced enhancement of emission and aggregation-induced circularly polarized luminescence. The rates of the association and dissociation of the assemblies were significantly reduced in toluene, and the non-helical structures formed in chloroform were surprisingly memorized. PMID:26108199

  18. 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.

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

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as ??(w)(0) = 1206 ± 2 J/mol and ?H(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234

  20. How intermolecular charge transfer influences the air-water interface.

    PubMed

    Wick, Collin D; Lee, Alexis J; Rick, Steven W

    2012-10-21

    The interfacial properties of three water models that allow for intermolecular charge rearrangement were examined with molecular dynamics simulations. They included the TIP4P water model, the TIP4P-FQ water model, which recently were modified to include intermolecular charge transfer [A. J. Lee and S. W. Rick, J. Chem. Phys. 134, 184507 (2011)]. Furthermore, another model with intermolecular charge transfer was developed for this work that was both flexible and polarizable. The effect of including intermolecular charge transfer is modest on most interfacial properties, including surface tension, electrostatic potential, interfacial dipole, and structure. However, a negative charge was found to build up at the air-water interface, but much smaller than has been measured experimentally. PMID:23083178

  1. Intermolecular potentials for simulations of liquid imidazolium salts

    NASA Astrophysics Data System (ADS)

    Hanke, C. G.; Price, S. L.; Lynden-Bell, R. M.

    Intermolecular potentials suitable for molecular dynamics or Monte Carlo simulations have been developed for dimethyl imidazolium and methyl ethyl imidazolium ions. The predicted crystal structures were compared with experimental crystal structures for chloride and PF6- salts and found to be satisfactory when the dominant electrostatic interactions were modelled by either an accurate distributed multipole description or a simplified atomic point charge model. A further simplification of using united atoms in place of methyl or methylene groups on the side chains gave a much less satisfactory reproduction of the crystal structures. Liquid dimethyl imidazolium chloride and dimethyl imidazolium PF6-were simulated using the explicit atom and united atom potentials. The local structure showed a strong preference for the chloride ions to be located in certain regions around the cation, and a similar, but less strong localization of the larger PF6-. Significant differences in density and diffusion rates were found when the explicit atom model was replaced by the cheaper united atom model, showing that the latter potential is significantly poorer for modelling both the static solid and dynamic liquid simulations.

  2. Comparison of interionic/intermolecular vibrational dynamics between ionic liquids and concentrated electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki

    2009-12-01

    In this study, we have compared the interionic/intermolecular vibrational dynamics of ionic liquids (ILs) and concentrated electrolyte solutions measured by femtosecond optically heterodyne-detected Raman-induced Kerr effect spectroscopy. A typical anion in ILs, bis(trifluoromethanesulfonyl)amide ([NTf2]-), has been chosen as the anion for the sample ILs and concentrated electrolyte solutions. ILs used in this study are 1-butyl-3-methylimidazolium, 1-butylpyridinium, N-butyl-N,N,N-triethylammonium, and 1-butyl-1-methylpyrrolidinium with [NTf2]-. Li[NTf2] solutions (˜3.3M) of water, methanol, propylene carbonate, and poly(ethylene glycol) have been selected as control samples. Kerr transients of the ILs and electrolyte solutions show intra- and interionic/intermolecular vibrational dynamics followed by slow picosecond overdamped relaxation. Fourier transform Kerr spectra have shown a difference in the relative intensities of intraionic vibrational bands of [NTf2]- (280-350 cm-1) between the ILs and electrolyte solutions. The origin of the difference is attributed to the change in the conformational equilibrium between cisoid and transoid forms of [NTf2]-, which is caused by a favorable stabilization of dipolar cisoid form due to Li+ and dipolar solvent molecules in the electrolyte solutions. Low-frequency Kerr spectra (0-200 cm-1) exhibit unique features with the variation of cation and solvent species. The aromatic ILs have a prominent high-frequency librational motion at about 100 cm-1 in contrast to the case for the nonaromatic ones. The common structure of the spectra observed at about 20 cm-1 likely comes from an interionic motion of [NTf2]-. The nonaromatic ILs allow a fair comparison with the electrolyte solutions of propylene carbonate and poly(ethylene glycol) because of the structural similarities. The comparison based on the first moment of the interionic/intermolecular vibrational spectrum suggests the stronger interionic/intermolecular interaction in the concentrated electrolyte solutions than the ILs.

  3. Intermolecular Interaction by Apical Oxygen in Titanyl Phthalocyanine

    NASA Astrophysics Data System (ADS)

    Harada, Yoshihisa; Tokushima, Takashi; Takata, Yasutaka; Kamakura, Nozomu; Takeuchi, Tomoyuki; Kobayashi, Keisuke; Shirota, Yasuhiko; Shin, Shik

    2005-08-01

    Local charge distribution around the titanium atom of amorphous and ?-crystalline TiOPc films was investigated using Ti 2 p X-ray absorption and emission spectroscopy. The X-ray emission spectra show two characteristic features that correspond to charge transfer states that result from in-plane Ti-N and apical Ti-O hybridizations. In the amorphous phase, the Ti-O charge transfer state has both localized and delocalized properties, whereas in the ?-crystalline phase it has only the delocalized property. These different properties evidence the role of the oxygen atom in forming a network with a neighboring molecule and in balancing the total dipole moment in the ?-crystalline phase.

  4. 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.

  5. AnEffective Approach for TeachingIntermolecularInteractions

    E-print Network

    Campanario, Juan Miguel

    properties. This device should be useful in teaching chemistry in the classroom. This paper has two sections are interested in this matter may use the samples in the classroom as they are. Molecular Electrostatic Potential: Defihition and Calculation Like electron density, electrostatic potential is a physical property and may

  6. Intermolecular interaction in complexes of tetracyanoethylene with amines

    Microsoft Academic Search

    V. V. Pen'kovskii

    1972-01-01

    Solutions of tetracyanoethylene (TCE) in pyridine and its homologs (piperidine and triethylamine) and also a solution of the complex of 2,2'-dipyridyl with TCE in acetone were investigated. The EPR spectra of these systems show hyperfine structure of nine components with splitting constants characteristic of TCE radical anions. This indicates complete electron transfer from the nitrogen atom in the amine to

  7. Proinsulin Intermolecular Interactions during Secretory Trafficking in Pancreatic ? Cells*

    PubMed Central

    Haataja, Leena; Snapp, Erik; Wright, Jordan; Liu, Ming; Hardy, Alexandre B.; Wheeler, Michael B.; Markwardt, Michele L.; Rizzo, Mark; Arvan, Peter

    2013-01-01

    Classically, exit from the endoplasmic reticulum (ER) is rate-limiting for secretory protein trafficking because protein folding/assembly occurs there. In this study, we have exploited “hPro-CpepSfGFP,” a human proinsulin bearing “superfolder” green fluorescent C-peptide expressed in pancreatic ? cells where it is processed to human insulin and CpepSfGFP. Remarkably, steady-state accumulation of hPro-CpepSfGFP and endogenous proinsulin is in the Golgi region, as if final stages of protein folding/assembly were occurring there. The Golgi regional distribution of proinsulin is dynamic, influenced by fasting/refeeding, and increased with ? cell zinc deficiency. However, coexpression of ER-entrapped mutant proinsulin-C(A7)Y shifts the steady-state distribution of wild-type proinsulin to the ER. Endogenous proinsulin coprecipitates with hPro-CpepSfGFP and even more so with hProC(A7)Y-CpepSfGFP. Using Cerulean and Venus-tagged proinsulins, we find that both WT-WT and WT-mutant proinsulin pairs exhibit FRET. The data demonstrate that wild-type proinsulin dimerizes within the ER but accumulates at a poorly recognized slow step within the Golgi region, reflecting either slow kinetics of proinsulin hexamerization, steps in formation of nascent secretory granules, or other unknown molecular events. However, in the presence of ongoing misfolding of a subpopulation of proinsulin in ? cells, the rate-limiting step in transport of the remaining proinsulin shifts to the ER. PMID:23223446

  8. 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.

  9. Nonlinear Dynamics of Bose-Einstein Condensates with Long-Range Interactions

    SciTech Connect

    Wunner, G.; Cartarius, H.; Fabcic, T.; Koeberle, P.; Main, J.; Schwidder, T. [Institut fuer Theoretische Physik 1, Universitaet Stuttgart, 70550 Stuttgart (Germany)

    2008-11-13

    The motto of this paper is: Let's face Bose-Einstein condensation through nonlinear dynamics. We do this by choosing variational forms of the condensate wave functions (of given symmetry classes), which convert the Bose-Einstein condensates via the time-dependent Gross-Pitaevskii equation into Hamiltonian systems that can be studied using the methods of nonlinear dynamics. We consider in particular cold quantum gases where long-range interactions between the neutral atoms are present, in addition to the conventional short-range contact interaction, viz. gravity-like interactions, and dipole-dipole interactions. The results obtained serve as a useful guide in the search for nonlinear dynamics effects in numerically exact quantum calculations for Bose-Einstein condensates. A main result is the prediction of the existence of stable islands as well as chaotic regions for excited states of dipolar condensates, which could be checked experimentally.

  10. Effect of spacer layer thickness on magnetic interactions in self-assembled single domain iron nanoparticles

    SciTech Connect

    Herndon, Nichole B [ORNL; Ho, S [Oak Ridge National Laboratory (ORNL); Abiade, J. [North Carolina A& T State University; Pai, Devdas M. [North Carolina A& T State University; Sankar, Jag [North Carolina A& T State University; Pennycook, Stephen J [ORNL

    2009-01-01

    The magnetic characteristics of iron nanoparticles embedded in an alumina thin film matrix have been studied as a function of spacer layer thickness. Alumina as well as iron nanoparticles were deposited in a multilayered geometry using sequential pulsed laser deposition. The role of spacer layer thickness was investigated by making layered thin film composites with three different spacer layer thicknesses 6, 12, and 18 nm with fixed iron particle size of 13 nm. Intralayer magnetic interactions being the same in each sample, the variation in coercivity and saturation magnetization is attributed to thickness dependent interlayer magnetic interactions of three types: exchange, strong dipolar, and weak dipolar. A thin film composite multilayer structure offers a continuously tunable strength of interparticle dipole-dipole interaction and is thus well suited for studies of the influence of interaction on the magnetic properties of small magnetic particle systems.

  11. Metal containing cryptands as hosts for anions: evaluation of Cu(i)X and ?X interactions in halide-tricopper(i) complexes through relativistic DFT calculations.

    PubMed

    Ponce-Vargas, Miguel; Muñoz-Castro, Alvaro

    2015-07-01

    More selective than crown ethers, cryptands arise as suitable hosts for several ions, with the size of the cavity and the behavior of the atoms belonging to the structure being the main factors governing their selectivity. Similar to metallacrowns, inorganic counterparts of crown ethers, the presence of metal centers in cryptands can offer significant advantages in terms of ion recognition as they provide positively charged sites, which allow them to encapsulate anions. Here, through density functional methodologies, we evaluate the preference of a tricopper(i) cryptand host toward a series of halide ions ranging from the hard fluoride to the soft iodide, where the more intense interactions are established with the hardest one, and the electrostatic term is the more relevant contributor to total interaction energy. Upon exploration of this electrostatic contribution in more detail, it is observed that as the guest becomes softer, the increase of higher order Coulombic terms, such as dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole, acquires more relevance on going from 9.22% to 41.25%, denoting the key role and variation of such forces in inclusion systems with metal-containing hosts. PMID:26120065

  12. Copper-Catalyzed Intermolecular Asymmetric Propargylic Dearomatization of Indoles.

    PubMed

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

    2015-06-22

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

  13. Probing intermolecular potentials with dynamic and kinetic observables

    Microsoft Academic Search

    1991-01-01

    The connection between intermolecular potentials and a variety of dynamic and kinetic observables is studied through the use of functional sensitivity analysis. Equations were derived for the functional derivatives of inelastic cross sections, rate constants, energy level populations, and transport and relaxation cross sections with respect to a variation in the potential surface. Five different studies were performed. Three of

  14. A reliable semi-empirical approach for evaluating the isotropic intermolecular forces between closed-shell systems

    Microsoft Academic Search

    Kin-Chue Ng; William J. Meath; A. R. Allnatt

    1979-01-01

    A relatively simple tractable scheme for the evaluation of the isotropic intermolecular potential between two closed-shell systems, which contains one adjustable parameter, is proposed and tested using the He-He, Ne-Ne, Ar-Ar, Kr-Kr, and H2-H2 interactions as models. The approach is based on expressing the potential as a sum of exchange (Ex) and coulomb (Ec) contributions. A semi-empirical approximation, which is

  15. Driven-dissipative dynamics of a strongly interacting Rydberg gas

    E-print Network

    A. W. Glaetzle; R. Nath; B. Zhao; G. Pupillo; P. Zoller

    2012-07-11

    We study the non-equilibrium many-body dynamics of a cold gas of ground state alkali atoms weakly admixed by Rydberg states with laser light. On a timescale shorter than the lifetime of the dressed states, effective dipole-dipole or van der Waals interactions between atoms can lead to the formation of strongly correlated phases, such as atomic crystals. Using a semiclassical approach, we study the long-time dynamics where decoherence and dissipative processes due to spontaneous emission and blackbody radiation dominate, leading to heating and melting of atomic crystals as well as particle losses. These effects can be substantially mitigated by performing active laser cooling in the presence of atomic dressing.

  16. 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.

  17. The interaction of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells.

    PubMed

    Kim, Sung-Jo; Kim, Jong-Hyun

    2014-04-21

    We have investigated interactions of colloidal particles with weak homeotropic anchoring energy in homogeneous nematic liquid crystal cells. Particle-wall and inter-particle interactions were observed experimentally and analyzed using typical dipole-dipole and quadrupole-quadrupole interactions, including substrate effects as the image charges. Both experimental results matched well with the calculated results for the effective particle radius reflecting the weak anchoring. The effective radius is reduced by the amount of extrapolation length than the actual particle radius. The effective radii of polyethylene micro-particles were reduced to a coefficient ? (0.78 ? ? ? 0.52) times the actual radius with anchoring coefficients in the range of 3.8 × 10(-6) to 1.4 × 10(-6) J m(-2). The anchoring energy of the particles is, therefore, a key component for explaining liquid crystal colloidal systems. PMID:24647470

  18. 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

  19. 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.

  20. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    NASA Astrophysics Data System (ADS)

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2015-06-01

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.

  1. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.

    PubMed

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2015-06-28

    We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data. PMID:26133428

  2. 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.

  3. Direct simulation Monte Carlo method for an arbitrary intermolecular potential

    NASA Astrophysics Data System (ADS)

    Sharipov, Felix; Strapasson, José L.

    2012-01-01

    A scheme to implement an arbitrary intermolecular potential into the direct simulation Monte Carlo method is proposed. To illustrate the scheme, two benchmark problems are solved employing the Lennard-Jones potential. Since the computational effort of the new scheme is comparable with that of the hard sphere model of molecules, it can completely substitute the widely used models such as variable hard spheres and variable soft spheres.

  4. Study of intermolecular effects in linear polymers by magnetic susceptibility

    Microsoft Academic Search

    F. J. Baltá-Calleja; J. M. Barrales-Rienda

    1972-01-01

    The diamagnetic susceptibility of poly(2,6-dimethyl-1,4-phenylene) oxide (PPO) and polyethylene sebacate (PES) precipitated from diluted solution was measured with reference to the additivity of atomic susceptibilities, in a wide range of molecular weights. The experimentally obtained linear relationship between molecular susceptibility and degree of polymerization permits the derivation, for both polymer systems, of an intermolecular constant ?k, characteristic for the crystalline

  5. 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

  6. Intermolecular ?-Strand Networks Avoid Hub Residues and Favor Low Interconnectedness: A Potential Protection Mechanism against Chain Dissociation upon Mutation

    PubMed Central

    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

  7. Intra- and intermolecular hydrogen bonding in acetylacetone and benzoylacetone derived enaminone derivatives

    NASA Astrophysics Data System (ADS)

    Lazi?, Vedrana; Jurkovi?, Mihaela; Jedna?ak, Tomislav; Hrenar, Tomica; Vukovi?, Jelena Parlov; Novak, Predrag

    2015-01-01

    The structure and hydrogen bonding in solution of acetylacetone and benzoylacetone derived enaminone derivatives, 1a-1d and 2a-2d, have been studied by a combination of experimental (NMR and UV spectroscopies) and theoretical (PM6 and DFT) methods. It has been shown that all studied compounds predominantly existed in the localised keto-amine tautomeric form in solution as found also in the solid state. Significant line-broadening and down-field chemical shifts of NH and OH protons have strongly indicated that both groups formed hydrogen bonds, which has further been supported by quantum chemical calculations. Temperature and concentration dependent NMR measurements have pointed towards the fact that NH protons are engaged in strong intramolecular hydrogen bonds of the NH⋯Odbnd C type in both solvents. On the other hand, OH protons are involved in weaker intermolecular hydrogen bonding with solvent molecules in DMSO, while in chloroform intermolecular interactions between two molecules dominate. The results presented in this paper can be used for better understanding and further exploiting properties these ligands possess, especially their bioactivity.

  8. Using Voronoi tessellations to assess nanoparticle-nanoparticle interactions and ordering in monolayer films formed through electrophoretic deposition.

    PubMed

    Krejci, Alex J; Thomas, Colin G W; Mandal, Jyotirmoy; Gonzalo-Juan, Isabel; He, Weidong; Stillwell, Ryan L; Park, Ju-Hyun; Prasai, Dhiraj; Volkov, Vyacheslav; Bolotin, Kirill I; Dickerson, James H

    2013-02-14

    Monolayers of iron oxide nanoparticles of two different sizes, 9.6 nm and 16.5 nm, were fabricated through electrophoretic deposition. The arrangements of nanoparticles within the films were analyzed using the technique of Voronoi tessellations. These analyses indicated that the films possessed equivalent degrees of ordering, and that the films were uniform over centimeter length scales. Precise measurements of the interparticle spacing were obtained, and the magnitudes of magnetic dipole interactions were calculated. The dipole-dipole interaction among the larger nanoparticles was 14 times larger than that of the smaller nanoparticles, indicating that magnetic coupling interactions could not have been the lone source of ordering in the system. PMID:22908936

  9. Probing the interaction mode in hydrophilic interaction chromatography.

    PubMed

    Dinh, Ngoc Phuoc; Jonsson, Tobias; Irgum, Knut

    2011-09-01

    This work aims at characterizing interactions between a select set of probes and 22 hydrophilic and polar commercial stationary phases, to develop an understanding of the relationship between the chemical properties of those phases and their interplay with the eluent and solutes in hydrophilic interaction chromatography. "Hydrophilic interaction" is a somewhat inexact term, and an attempt was therefore made to characterize the interactions involved in HILIC as hydrophilic, hydrophobic, electrostatic, hydrogen bonding, dipole-dipole, ?-? interaction, and shape-selectivity. Each specific interaction was quantified from the separation factors of a pair of similar substances of which one had properties promoting the interaction mode being probed while the other did not. The effects of particle size and pore size of the phases on retention and selectivity were also studied. The phases investigated covered a wide range of surface functional groups including zwitterionic (sulfobetaine and phosphocholine), neutral (amide and hydroxyl), cationic (amine), and anionic (sulfonic acid and silanol). Principal component analysis of the data showed that partitioning was a dominating mechanism for uncharged solutes in HILIC. However, correlations between functional groups and interactions were also observed, which confirms that the HILIC retention mechanism is partly contributed by adsorption mechanisms involving electrostatic interaction and multipoint hydrogen bonding. Phases with smaller pore diameters yielded longer retention of solutes, but did not significantly change the column selectivities. The particle diameter had no significant effect, neither on retention, nor on the selectivities. An increased water content in the eluent reduced the multipoint hydrogen bonding interactions, while an increased electrolyte concentration lowered the selectivities of the tested columns and made their interaction patterns more similar. PMID:21803363

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

    PubMed

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

    2014-12-11

    The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled ?-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles. PMID:25419869

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

    NASA Astrophysics Data System (ADS)

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

    2002-04-01

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

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

    PubMed

    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. PMID:23927242

  14. 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.

  15. 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.

  16. Theory of correlations in strongly interacting fluids of two-dimensional dipolar bosons

    NASA Astrophysics Data System (ADS)

    Abedinpour, Saeed H.; Asgari, Reza; Polini, Marco

    2012-10-01

    Ground-state properties of a two-dimensional fluid of bosons with repulsive dipole-dipole interactions are studied by means of the Euler-Lagrange hypernetted-chain approximation. We present a self-consistent semianalytical theory of the pair distribution function g(r) and ground-state energy of this system. Our approach is based on the solution of a zero-energy scattering Schrödinger equation for the “pair amplitude” g(r) with an effective potential from Jastrow-Feenberg correlations. We find excellent agreement with quantum Monte Carlo results over a wide range of coupling strength, nearly up to the critical coupling for the liquid-to-crystal quantum phase transition. We also calculate the one-body density matrix and related quantities, such as the momentum distribution function and the condensate fraction.

  17. Intermolecular radical carbofluorination of non-activated alkenes.

    PubMed

    Kindt, Stephanie; Heinrich, Markus R

    2014-11-17

    The Meerwein arylation has recently become an even more powerful tool for the functionalization of alkenes. Besides the attachment of an aryl group, radical reactions of this type allow the introduction of several different heteroatoms and a broad variety of alkenes are meanwhile tolerated as substrates. Closing a long-standing gap of the methodology, this communication describes the first intermolecular Meerwein-type carbofluorination. In metal-free reactions, arylalkyl fluorides were obtained from arylhydrazines and alkenes with Selectfluor acting as oxidant and as radical fluorine source. PMID:25303212

  18. Gold-catalyzed intermolecular anti-markovnikov hydroamination of alkylidenecyclopropanes.

    PubMed

    Timmerman, Jacob C; Robertson, Bradley D; Widenhoefer, Ross A

    2015-02-01

    The cationic gold phosphine complex [{PCy2 (o-biphenyl)}Au(NCMe)](+) SbF6 (-) (Cy=cyclohexyl) catalyzes the intermolecular, anti-Markovnikov hydroamination reaction of monosubstituted and cis- and trans-disubstituted alkylidenecyclopropanes (ACPs) with imidazolidin-2-ones and other nucleophiles. This reaction forms 1-cyclopropyl alkylamine derivatives in high yield and with high regio- and diastereoselectivity. NMR spectroscopic analysis of gold ?-ACP complexes and control experiments point to the sp?hybridization of the ACP internal alkene carbon atom as controlling the regiochemistry of the ACP hydroamination reaction. PMID:25533892

  19. Observation and characterization of intermolecular homonuclear single-quantum coherences in liquid nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Chen, Zhong; Chen, Zhiwei; Zhong, Jianhui

    2002-11-01

    Intermolecular zero-quantum and double-quantum coherences (iZQCs and iDQCs) are frequently discussed in literature since they may provide novel contrast mechanisms in magnetic resonance imaging and possibilities for high-resolution spectra in an inhomogeneous and unstable magnetic field. In a previous paper [J. Chem. Phys. 115, 10769 (2001)], we have studied both theoretically and experimentally the properties of iZQC and iDQC nuclear magnetic resonance (NMR) signals related to intermolecular dipolar interactions in two-component systems. In this paper, the investigation is extended to homonuclear intermolecular single-quantum coherences (iSQCs) from the second-order spin interactions, which have not been observed and studied previously. Selective excitation was used to suppress the strong conventional single-spin single-quantum signals. A combination of dipolar field treatment and Torrey equation was used to derive a general theoretical expression for the time evolution of spins with arbitrary flip angles of rf pulses. The expression was used to predict the optimal conditions for iSQCs among highly polarized spins in liquid. Dependence of the iSQC signals on the experimental parameters was measured and analyzed to verify the theoretical predictions. For the first time, signals from pure homonuclear two-spin iSQCs free of much larger conventional single-spin single-quantum signals, and intermolecular iSQC cross peaks in homonuclear pulsed-field gradient COSY experiments were observed and characterized, in one- and two-dimensional (1D and 2D) experiments, respectively. The use of coherence-selection gradients tilted at the magic angle results in the suppression of iSQC cross peaks. It provides strong evidence that the observed signals originate from distant dipolar interactions. Relaxation and diffusion properties of iSQCs in multiple-component samples were characterized and analyzed as well as the optimal rf flip angles. Theoretical and experimental results presented herein demonstrate that the signals from the homonuclear second-order iSQCs not only have a similar signal intensity as iZQCs or iDQCs, all of which are much stronger than that from three-spin iSQCs reported previously, but also provide spatial information related to dipolar correlation scales similar to iZQCs and iDQCs, which is not present in conventional SQC experiments. All 1D and 2D NMR experimental observations based on single- and multiple-component samples are in excellent agreement with the theoretical predictions. The quantitative study of iSQCs provides a better understanding of their unique mechanisms, and may find useful applications in NMR analyses such as sample purification and/or preparation of metabolites, biofluids, and natural compounds dissolved in nondeuterated solvents.

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

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-07-01

    Clear evidence for the existence of intermolecular carbon-carbon (CC), nitrogen-nitrogen (NN) and oxygen-oxygen (OO) interactions between atoms in similar chemical environments in homogeneous dimers of organic dipolar molecules has been obtained from molecular orbital (MO), natural bond orbital (NBO) and atoms-in-molecule (AIM) electron density analyses at the M06L/6-311++G(d,p) level of density functional theory (DFT). These XX type interactions are mainly the result of local polarization effects, causing segregation of electron-rich and electron-deficient regions in the X atoms, leading to complementary electrostatic interactions. NBO analysis provides evidence of charge transfer between the two X atoms. Even in symmetrical molecules such as acetylene, induced dipoles in the dimer create CC bonding interactions. The strength of this type of interaction increases with increase in the dipole moment of the molecule. Energy decomposition analysis (EDA) shows that the electrostatic component of the interaction energy (Eint) is very high, up to 95.86%. The CC interactions between similar carbon atoms are located for several crystal structures obtained from the literature. In addition, MO, AIM and electrostatic potential analyses support interactions between similar oxygen (OO) and nitrogen (NN) atoms in a variety of molecular dimers. Good prediction of Eint is achieved in terms of the total gain in electron density at non-covalently interacting intermolecular bonds (??) and the monomer dipole moment (?). A rigorously tested QSAR equation has been derived to predict Eint for all dimer systems:This equation suggests that the polarization-induced bonding interaction between atoms in a similar chemical environment could well be a general chemical phenomenon. The results have been further validated by different density functional methods and also by G3MP2 method. PMID:26103886

  1. 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

  2. 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

  3. 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.

  4. A combined quantum chemistry and classical molecular interaction energy method for the determination of crystal geometries and energies

    Microsoft Academic Search

    Gwon Hee Ko; William H. Fink

    2002-01-01

    Theoretical molecular solid crystal structure optimization presents many computational challenges. Calculation of both intramolecular interactions and intermolecular interactions are major obstacles. In this study, the intramolecular interactions are treated quantum mechanically and the intermolecular interactions are approximated by a force field, which is in part determined by a partial charge analysis of the quantum treatment. This combined approach, called the

  5. Energy transfer with migration. Generalization of the Yokota-Tanimoto model for any kind of multipole interaction

    NASA Astrophysics Data System (ADS)

    Martín, I. R.; Rodríguez, V. D.; Rodríguez-Mendoza, U. R.; Lavín, V.; Montoya, E.; Jaque, D.

    1999-07-01

    The dynamics of luminescence decay is analyzed within the general scenario of randomly distributed ions with whatever multipole interaction, taking into account energy transfer and migration processes among them. By applying Padé approximants to the Allinger and Blumen expression for the excited state population, a simple expression has been obtained which can be easily fitted to experimental data. This expression can be considered a generalization of the dipole-dipole Yokota-Tanimoto equation. On the other hand, the decay curves from the 5D3 level of the Tb3+ ions in fluorozincate glasses have been measured for different Tb3+ concentrations. The results are analyzed in the framework of the proposed expression.

  6. H3O+···H2O: comparison between some analytical forms of the intermolecular energy

    NASA Astrophysics Data System (ADS)

    Kochanski, E.

    1986-10-01

    A comparison between results obtained using different analytical expressions for the intermolecular energy of H 3O +⋯H 2O is presented for 33 geometries (6 geometrical configurations and different intermolecular distances). These values are compared with SCF energies in order to estimate the validity of the approximations.

  7. Intermolecular vibrational energy transfers in liquids and solids.

    PubMed

    Chen, Hailong; Wen, Xiewen; Guo, Xunmin; Zheng, Junrong

    2014-07-21

    Resonant and nonresonant intermolecular vibrational energy transfers in KSCN/KSC(13)N/KS(13)C(15)N aqueous and DMF solutions and crystals are studied. Both energy-gap and temperature dependent measurements reveal some surprising results, e.g. inverted energy-gap dependent energy transfer rates and opposite temperature dependences of resonant and nonresonant energy transfer rates. Two competing mechanisms are proposed to be responsible for the experimental observations. The first one is the dephasing mechanism in which the measured energy transfer rate originates from the dephasing of the energy donor-acceptor coherence, and the second one is the phonon-compensation mechanism derived from the second order perturbation. It is found that both the nonresonant energy transfers in the liquids and resonant energy transfers in both liquids and solids can be well described by the first mechanism. The second mechanism explains the nonresonant energy transfers in one series of the solid samples very well. PMID:24899537

  8. Intermolecular coulomb decay at weakly coupled heterogeneous interfaces.

    PubMed

    Grieves, Gregory A; Orlando, Thomas M

    2011-07-01

    Surface ejection of H(+)(H(2)O)(n=1-8) from low energy electron irradiated water clusters adsorbed on graphite and graphite with overlayers of Ar, Kr or Xe results from intermolecular Coulomb decay (ICD) at the mixed interface. Inner valence holes in water (2a(1)(-1)), Ar (3s(-1)), Kr (4s(-1)), and Xe (5s(-1)) correlate with the cluster appearance thresholds and initiate ICD. Proton transfer occurs during or immediately after ICD and the resultant Coulomb explosion leads to H(+)(H(2)O)(n=1-8) desorption with kinetic energies that vary with initiating state, final state, and interatomic or molecular distances. PMID:21797555

  9. Nonlinear dynamics of globular proteins

    SciTech Connect

    Lomdahl, P.S.

    1983-01-01

    Some ongoing work aimed at generalizing DAVYDOV's ideas to a real globular protein is described. So far, a computer code, GLOP, which calculates amide-I bond energy evolution on a globular protein has been developed and tested. The code is quite versatile and takes as input the coordinates of a protein. The full geometry of the molecule is then taken into account when the dipole-dipole interaction between peptide groups is calculated. The amide-I energy is coupled to one intramolecular excitation, but can without difficulty be extended to more or to include intermolecular excitations.

  10. Magnetic moment oscillation in ammonium perchlorate in a DC SQUID-based magnetic resonance experiment

    NASA Astrophysics Data System (ADS)

    Montero, V.; Cernicchiaro, G.

    In this work we describe experimental results in which a DC SQUID (superconducting quantum interference device) is used as free induction decay detector. Measurements of a solid ammonium perchlorate (NH 4ClO 4) sample were performed, in zero field, at 4.2 K. Unexpected magnetic moment oscillations were detected at 1.5 kHz. The computation of the magnetic fields suggests that the proton nuclear magnetic resonance may explain the measured resonance, considering reorientation of the ammonium group by quantum tunneling of protons and a magnetic proton dipole-dipole intermolecular interaction model.

  11. Intermolecular electron transfer promoted by directional donor-acceptor attractions in self-assembled diketopyrrolopyrrole-thiophene films.

    PubMed

    Liu, Huiying; Jia, Hui; Wang, Lanfen; Wu, Yishi; Zhan, Chuanlang; Fu, Hongbing; Yao, Jiannian

    2012-11-01

    The photophysics of a symmetric triad consisting of two bithiophene (BT) units covalently linked to a central diketopyrrolopyrrole unit (DPP) has been investigated both in dichloromethane and in the thin film. The DPP-BT film exhibits a red-shifted low-energy absorption band compared to its solution, which is indicative of efficient ?-? interactions in the solid-state phase. The steady-state and time-resolved fluorescence results revealed that the photoluminescence was subjected to severe emission quenching when DPP-BT changes from its solution phase to its film form. Further femtosecond transient absorption studies clarified that rapid intermolecular electron transfer accounts for the considerable fluorescence quenching event. The structural characterization of DPP-BT nanobelts, based on GIXRD and SAED patterns, suggested that the composite may be self-assembled into a slipped face-to-face configuration in the film, providing compact interlayer D-A interactions. As a result, intermolecular electron transfer is promoted by the favorable donor-acceptor attractions between the adjacent molecules. Moreover, this packing configuration provides a moderate channel for charge transportation. The hole mobility, which was measured based on a single-belt field-effect transistor, was found to be around 0.07 cm(2) V(-1) s(-1). Our observation reveals the role of spatial orientation in photophysical processes and the consequential semiconductor performance, providing guidance for the development and self-assembly of new opto-electronic molecules. PMID:22951990

  12. Determination of a silane intermolecular force field potential model from an ab initio calculation

    SciTech Connect

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng [Institute of Applied Mechanics, National Taiwan University, Taipei 10617, Taiwan (China)

    2010-12-15

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  13. 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.

  14. Photoinduced intermolecular electron transfer in complex liquids: Experiment and theory

    NASA Astrophysics Data System (ADS)

    Tavernier, H. L.; Kalashnikov, M. M.; Fayer, M. D.

    2000-12-01

    Photoinduced intermolecular electron transfer between Rhodamine 3B and N,N-dimethylaniline has been studied in a series of seven liquids: acetonitrile, ethanol, propylene glycol, and mixtures of ethanol, 2-butanol, ethylene glycol, propylene glycol, and glycerol. In each liquid, the donor and acceptors have different diffusion constants and experience distinct dielectric properties. Ps time-dependent fluorescence measurements and steady-state fluorescence yield measurements were made and analyzed using a detailed statistical mechanical theory that includes a distance-dependent Marcus rate constant, diffusion with the hydrodynamic effect, and solvent structure. All solvent-dependent parameters necessary for calculations were measured, including dielectric constants, diffusion constants, and redox potentials, leaving the electronic coupling unknown. Taking the distance-dependence of the coupling to be ?=1 Å-1, data were fit to a single parameter, the coupling matrix element at contact, J0. The theory is able to reproduce both the functional form of the time-dependence and the concentration-dependence of the data in all seven liquids by fitting only J0. Despite the substantial differences in the properties of the experimental systems studied, fits to the data are very good and the values for J0 are very similar for all solvents.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  16. Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences.

    PubMed

    Chen, Zhong; Cai, Shuhui; Chen, Zhiwei; Zhong, Jianhui

    2009-02-28

    A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry. PMID:19256612

  17. Fast acquisition of high-resolution NMR spectra in inhomogeneous fields via intermolecular double-quantum coherences

    PubMed Central

    Chen, Zhong; Cai, Shuhui; Chen, Zhiwei; Zhong, Jianhui

    2009-01-01

    A pulse sequence, IDEAL-II, is proposed based on the concept of intermolecular dipolar-interaction enhanced all lines [Z. Chen et al., J. Am. Chem. Soc. 126, 446 (2004)] for obtaining one-dimensional (1D) high-resolution liquid NMR spectra in inhomogeneous fields via two-dimensional acquisitions. With the new acquisition scheme, the range of magnetic field inhomogeneity rather than chemical shift is sampled in the indirect dimension. This enables a great reduction in acquisition time and amount of data, much improved over the original IDEAL implementation. It is applicable to both isolated and J-coupled spin systems in liquid. For the latter, apparent J coupling constants are magnified threefold in spectra obtained with this sequence. This allows a more accurate measurement of J coupling constants in the cases of small J coupling constants or large inhomogeneous fields. Analytical expression was derived based on intermolecular multiple-quantum coherence treatments. Solution samples that were purposely deshimmed and biological samples with intrinsic field inhomogeneities were tested. Experimental results demonstrate that this sequence retains useful structural information including chemical shifts, relative peak areas, and multiplet patterns of J coupling even when the field inhomogeneity is severe enough to almost erase all spectroscopic information with conventional 1D single-quantum coherence techniques. This sequence is more applicable to weakly coupled and uncoupled spin systems, potentially useful for studying metabolites in in vivo NMR spectroscopy and for characterizing technologically important new materials in combinatorial chemistry. PMID:19256612

  18. Order induced by dipolar interactions in a geometrically frustrated antiferromagnet

    NASA Astrophysics Data System (ADS)

    Palmer, S. E.; Chalker, J. T.

    2000-07-01

    We study the classical Heisenberg model for spins on a pyrochlore lattice interacting via long-range dipole-dipole forces and nearest-neighbor exchange. Antiferromagnetic exchange alone is known not to induce ordering in this system. We analyze low-temperature order resulting from the combined interactions, both by using a mean-field approach and by examining the energy cost of fluctuations about an ordered state. We discuss behavior as a function of the ratio of the dipolar and exchange interaction strengths and find two types of ordered phase. Below a certain value of this ratio, we find that the system orders in a four-sublattice Néel state. For interaction strengths above this critical ratio, the system orders with an incommensurate wave vector. We relate our results to the recent experimental work and reproduce and extend the theoretical calculations on the pyrochlore compound, Gd2Ti2O7, by N. P. Raju, M. Dion, M. J. P. Gingras, T. E. Mason, and J. E. Greedan, Phys. Rev. B 59, 14 489 (1999).

  19. 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)

  20. Intermolecular and intramolecular FRET between two spectrally overlapping green fluorescent protein variants fused to two

    E-print Network

    573 Intermolecular and intramolecular FRET between two spectrally overlapping green fluorescent fluorescent proteins within a living cell and follow the time course of the changes in FRET corresponding cyan fluorescent protein FLIM fluorescence lifetime imaging microscopy FRET fluorescence resonance

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

    E-print Network

    Rubina, Marina; Sherrill, William M.; Barkov, Alexey Yu; Rubin, Michael

    2014-07-07

    A novel class of chiral phosphanyl-oxazoline (PHOX) ligands with a conformationally rigid cyclopropyl backbone was synthesized and tested in the intermolecular asymmetric Heck reaction. Mechanistic modelling and crystallographic studies were used...

  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. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties.

    PubMed

    Dalvit, Claudio; Vulpetti, Anna

    2012-02-01

    A correlation between 19F NMR isotropic chemical shift and close intermolecular F???H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F???X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F???H distance and F???H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target. PMID:22262517

  4. Vibrational dependence of an intermolecular potential for H2O-He system

    NASA Astrophysics Data System (ADS)

    Petrova, T. M.; Solodov, A. M.; Solodov, A. A.; Starikov, V. I.

    2013-11-01

    The intermolecular interaction potential, taken as the sum of pair potentials which, in turn, were modeled by the Lennard-Jones potential has been determined by means of nonlinear least squares fitting its parameters to the experimental data on the lines broadening (?) and shift (?) coefficients. The data on ? and ? for nine vibration bands ?1, ?3, 2?2, ?1+?2, ?2+?3, 2?1, ?1+?3, 2?2+?3 and ?1+?2+?3 have been obtained from the analysis of the H2O-He absorption spectra, recorded from 3000 to 9000 cm-1 with help of IFS 125HR Fourier spectrometer at room temperature, spectral resolution of 0.01 cm-1 and in wide pressure range of He. Additionally we use literature data for rotational band (˜180 GHz) and ?2 band (1850-2140 cm-1). The vibrational and rotational dependence of the potential parameters as well as the temperature dependence of the calculated lines broadening coefficients have been demonstrated.

  5. Intermolecular multiple quantum coherences at high magnetic field: the nonlinear regime.

    PubMed

    Marques, J P; Grant, S; Blackband, S; Bowtell, R W

    2005-10-22

    Experiments have been carried at magnetic-field strengths of 9.4, 14.1, and 17.6 T to explore the evolution of intermolecular multiple quantum coherences in the nonlinear regime where the system evolves for times that are much greater than the characteristic time of action of the long-range dipolar field, tau(d). The results show the expected Bessel function form of the recorded signal as a function of time of evolution, with evident zeros and sign changes. As expected, the rate of signal evolution increases at higher-field strengths as a result of the increased equilibrium magnetization. A numerical method for calculating the evolution of magnetization under the action of the distant dipolar field, relaxation, and diffusion that is based on Fourier analysis of the magnetization distribution has been applied to the correlated two-dimensional spectroscopy revamped by asymmetric z-gradient echo detection sequence in the nonlinear regime and shown to produce results that are in good agreement with experimental data acquired at different magnetic fields and rates of spatial modulation. Experiments and simulations have also been used to explore the evolution of magnetization in a mixture of two interacting spin species in the nonlinear regime. PMID:16268701

  6. 3,5-Dimethyl-1,3,5-oxadiazane-2,4,6-trione: short intermolecular contacts determining the crystal packing.

    PubMed

    Geith, Janna; Klapötke, Thomas M; Mayer, Peter; Schulz, Axel; Weigand, Jan J

    2005-09-01

    In the title compound, C5H6N2O4, the molecules lie across a crystallographic mirror plane. The compound lacks traditional hydrogen-bond donors, and hence crystals are held together by unusual C=O...O, O...C and weak C-H...O interactions, forming layers. Adjacent layers are arranged in an antiparallel manner, yielding an ABA layer sequence. The intermolecular contacts are quite short; a topological analysis of charge density based on density-functional-theory calculations was used for consideration of these short contacts and indicated a strong attractive bonding closed-shell interaction between these atoms in the crystal structure. PMID:16143776

  7. Investigating nanoparticle interactions from interparticle-to-nanocomposite

    NASA Astrophysics Data System (ADS)

    Desautels, R. D.; Skoropata, E.; Rowe, M.; van Lierop, J.

    2015-05-01

    A series of core/shell Fe-oxide/SiO2 nanoparticles were produced to form Fe-oxide (1:1 Fe3O4 and ?-Fe2O3) cores with diameters of approximately 4.6 nm and shell thicknesses ranging from 3.6 to 5.4 nm. Hot press sintering of core/shell nanoparticles created a nanocomposite of Fe-oxide nanoparticles in a SiO2 matrix. The presence of an iron-orthosilicate at the core-shell interface defines the intrinsic magnetic properties of the nanoparticle systems, resulting in an increase in magnetic anisotropy with thicker SiO2 shell. We find that dipole-dipole interactions are mediated by the overall SiO2 shell, and that these interactions are coupling neighbouring particles' magnetization with increasing correlation lengths. When the nanoparticles from a composite material, packing significantly increases the interaction strengths, altering the overall magnetization of the system so that the iron-oxide cores present an approximate 25% increase in (saturation) magnetization to a bulk-like (˜80 emu/g) value.

  8. The Nanoscale Biophysics of Microscale Cell Adhesion

    E-print Network

    Tees, David F.J.

    in solution ­ Receptor is molecule bound to a surface (cell or glass/plastic substrate) · For cell attached to a substrate. #12;Mechanical Forces in Biology · Phenomena for which mechanical forces play: ­ Charge-charge interactions ­ charge-dipole, dipole-dipole interactions ­ Hydrophobic interactions

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

    PubMed

    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. PMID:24028120

  10. 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.

  11. The energy parameters of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane polymorphs and their phase transitions

    NASA Astrophysics Data System (ADS)

    Golovina, N. I.; Utenyshev, A. N.; Bozhenko, K. V.; Chukanov, N. V.; Zakharov, V. V.; Korsounskii, B. L.

    2009-07-01

    The calculated dispersion and electrostatic intermolecular interaction energies in crystals of ?, ?(H2O), and ? polymorphs of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazawurtzitane (HNIW) were compared. Preliminarily, nonempirical quantum-chemical calculations of the three compounds with complete geometry optimization were performed using the GAUSSIAN-03 package and density functional theory. The dispersion intermolecular interaction energy was calculated with the “6-exp” potential. The van der Waals and dipole-dipole interaction energies were substantially different in crystals of different HNIW polymorphs, but total energy changes in phase transitions were close to zero. The calculated ? > ? and ?(H2O) > ? phase transition energies were close to the experimental values determined using a differential calorimeter. Dehydration substantially influenced the kinetics and heat effects of polymorphic transitions.

  12. 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...

  13. Gold(I)-Catalyzed Intra-and Intermolecular Hydroamination of Unactivated Junliang Zhang, Cai-Guang Yang, and Chuan He*

    E-print Network

    He, Chuan

    -based molecules, such as amines, anilines, carboxyamides, carbamates, alkylsulfona- mides, or sulfamates that carbamates also work as nucleophiles in intramolecular additions. Table 1. Intermolecular Hydroamination

  14. Quantitation of intermolecular dipolar effects in NMR spectroscopy and high order MSE MR imaging.

    PubMed

    Chen, Z; Kennedy, S D; Zhong, J

    2000-12-01

    An analytical expression for intermolecular dipolar effects was derived for the CRAZED sequence with an arbitrary flip angle of the second RF pulse and time-varying gradients. A combination of the demagnetizing field theory and product operator formalism was utilized in the derivation. It is demonstrated that the time-averaged, not instantaneous, orientation of the applied gradients determines the contributions of long-range intermolecular dipole effects. An imaging sequence to detect intermolecular dipolar effects was designed. The second- and third-order multiple spin echo (MSE) NMR signals of swine muscle were observed and were found to be in good agreement with the theoretical predictions. MSE images of a water phantom with nth orders (n = 2, - 3, - 4, and - 5) were also obtained, and their relative signal intensities and optimized TE values were elucidated and compared with the theoretical prediction. PMID:11154953

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

    PubMed

    Chiue, Hiroko; Yamazoye, Tsutako; Matsumura, Sueo

    2015-06-01

    Previous studies have shown that fibrous collagen undergoes intermolecular cross-linking at multiple sites of the elongated triple-helical regions among adjacent juxtaposed collagen molecules on incubation with a very high concentration of reducing sugar such as 200 mM ribose, and the similarity of the changes in its physicochemical properties to that of senescent collagen aged in vivo has been emphasized. In the present study, however, it was found that when incubated with less than 30 mM ribose, fibrous collagen underwent intermolecular cross-linking primarily between the telopeptide region of a collagen molecule and the triple-helical region of another adjacent collagen molecule, and intermolecular cross-linking between the triple-helical regions of adjacent collagen molecules was very small. Physiological significance of the previous studies thus needs to be reevaluated. PMID:25892520

  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. In vivo intermolecular double-quantum imaging on a clinical 1.5 T MR scanner.

    PubMed

    Zhong, J; Chen, Z; Kwok, E

    2000-03-01

    A novel MRI method based on the intermolecular double-quantum coherence (DQC) for soft tissues is described. DQC images of human brain were obtained for the first time on a whole-body 1.5 T scanner. The combination of quantum and classical formalisms was used to characterize multiple-quantum coherences, and to aid in the design of a DQC imaging sequence. The theoretical analysis suggests that signals from the intermolecular DQCs have higher sensitivity than those from the zero-quantum coherence (ZQC) for human brain, and the sensitivity increases with increased field strength. The DQC signal may provide a new form of contrast for MRI. PMID:10725874

  18. Infrared spectra of ice and water from first principles: intra vs. intermolecular dipole correlations

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Sharma, Manu; Resta, Raffaele; Galli, Giulia; Car, Roberto

    2008-03-01

    We report simulated infrared (IR) spectra of deuterated ice and water using Car-Parrinello molecular dynamics with maximally localized Wannier functions. Experimental features of both ice and water are accurately reproduced within the harmonic approximation. Calculated line shapes are further decomposed in terms of intra and intermolecular dipole correlation functions with spatial resolution. This approach proves to be very useful to understand the origin of spectral features and the nature of the underlying hydrogen-bond (H-bond) network. We find that intermolecular dynamic charge fluctuations play a crucial role over the entire frequency range.

  19. Quantum phases of hardcore bosons with long-range interactions on a square lattice

    NASA Astrophysics Data System (ADS)

    Yamamoto, Daisuke; Masaki, Akiko; Danshita, Ippei

    2012-08-01

    We study the ground-state phase diagrams of hardcore bosons with long-range interactions on a square lattice using the linear spin-wave theory and a cluster mean-field method. Specifically, we consider the two types of long-range interaction: One consists only of the nearest- and next-nearest-neighbor interactions, and the other is the dipole-dipole interaction that decays with the interparticle distance r as ˜r-3. It is known from previous analyses by quantum Monte Carlo methods that a checkerboard supersolid (CSS) is absent in the ground-state phase diagram of the former case while it is present in the latter. In the former, we find that quantum fluctuations around mean-field solutions are enhanced by the direct competition between the checkerboard and striped solid orders and that they destabilize the CSS phase. On the other hand, the emergence of the CSS phase in the latter case can be attributed to the absence of such a competition with other solid orders. We also show that the cluster mean-field method allows for the determination of phase boundaries in a precise quantitative manner when scaling with respect to the cluster size is taken into account. It is found that the phase transition between the superfluid and the solid (or CSS) is of the first order in the vicinity of the particle-hole symmetric line.

  20. BPS Force Balances via Spin-Spin Interactions

    E-print Network

    David Kastor; Jennie Traschen

    1998-11-10

    We study two systems of BPS solitons in which spin-spin interactions are important in establishing the force balances which allow static, multi-soliton solutions to exist. Solitons in the Israel-Wilson-Perjes (IWP) spacetimes each carry arbitrary, classical angular momenta. Solitons in the Aichelburg-Embacher "superpartner" spacetimes carry quantum mechanical spin, which originates in the zero-modes of the gravitino field of N=2 supergravity in an extreme Reissner-Nordstrom background. In each case we find a cancellation between gravitational spin-spin and magnetic dipole-dipole forces, in addition to the usual one between Newtonian gravitational attraction and Coulombic electrostatic repulsion. In both cases, we analyze the forces between two solitons by treating one of the solitons as a probe or test particle, with the appropriate properties, moving in the background of the other. In the IWP case, the equation of motion for a spinning test particle, originally due to Papapetrou, includes a coupling between the background curvature and the spin of the test particle. In the superpartner case, the relevant equation of motion follows from a kappa-symmetric superparticle action.

  1. THE DIFFERENCE IN THE INTERMOLECULAR FORCES OF HâO AND DâO

    Microsoft Academic Search

    E. Whalley

    1957-01-01

    The lattice energy of a compound at O deg K can be obtained from the ; heat of sublimation at O deg K, the zero-point energies due to the various ; intermolecular vibrations, and the difference between the crystal and the gas in ; the intramolecular zero-point energies. The difference in the lattice energies ; of isotopic molecules which have

  2. 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.

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

    Microsoft Academic Search

    1997-01-01

    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.

  4. Importance of the Donor:Fullerene Intermolecular Arrangement for High-Efficiency Organic Photovoltaics

    E-print Network

    McGehee, Michael

    -accepting materials. Furthermore, external quantum efficiency measurements of the charge-transfer state and solidImportance of the Donor:Fullerene Intermolecular Arrangement for High-Efficiency Organic of some of the most efficient polymers utilized in polymer:fullerene PV devices, combined with an analysis

  5. Visible-Light-Driven Intermolecular [2+2] Cycloadditions between Coumarin-3-Carboxylates and Acrylamide Analogs.

    PubMed

    Liu, Qiang; Zhu, Fu-Ping; Jin, Xiao-Ling; Wang, Xiao-Ju; Chen, Han; Wu, Li-Zhu

    2015-07-13

    This paper reports a room temperature visible-light-driven protocol for the intermolecular [2+2] cycloadditions between coumarin-3-carboxylates and acrylamides analogs by an energy-transfer process. Using an iridium complex FIrPic as a photosensitizer and a 3?W blue LED as a light source, an array of cyclobutabenzocypyranones were prepared in moderate to excellent yields. PMID:26096526

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

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han [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.

  7. An exact quantum Monte Carlo calculation of the helium-helium intermolecular potential

    E-print Network

    Anderson, James B.

    An exact quantum Monte Carlo calculation of the helium-helium intermolecular potential James B Monte Carlo method used is exact in that it requires no mathematical or physical approximations beyond those of the Schriidinger equation. As in most Monte Carlo methods there is a statistical or sampling

  8. 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

  9. 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…

  10. 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

  11. Casimir-Polder intermolecular forces in minimal length theories

    SciTech Connect

    Panella, O. [INFN, Sezione di Perugia, Via A. Pascoli, I-06123, Perugia (Italy)

    2007-08-15

    Generalized uncertainty relations are known to provide a minimal length ({Dirac_h}/2{pi}){radical}({beta}). The effect of such minimal length in the Casimir-Polder interactions between neutral atoms (molecules) is studied. The first order correction term in the minimal uncertainty parameter is derived and found to describe an attractive potential scaling as r{sup -9}, as opposed to the well-known r{sup -7} long range retarded potential.

  12. 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.

  13. Intermolecular forces and molecular dynamics simulation of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) using symmetry adapted perturbation theory.

    PubMed

    Taylor, DeCarlos E

    2013-04-25

    The dimer potential energy surface (PES) of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) has been explored using symmetry adapted perturbation theory based on a Kohn-Sham density functional theory description of the monomers [SAPT(DFT)]. An intermolecular potential energy function was parametrized using a grid of 880 ab initio SAPT(DFT) dimer interaction energies, and the function was used to identify stationary points on the SAPT(DFT) dimer PES. It is shown that there exists a variety of minima with a range of bonding configurations and ab initio analyses of the interaction energy components, along with radial cross sections of the PES near each minimum, are presented. Results of isothermal-isostress molecular dynamics simulations are reported, and the simulated structure, thermal expansion, sublimation enthalpy, and bulk modulus of the TATB crystal, based on the SAPT(DFT) interaction potential, are in good agreement with experiment. PMID:23565605

  14. Intermolecular bonding and vibrations of phenol?H2O (D2O)

    NASA Astrophysics Data System (ADS)

    Schütz, Martin; Bürgi, Thomas; Leutwyler, Samuel; Fischer, Thomas

    1993-03-01

    Extensive ab initio calculations of the phenol?H2O complex were performed at the Hartree-Fock level, using the 6-31G(d,p) and 6-311++G(d,p) basis sets. Fully energy-minimized geometries were obtained for (a) the equilibrium structure, which has a translinear H bond and the H2O plane orthogonal to the phenol plane, similar to (H2O)2; (b) the lowest-energy transition state structure, which is nonplanar (C1 symmetry) and has the H2O moiety rotated by ±90°. The calculated MP2/6-311G++(d,p) binding energy including basis set superposition error corrections is 6.08 kcal/mol; the barrier for internal rotation around the H bond is only 0.4 kcal/mol. Intra- and intermolecular harmonic vibrational frequencies were calculated for a number of different isotopomers of phenol?H2O. Anharmonic intermolecular vibrational frequencies were computed for several intermolecular vibrations; anharmonic corrections are very large for the ?2 intermolecular wag. Furthermore, the H2O torsion ? around the H-bond axis, and the ?2 mode are strongly anharmonically coupled, and a two-dimensional ?/?2 potential energy surface was explored. The role of tunneling splitting due to the torsional mode is discussed and tunnel splittings are estimated for the calculated range of barriers. The theoretical studies were complemented by a detailed spectroscopic study of h-phenol?H2O and d-phenol?D2O employing two-color resonance-two-photon ionization and dispersed fluorescence emission techniques, which extends earlier spectroscopic studies of this system. The ?1 and ?2 wags of both isotopomers in the S0 and S1 electronic states are newly assigned, as well as several other weaker transitions. Tunneling splittings due to the torsional mode may be important in the S0 state in conjunction with the excitation of the intermolecular ? and ?2 modes.

  15. Localized excitations in discrete nonlinear Schrödinger systems: Effects of nonlocal dispersive interactions and noise

    NASA Astrophysics Data System (ADS)

    Rasmussen, K. Ø.; Christiansen, P. L.; Johansson, M.; Gaididei, Yu. B.; Mingaleev, S. F.

    1998-03-01

    A one-dimensional discrete nonlinear Schrödinger (DNLS) model with the power dependence, r- s on the distance r, of dispersive interactions is proposed. The stationary states of the system are studied both analytically and numerically. Two kinds of trial functions, exp-like and sech-like are exploited and the results of both approaches are compared. Both on-site and inter-site stationary states are investigated. It is shown that for s sufficiently large all features of the model are qualitatively the same as in the DNLS model with nearest-neighbor interaction. For s less than some critical value, scr, there is an interval of bistability where two stable stationary states exist at each excitation number. The bistability of on-site solitons may occur for dipole-dipole dispersive interaction ( s = 3), while scr for inter-site solitions is close to 2.1. In the framework of the DNLS equation with nearest-neighbor coupling we discuss the stability of highly localized, “breather-like”, excitations under the influence of thermal fluctuations. Numerical analysis shows that the lifetime of the breather is always finite and in a large parameter region inversely proportional to the noise variance for fixed damping and nonlinearity. We also find that the decay rate of the breather decreases with increasing nonlinearity and with increasing damping.

  16. Intermolecular repulsion through interfacial attraction: toward engineering of polymorphs.

    PubMed

    Kudernac, Tibor; Sändig, Nadja; Fernández Landaluce, Tatiana; van Wees, Bart J; Rudolf, Petra; Katsonis, Nathalie; Zerbetto, Francesco; Feringa, Ben L

    2009-11-01

    Understanding the formation of crystalline polymorphs is of importance for various applications of materials science. Polymorphism of Schiff base derivatives has recently attracted considerable attention because of its influence on photochromic and thermochromic properties of their 3D crystals. The present investigation extends the study of Schiff base polymorphism to the molecular level by using a combination of scanning tunneling microscopy at the liquid/solid interface and molecular modeling. It is demonstrated that polymorphism of 4-(dodecyloxy)-N-(4-dodecylphenyl)-2-hydroxybenzaldimine (PHB), a Schiff base substituted by alkyl side chains, can occur in 2D crystals when PHB is adsorbed on a surface that is able to exchange charge with the molecule. In particular, on Au(111), PHB molecules self-organize not only into a columnar packing but also in dimer structures. Theoretical and experimental results demonstrate that the dimer-based structure observed on Au(111) originates from molecule/surface interactions, which in turn modify molecule/molecule interactions. The results highlight that the Au(111) substrate is far from being a passive part of the self-assembled system and plays a crucial role in the morphology of 2D polymorphs. PMID:19827775

  17. Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.

    PubMed

    Oliva, Romina; Chermak, Edrisse; Cavallo, Luigi

    2015-01-01

    In view of the increasing interest both in inhibitors of protein-protein interactions and in protein drugs themselves, analysis of the three-dimensional structure of protein-protein complexes is assuming greater relevance in drug design. In the many cases where an experimental structure is not available, protein-protein docking becomes the method of choice for predicting the arrangement of the complex. However, reliably scoring protein-protein docking poses is still an unsolved problem. As a consequence, the screening of many docking models is usually required in the analysis step, to possibly single out the correct ones. Here, making use of exemplary cases, we review our recently introduced methods for the analysis of protein complex structures and for the scoring of protein docking poses, based on the use of inter-residue contacts and their visualization in inter-molecular contact maps. We also show that the ensemble of tools we developed can be used in the context of rational drug design targeting protein-protein interactions. PMID:26140438

  18. 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.

  19. Coupling of electrons to intermolecular phonons in molecular charge transfer dimers: A resonance Raman study

    NASA Astrophysics Data System (ADS)

    Pedron, D.; Speghini, A.; Mulloni, V.; Bozio, R.

    1995-08-01

    We report resonance Raman scattering (RRS) spectra and Raman excitation profiles (REP) of a system containing ? dimers of identical molecular radical ions measured with laser excitation in resonance with the charge transfer (CT) transition. A Peierls-Hubbard (PH) Hamiltonian has been used to model the investigated system and to calculate its optical and RRS properties. Results are reported for two polyoxometallate salts of tetrathiafulvalene (TTF), namely (TTF)2(W6O19) and (TTF)2(Mo6O19) whose structures contain almost isolated (TTF+)2 dimers. The RRS spectra of (TTF)2(W6O19), measured in resonance with the CT absorption band centered at 832 nm, show three phonon modes located at 55, 90, and 116 cm-1 which are strongly resonance enhanced. These modes have been associated to the out-of-phase combinations of the translational motions of the two molecules composing the dimer. Such modes are effective in modulating the intradimer transfer integral, thus providing an efficient mechanism for coupling with the electronic system and for enhancement of the scattering intensity at resonance with the CT transition. The REP for the three strongly coupled modes of (TTF)2(W6O19) have been measured with laser excitation wavelengths ranging from 740 to 930 nm. Quantitative analysis of the REP data has been performed based on a perturbative solution of the PH model to second order in the electron-molecular-vibration (EMV) and electron-intermolecular-phonon (EIP) interactions. The CT absorption profile and the REP's have been calculated using a time correlator technique and the model parameters have been optimized in order to fit the experimental REP data. Infrared vibronic absorptions of (TTF)2(W6O19), originated by the EMV coupling, have been measured and independent information on the electronic parameters of the PH model have been derived. This has made the choice of the fitting parameters used for the REP calculations rather unambiguous and has allowed us to obtain, for the first time, reliable experimental estimates of the EIP coupling constants.

  20. Pentacene on Ag(111): Correlation of Bonding Distance with Intermolecular Interaction and Order

    E-print Network

    Schreiber, Frank

    charge carrier injection.4,5,9,10 However, despite extensive research efforts,11-13 the adsorption,2 In this context, the first organic layer on a (typically metal) electrode in such devices is crucial for charge injection into the functional organic film and is, therefore, subject of intense research interest.3

  1. A study of the intermolecular interactions of tolmetin/N-acetyl-L-tyrosine ethyl ester complex.

    PubMed

    Tito, Antonio; Jimenez-Lopez, Claudia; Kowalska, Agnieszka; Wysocki, Stanis?aw

    2009-06-01

    The formation of tolmetin/N-acetyl-l-tyrosine ethyl ester (ATEE) complex has been reported by means of both theoretical and experimental studies, including quantum mechanical calculations as well as UV-vis absorption, fluorescence and time-resolved spectroscopy measurements. It has been found that the fluorescence of ATEE is quenched due to the formation of a non-fluorescent complex between ATEE and tolmetin in the ground state. The geometrical parameters of ATEE/tolmetin complex have been determined with the use of the DFT method applying the B3LYP correlation-exchange functional and 6-31G(d) basis set. The results of experiments indicated the static ATEE quenching by tolmetin. Additionally, the experimental and theoretically predicted Gibbs free energy of complexation has been calculated. PMID:19181568

  2. Modeling Intermolecular Interactions in Nanotubes, Fullerenes and Graphite using a New Long-Range Potential

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Halicioglu, Timur; Han, Jie; Yang, Liu; Huo, Winifred (Technical Monitor)

    1998-01-01

    The cohesive energy and compressibility of strands of a single-wall nanotube rope has been computed using a new long-range potential energy function derived from accurate ab initio quantum chemistry calculations of the benzene dimer and calibrated for energetic and mechanical properties of graphite (at pressures up to 12 GPa). We also use this potential to calculate a variety of properties of carbon nanotubes (both single- and multi-wall) and fullerenes. Extensive comparisons are made with previously published potentials.

  3. 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 ...

  4. Intermolecular interactions in the ? phase of solid oxygen studied by infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Gorelli, Federico A.; Santoro, Mario; Ulivi, Lorenzo; Bini, Roberto

    1999-04-01

    The infrared spectra of solid oxygen, in the overtone region, have been measured in the ? and in the ? phases at low and room temperature up to 60 GPa. The two structured bands observed in the ? phase are assigned to the combination of the infrared active mode with itself and with the Raman active mode, respectively. Performing a deconvolution of the spectral profile the densities of states of the infrared and Raman active vibrational modes are obtained.

  5. FEATURE ARTICLE Unravelling the Origin of Intermolecular Interactions Using Absolutely Localized Molecular

    E-print Network

    Bell, Alexis T.

    to prohibit charge transfer. The second new feature is the ability to separate forward and back-donation and back-donation in synergic bonding in metal complexes. Additionally, it is demonstrated that this method-assembly and self-organization processes in supramolecular polymers, liquid crystals, and other supramolecular

  6. Intermolecular interactions and charge transfer in the 2:1 tetrathiafulvalene bromanil complex, (TTF)2-BA.

    PubMed

    García-Orduña, Pilar; Dahaoui, Slimane; Lecomte, Claude

    2011-06-01

    The crystal structure of the 2:1 charge-transfer complex of tetrathiafulvalene [2,2'-bis(1,3-dithiolylidene)] and bromanil (tetrabromo-1,4-benzoquinone) [(TTF)(2)-BA, (C(6)H(4)S(4))(2)-C(6)Br(4)O(2)] has been determined by X-ray diffraction at room temperature, 100 and 25 K. No structural phase transition occurs in the temperature range studied. The crystal is made of TTF-BA-TTF sandwich trimers. A charge-transfer estimation between donor and acceptor (0.2 e) molecules is proposed in comparison to the molecular geometries of TTF-BA and TTF and BA isolated molecules. Displacement parameters of the molecules have been modeled with the TLS formalism. PMID:21586832

  7. Interaction between polymer constituents and the structure of biopolymers

    NASA Technical Reports Server (NTRS)

    Rein, R.

    1974-01-01

    The paper reviews the current status of methods for calculating intermolecular interactions between biopolymer units. The nature of forces contributing to the various domains of intermolecular separations is investigated, and various approximations applicable in the respective regions are examined. The predictive value of current theory is tested by establishing a connection with macroscopic properties and comparing the theoretical predicted values with those derived from experimental data. This has led to the introduction of a statistical model describing DNA.

  8. Detection and characterization of individual intermolecular bonds using optical tweezers.

    PubMed Central

    Stout, A L

    2001-01-01

    The development of scanning probe techniques has made it possible to examine protein-protein interactions at the level of individual molecular pairs. A calibrated optical tweezers, along with immunoglobulin G (IgG)-coated polystyrene microspheres, has been used to detect individual surface-linked Staphylococcus protein A (SpA) molecules and to characterize the strength of the noncovalent IgG-SpA bond. Microspheres containing, on average, less than one IgG per contact area were held in the optical trap while an SpA-coated substrate was scanned beneath them at a distance of approximately 50 nm. This geometry allows the trapped bead to make contact with the surface, from bond formation to rupture, and results in an enhancement of the force applied to a bond due to leverage supplied by the bead itself. Experiments yielded median single-bond rupture forces from 25 to 44 pN for IgG from four mammalian species, in general agreement with predictions based on free energies of association obtained from solution equilibrium constants. PMID:11371470

  9. 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

  10. Identifiability of competitive intermolecular three-state excited-state processes

    NASA Astrophysics Data System (ADS)

    Boens, Noël; Kowalczyk, Andrzej

    1996-09-01

    The conditions necessary for the recovery of the rateconstants from flourescence decay traces due to competitive intermolecular three-state excited-state processes are investigated. The studied system models a situation where an excited-state species can react competitively with both co-reactants X and Y. It is demonstrated theoretically that, if fluorescence decay traces at two concentrations of X and two concentrations of Y are available, all seven rate constants can always be recovered. In contrast to previously studied intermolecular two-state and three-state excited-state processes, it is not required to obtain a fluorescence decay at [X] = [Y] = 0 Mto assign unique numerical values to all rate constants.

  11. Communication: Relationships between Intermolecular potential, thermodynamics, and dynamic scaling in viscous systems.

    PubMed

    Grzybowski, A; Paluch, M; Grzybowska, K; Haracz, S

    2010-10-28

    In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the "thermodynamic scaling" idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems. PMID:21033768

  12. Communication: Relationships between Intermolecular potential, thermodynamics, and dynamic scaling in viscous systems

    NASA Astrophysics Data System (ADS)

    Grzybowski, A.; Paluch, M.; Grzybowska, K.; Haracz, S.

    2010-10-01

    In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the "thermodynamic scaling" idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems.

  13. Implementation of the Voronoi-Delaunay Method for Analysis of Intermolecular Voids

    Microsoft Academic Search

    Alexey V. Anikeenko; M. G. Alinchenko; V. P. Voloshin; Nikolai N. Medvedev; Marina L. Gavrilova; P. Jedlovszky

    2004-01-01

    \\u000a Voronoi diagram and Delaunay tessellation have been used for a long time for structural analysis of computer simulation of\\u000a simple liquids and glasses. However the method needs a generalization to be applicable to molecular and biological systems.\\u000a Crucial points of implementation of the method for analysis of intermolecular voids in 3D are discussed in this paper. The\\u000a main geometrical constructions

  14. Asymmetric Rh-catalyzed intermolecular hydroacylation of 1,5-hexadiene with salicylaldehyde.

    PubMed

    Inui, Yasuhiro; Tanaka, Masakazu; Imai, Masanori; Tanaka, Keitaro; Suemune, Hiroshi

    2009-10-01

    Asymmetric intermolecular hydroacylation between salicylaldehyde (1) and 1,5-hexadiene (2) using a combination of [RhCl(C(8)H(14))(2)](2) (0.10 eq), (S)-BINAP (0.10 eq), and ZnBr(2) (0.20 eq) afforded an enantiomerically enriched hydroacylated product iso-3 of 84% ee, along with an achiral product normal-3. PMID:19801881

  15. Ruthenium-catalyzed intermolecular [2+2+2] alkyne cyclotrimerization in aqueous media under microwave irradiation

    Microsoft Academic Search

    Victorio Cadierno; Javier Francos; Sergio E. García-Garrido; José Gimeno

    2011-01-01

    The ability of the bis(allyl)-ruthenium(IV) complex [{RuCl(µ-Cl)(?: ?-C10H16)}2] (C10H16=2,7-dimethylocta-2,6-diene-1,8-diyl) to promote intermolecular [2+2+2] alkyne cyclotrimerization reactions in aqueous media under microwave (MW) irradiation has been evaluated. Advantages and disadvantages of using MW vs. conventional thermal heating are discussed.

  16. Total Synthesis and Structural Reassignment of Lyngbyaloside C Highlighted by Intermolecular Ketene Esterification.

    PubMed

    Chang, Chia-Fu; Stefan, Eric; Taylor, Richard E

    2015-07-20

    Lyngbyaloside C, a classic macrolide, isolated from Lyngbya bouilloni, has shown moderate anticancer activity against several cancer cell lines. Here, we report the first total synthesis and stereochemical configuration reassignment of lyngbyaloside C. The synthesis highlights a one-pot intermolecular ketene esterification reaction to form the crucial tertiary ester and tetrahydropyran. In addition, a novel and concise synthetic pathway towards the 1,3-syn secondary, tertiary diol fragment is described using a regio- and stereospecific electrophilic ether transfer reaction. PMID:26101039

  17. Separation and characterization of different signals from intermolecular three-spin orders in solution NMR.

    PubMed

    Chen, Zhong; Chen, Zhi-Wei; Hwang, Dennis W; Zhong, Jianhui; Hwang, Lian-Pin

    2004-12-01

    In this paper, signals originating from a pure specific coherence of intermolecular three-spin orders were separated and characterized experimentally in highly polarized two-component spin systems. A modified CRAZED sequence with selective radio-frequency excitation was designed to separate the small signals from the strong conventional single-spin single-quantum signals. General theoretical expressions of the pulse sequence with arbitrary flip angle pulses were derived using dipolar field treatment. The expressions were used to predict the relaxation and diffusion properties and optimal experimental parameters such as flip angles. For the first time, relaxation and diffusion properties of pure intermolecular single-quantum, double-quantum, and triple-quantum coherences of three-spin orders were characterized and analyzed in one-dimensional experiments. All experimental observations are in excellent agreement with the theoretical predictions. The theoretical results show that the quantum-mechanical treatment leads to exactly the same predictions as the dipolar field treatment. The quantitative study of intermolecular multiple-quantum coherences of three-spin orders presented herein provides a better understanding of their mechanisms. PMID:15546750

  18. Electrochemiluminescence-based detection method of lead(ii) ion via dual enhancement of intermolecular and intramolecular co-reaction.

    PubMed

    Deng, Wei; Hong, Lin-Ru; Zhao, Min; Zhuo, Ying; Gao, Ming

    2015-06-21

    A novel analytical method to design a highly selective and sensitive detection technique for lead(ii) ions (Pb(2+)) detection was developed based on an electrochemiluminescence (ECL) sensor, taking advantage of the high specificity of the aptamer for Pb(2+) and the use of both intermolecular and intramolecular co-reaction to achieve signal enhancement. For sensing interface construction, l-cysteine (Cys) and gold nanostructured layers were electrodeposited on the electrode surface successively, which afforded a large surface area to anchor massive thiol-terminated auxiliary probes (APs) via a thiol-Au interaction. Then, a DNA duplex was generated based on the hybridization of the APs with capture probes (CPs, Pb(2+) specific aptamers). In the presence of Pb(2+), Pb(2+)-induced aptamers were released from the DNA duplex via the formation of a Pb(2+)-stabilized G-quadruplex, accompanied by leaving the single CPs on the sensing interface. Herein, the ruthenium(ii) complexes with functional groups of -COOH (Ru-COOH) were covalently bonded on the polyamidoamine dendrimers with amine end groups (PAMAM), which were capped by the high-index-faceted Au nanoparticles (HIFAuNPs) to obtain the ECL signal labels of Ru-PAMAM-HIFAuNPs. Then, the detection probes (DPs) of amino-terminated Pb(2+) specific aptamers were tagged with the Ru-PAMAM-HIFAuNPs. It was demonstrated that the covalent bonding of PAMAM and Ru-COOH could generate a self-enhanced ECL luminophore by an intramolecular co-reaction and the use of a Cys layer modified electrode could enhance the ECL by the intermolecular co-reaction of Cys and Ru-COOH, which lead to a significant enhancement of the ECL response. Based on this analytical method, the ECL signal increased with Pb(2+) concentration which presented a linear relationship in the range 1.0 × 10(-13)-1.0 × 10(-7) M with the detection limit of 4.0 × 10(-14) M. The proposed approach was also successfully utilized for the determination of Pb(2+) in soil samples. PMID:25915114

  19. Direct computer simulation of water-mediated force between supported phospholipid membranes

    NASA Astrophysics Data System (ADS)

    Pertsin, Alexander; Platonov, Dmitry; Grunze, Michael

    2005-06-01

    The grand canonical Monte Carlo technique is used to calculate the water-mediated force operating between two supported 1,2-dilauroyl-DL-phosphatidylethanolamine (DLPE) membranes in the short separation range. The intra- and intermolecular interactions in the system are described with a combination of an AMBER-based force field for DLPE and a TIP4P model for water. The long range contributions to the electrostatic interaction energy are treated in the dipole-dipole group-based approximation. The total water-mediated force is analyzed in terms of its hydration component and the component due to the direct interaction between the membranes. The latter is, in addition, partitioned into the electrostatic, van der Waals, and steric repulsion contributions to give an idea of their relative significance in the water-mediated interaction of the membranes.

  20. Syntheses, spectroscopic and structural properties of phenoxysilyl compounds: X-ray structures, FT-IR and DFT calculations

    NASA Astrophysics Data System (ADS)

    Jab?o?ska, Agnieszka; Ponikiewski, ?ukasz; Ejsmont, Krzysztof; Herman, Aleksander; Do??ga, Anna

    2013-12-01

    The reaction of silicon disulfide with alkylphenols yields tetraphenoxysilane, cyclodisilthiane and silanethiol. The outcome of the reaction depends on the presence of the steric hindrance in the ortho position on the reacting phenol. New products of the reaction of silicon disulfide with phenols are characterized by FT-IR, NMR, X-ray diffraction and DFT calculations. The intramolecular interactions in the compounds are mainly XH---? (X = C, S) whereas the intermolecular interactions are either very weak CH---?/CH---O contacts found in aryloxysilane or electrostatic dipole-dipole attraction in cyclodisilthiane and silanethiol. The S-H---? interactions in the obtained silanethiol are analyzed with the use of DFT/GGA BLYP-D XC potentials. The energy of intramolecular S-H---? interaction is estimated.

  1. Argentophilic interactions.

    PubMed

    Schmidbaur, Hubert; Schier, Annette

    2015-01-12

    The decade 1990-2000 saw a growing interest in aurophilic interactions in gold chemistry. These interactions were found to influence significantly a variety of structural and other physical characteristics of gold(I) compounds. The attention paid to this unusual and counterintuitive type of intra- and intermolecular bonding between seemingly closed-shell metal centers has rapidly been extended to also include silver chemistry. Hundreds of experimental and computational studies have since been dedicated to the argentophilicity phenomenon. The results of this development are reviewed herein focusing on molecular systems where two or more silver(I) centers are in close contact leading to specific structural characteristics and a variety of novel physical properties. These include strongly modified ligand-to-metal charge-transfer processes observed in absorption and emission spectroscopy, but also colossal positive and negative thermal expansion on the one hand and unprecedented negative linear compressibility of crystal parameters on the other. PMID:25393553

  2. The inclusion of density fluctuations in the theory of adsorption of laterally interacting molecules on microcrystalline particles

    NASA Astrophysics Data System (ADS)

    Tovbin, Yu. K.

    2012-07-01

    Equations for the isotherms of adsorption of pure substances on small inhomogeneous crystalline particles with taking into account density fluctuations and intermolecular interactions in the quasi-chemical approximation were obtained for the first time.

  3. Intramolecular vibrational energy redistribution and intermolecular energy transfer of benzene in supercritical CO 2: measurements from the gas phase up to liquid densities

    NASA Astrophysics Data System (ADS)

    von Benten, R.; Charvat, A.; Link, O.; Abel, B.; Schwarzer, D.

    2004-03-01

    Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within ? IVR(1)<0.5 ps. The slower IVR component has a time constant of ? IVR(2)=(48±5) ps in the gas phase and in scCO 2 is accelerated by interactions with the solvent. At the highest CO 2 density it is reduced to ? IVR(2)=(6±1) ps. The corresponding IVR rate constants show a similar density dependence as the VET rate constants. Model calculations suggest that both quantities correlate with the local CO 2 density in the immediate surrounding of the benzene molecule.

  4. 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.

  5. Predicting Noncovalent Interactions with Nonlocal Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Hooper, Joe; Romero, Nichols A.; Zerilli, Frank

    2007-12-01

    We assess the accuracy of a recently developed nonlocal density functional in treating van der Waals molecular systems. This new functional contains a non-empirical treatment of dispersion interactions and exhibits the appropriate behavior in the high-density limit. We present results for three model noncovalently bonded systems: the methane-benzene complex, a dimethylnitramine dimer, and a dimer of triaminotrinitrobenzene in its crystalline symmetry. Predicted interaction energies are greatly improved with this new approach as compared to conventional density functionals. Intermolecular distances are also improved, though the degree of improvement varies with the character of the intermolecular interactions, with dispersion dominated systems showing the greatest improvement.

  6. Interaction Interaction

    E-print Network

    Hehner, Eric C.R.

    Interaction 1/54 #12;Interaction shared variables 2/54 #12;Interaction shared variables can be read and written by any process (most interaction) 3/54 #12;Interaction shared variables can be read and written by any process (most interaction) difficult to implement 4/54 #12;Interaction shared variables can

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

    PubMed

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

    2014-01-01

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

  8. Intermolecular hydroaminoalkylation of alkenes and dienes using a titanium mono(formamidinate) catalyst.

    PubMed

    Dörfler, Jaika; Preuß, Till; Brahms, Christian; Scheuer, Dennis; Doye, Sven

    2015-07-01

    An easily accessible formamidinate ligand-bearing titanium complex initially synthesized by Eisen et al. is used as catalyst for intermolecular hydroaminoalkylation reactions of unactivated, sterically demanding 1,1- and 1,2-disubstituted alkenes and styrenes with secondary amines. The corresponding reactions, which have never been achieved with titanium catalysts before, take place with excellent regioselectivity (up to 99?:?1) and in addition, corresponding reactions of 1,3-butadienes with N-methylbenzylamine are also described for the first time. PMID:25679294

  9. Catalytic Asymmetric Synthesis of 8-Oxabicyclooctanes by Intermolecular [5+2] Pyrylium Cycloadditions**

    PubMed Central

    Witten, Michael R.

    2014-01-01

    Highly enantioselective intermolecular [5+2] cycloadditions of pyrylium ion intermediates with electron-rich alkenes are promoted by a dual catalyst system composed of an achiral thiourea and a chiral primary aminothiourea. The observed enantioselectivity is highly dependent on the substitution pattern of the 5? component, and the basis for this effect is analyzed using experimental and computational evidence. The resultant 8-oxabicyclo[3.2.1]octane derivatives possess a scaffold common in natural products and medicinally active compounds and are also versatile chiral building blocks for further manipulations. Several stereoselective complexity-generating transformations of the 8-oxabicyclooctane products are presented. PMID:24782332

  10. Hadamard-encoded localized high-resolution NMR spectroscopy via intermolecular double-quantum coherences

    NASA Astrophysics Data System (ADS)

    Ke, Hanping; Cai, Honghao; Lin, Yanqin; Lin, Liangjie; Cai, Shuhui; Chen, Zhong

    2015-02-01

    A scheme based on Hadamard encoding and intermolecular double-quantum coherences is designed to obtain localized one-dimensional high-resolution NMR spectra in inhomogeneous fields. Brief theoretical derivation was performed to illuminate its principle. Experiments were carried out on phantom solution and biological tissues to verify its effectiveness in yielding useful spectral information and efficiency in suppressing solvent signal even when the field inhomogeneity is sufficiently severe to erase almost all spectral information. This sequence may provide a promising way for analyzing heterogeneous biological tissues and chemical systems.

  11. Intermolecular hydrogen bonded and self-assembled ?-pleated sheet structures of ?-sulfidocarbonyls

    NASA Astrophysics Data System (ADS)

    Hussain, Sahid; Das, Gopal; Chaudhuri, Mihir K.

    2007-06-01

    The three crystal structures of ?-sulfidocarbonyls 1, 2 and 3 synthesized from the reaction of acryl amide with cystiene, 1,2-dithiol and 1,3-dithiols, respectively, in water catalyzed by borax, have been determined at 273 K. The characteristic features of the structures are self-assembly through intermolecular hydrogen bonding leading to infinite chains of molecules in one direction, in addition to the stacking of layers of such molecular chains in the perpendicular direction ultimately giving rise to ?-pleated sheets of 3D molecular network involving N-H⋯O, C-H⋯O and C-H⋯S bonding in the crystal lattice.

  12. Direct measurement of the intermolecular forces confining a single molecule in an entangled polymer solution

    E-print Network

    Rae M. Robertson; Douglas E. Smith

    2007-06-25

    We use optical tweezers to directly measure the intermolecular forces acting on a single polymer imposed by surrounding entangled polymers (115 kbp DNA, 1 mg/ml). A tube-like confining field was measured in accord with the key assumption of reptation models. A time-dependent harmonic potential opposed transverse displacement, in accord with recent simulation findings. A tube radius of 0.8 microns was determined, close to the predicted value (0.5 microns). Three relaxation modes (~0.4, 5 and 30 s) were measured following transverse displacement, consistent with predicted relaxation mechanisms.

  13. 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

  14. Cosolvent interactions in supercritical fluid solutions

    Microsoft Academic Search

    Michael P. Ekart; Karen L. Bennett; Susan M. Ekart; Gurdev S. Gurdial; Charles L. Liotta; Charles A. Eckert

    1993-01-01

    The addition of cosolvents to supercritical fluid (SCF) solvents can have large effects on solubilities, giving engineers the ability to tailor loadings and selectivities of solutes for difficult separations. It is necessary to have a better understanding of the special intermolecular interactions that occur in SCF solutions to predict the effects of cosolvents. The authors use a SCF chromatographic technique

  15. Conformational diversity in prion protein variants influences intermolecular [beta]-sheet formation

    SciTech Connect

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

  16. Improvement in the contrast of CEST MRI via intermolecular double quantum coherences.

    PubMed

    Zhang, Shengchun; Zhu, Xiaoqin; Chen, Zhong; Cai, Congbo; Lin, Tao; Zhong, Jianhui

    2008-07-21

    The tremendous potential of chemical exchange saturation transfer (CEST) agents as an emerging class of magnetic resonance imaging contrast media has been demonstrated in recent years. In a CEST experiment, a high CEST contrast is always welcome. However, when the exchange rate is low, which may happen in exchangeable solute protons of low concentration, it is usually hard to obtain an excellent CEST efficiency. Recently, we noted that the intermolecular multiple quantum coherence signal is more sensitive to the changes of the magnetization magnitude than a conventional single quantum coherence signal. Consequently, it may be easier when used in obtaining a CEST contrast. In this note, a modified COSY (two-dimensional correlated spectroscopy) revamped with an asymmetric Z-gradient echo detection (CRAZED) sequence combined with an off-resonance saturation pulse followed by a standard spin-echo imaging sequence was designed to obtain a better CEST contrast image based on the intermolecular double quantum coherence method. An analytical expression was derived from a dipolar field theory. Experiments were performed on an agar-glucose phantom, and the results demonstrate the feasibility of our method. PMID:18574314

  17. Intermolecular and Intramolecular Electron Transfer Processes from Excited Naphthalene Diimide Radical Anions.

    PubMed

    Fujitsuka, Mamoru; Kim, Sung Sik; Lu, Chao; Tojo, Sachiko; Majima, Tetsuro

    2015-06-18

    Excited radical ions are interesting reactive intermediates owing to powerful redox reactivities, which are applicable to various reactions. Although their reactivities have been examined for many years, their dynamics are not well-defined. In this study, we examined intermolecular and intramolecular electron transfer (ET) processes from excited radical anions of naphthalene-1,4,5,8-tetracarboxydiimide (NDI(•-)*). Intermolecular ET processes between NDI(•-)* and various electron acceptors were confirmed by transient absorption measurements during laser flash photolysis of NDI(•-) generated by pulse radiolysis. Although three different imide compounds were employed as acceptors for NDI(•-)*, the bimolecular ET rate constants were similar in each acceptor, indicating that ET is not the rate-determining step. Intramolecular ET processes were examined by applying femtosecond laser flash photolysis to two series of dyad compounds, where NDI was selectively reduced chemically. The distance dependence of the ET rate constants was described by a ? value of 0.3 Å(-1), which is similar or slightly smaller than the reported values for donor-acceptor dyads with phenylene spacers. Furthermore, by applying the Marcus theory to the driving force dependence of the ET rate constants, the electronic coupling for the present ET processes was determined. PMID:25397719

  18. Azide-water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy.

    PubMed

    Borek, Joanna; Perakis, Fivos; Kläsi, Felix; Garrett-Roe, Sean; Hamm, Peter

    2012-06-14

    We utilize two-color two-dimensional infrared spectroscopy to measure the intermolecular coupling between azide ions and their surrounding water molecules in order to gain information about the nature of hydrogen bonding of water to ions. Our findings indicate that the main spectral contribution to the intermolecular cross-peak comes from population transfer between the asymmetric stretch vibration of azide and the OD-stretch vibration of D(2)O. The azide-bound D(2)O bleach/stimulated emission signal, which is spectrally much narrower than its linear absorption spectrum, shows that the experiment is selective to solvation shell water molecules for population times up to ~500 fs. The waters around the ion are present in an electrostatically better defined environment. Afterwards, ~1 ps, the sample thermalizes and selectivity is lost. On the other hand, the excited state absorption signal of the azide-bound D(2)O is much broader. The asymmetry in spectral width between bleach/stimulated emission versus excited absorption has been observed in very much the same way for isotope-diluted ice Ih, where it has been attributed to the anharmonicity of the OD potential. PMID:22713053

  19. Azide-water intermolecular coupling measured by two-color two-dimensional infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Borek, Joanna; Perakis, Fivos; Kläsi, Felix; Garrett-Roe, Sean; Hamm, Peter

    2012-06-01

    We utilize two-color two-dimensional infrared spectroscopy to measure the intermolecular coupling between azide ions and their surrounding water molecules in order to gain information about the nature of hydrogen bonding of water to ions. Our findings indicate that the main spectral contribution to the intermolecular cross-peak comes from population transfer between the asymmetric stretch vibration of azide and the OD-stretch vibration of D2O. The azide-bound D2O bleach/stimulated emission signal, which is spectrally much narrower than its linear absorption spectrum, shows that the experiment is selective to solvation shell water molecules for population times up to ˜500 fs. The waters around the ion are present in an electrostatically better defined environment. Afterwards, ˜1 ps, the sample thermalizes and selectivity is lost. On the other hand, the excited state absorption signal of the azide-bound D2O is much broader. The asymmetry in spectral width between bleach/stimulated emission versus excited absorption has been observed in very much the same way for isotope-diluted ice Ih, where it has been attributed to the anharmonicity of the OD potential.

  20. 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

  1. 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.

  2. Competition between Intra- and Intermolecular Association of Chain Molecules with Water-like Solvent.

    PubMed

    Ballal, Deepti; Chapman, Walter G

    2015-06-01

    Fluid properties and phase behavior of systems such as glycol ethers, carboxylic acids, and proteins are affected by the competition between intra- and intermolecular hydrogen bonding. Here we study this competition by extending Wertheim's first-order thermodynamic perturbation theory to include intramolecular hydrogen bonding in chain molecules in the presence of an explicit water-like solvent. The theory derived here is found to be in good agreement with molecular simulation. It is shown that intramolecular association is most important for shorter chains at low temperature, low density, and high chain concentration. The theory is also extended into a density functional theory formalism to study the effect of intramolecular association on the structuring of the different segments of the molecules close to a hydrophobic surface. Intramolecular association is found to be enhanced close to the surface, with the total density of the system having the most effect on structuring close to the surface. PMID:25955880

  3. In Vivo Brown Adipose Tissue Detection and Characterization using Water-lipid Intermolecular Zero Quantum Coherences

    PubMed Central

    Branca, Rosa T.; Warren, Warren S.

    2010-01-01

    Brown Adipose Tissue (BAT) and White Adipose Tissue (WAT) depots are non-invasively characterized in vitro and in vivo in healthy and obese mice using intermolecular Zero-Quantum Coherence (iZQC) transitions between lipid and water spins. IZQCs enable selective detection of spatial correlation between water and lipid spins and thereby the hydration of fatty deposits with subvoxel resolution. At about a 100 micrometer distance scale, the major observed peaks are between water, methylene protons at 1.3ppm, and olefinic protons at 5.3 ppm. Our in vitro results show that the methylene-olefinic iZQC signal is strong both in BAT and in WAT, but that the water-methylene iZQC signal is characteristic only of BAT tissue. In vivo, the ratio of these peaks is substantially higher in lean or young mice than in old or obese mice. PMID:20939093

  4. Intermolecular explosives. [TNT, EDD, EAK, EARL, Amatol, EA, and Comp B 64 RDK

    SciTech Connect

    Akst, I.B.

    1985-01-01

    The steady-state detonation characteristics of a few intermolecular explosives are examined along with results of wedge experiments on initiation and reaction growth in one system (EAK), toward a better understanding of this class of explosives. The importance of factors such as products and their states, and temperature, to performance of these systems and explosives in general is discussed. Hydrogen compounds may be superior enough to carbon and its compounds as fuels and products for quick metal-accelerating explosives that the effect of the generally lower density is offset. High temperatures and condensation of solid products are probably the main causes of late appearance of energy in metal motion. The unusual shock sensitiveness and explosiveness of EAK are indicated by wedge results including pseudo-Pop-plots of overtaking waves, and by plots of shock velocity versus transit distance in the wedges. 20 refs., 10 figs., 2 tabs.

  5. Sequence-specific electron injection into DNA from an intermolecular electron donor

    PubMed Central

    Morinaga, Hironobu; Takenaka, Tomohiro; Hashiya, Fumitaka; Kizaki, Seiichiro; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2013-01-01

    Electron transfer in DNA has been intensively studied to elucidate its biological roles and for applications in bottom-up DNA nanotechnology. Recently, mechanisms of electron transfer to DNA have been investigated; however, most of the systems designed are intramolecular. Here, we synthesized pyrene-conjugated pyrrole-imidazole polyamides (PPIs) to achieve sequence-specific electron injection into DNA in an intermolecular fashion. Electron injection from PPIs into DNA was detected using 5-bromouracil as an electron acceptor. Twelve different 5-bromouracil-containing oligomers were synthesized to examine the electron-injection ability of PPI. Product analysis demonstrated that the electron transfer from PPIs was localized in a range of 8 bp from the binding site of the PPIs. These results demonstrate that PPIs can be a useful tool for sequence-specific electron injection. PMID:23439569

  6. 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.

  7. 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.

  8. New image contrast mechanisms in intermolecular double-quantum coherence human MR imaging.

    PubMed

    Zhong, J; Chen, Z; Kwok, E

    2000-08-01

    We have developed a novel magnetic resonance imaging (MRI) method based on the intermolecular double-quantum coherence (DQC) in humans. Combined quantum mechanical and classical formalisms were used to characterize the signal and to aid in the design of a DQC imaging sequence with conventional or echoplanar acquisitions. Imaging contrast was evaluated in volunteers using a 1.5-T clinical scanner. The results demonstrated that the DQC images have contrasts fundamentally different from the conventional images based on single-quantum coherence (SQC). Both our theoretical analysis and experiments suggest that signals from DQCs have a higher signal-to-noise ratio than those from zero-quantum coherence (ZQC) for human brain imaging. The new contrast in DQC imaging may be useful for the detection of varying microstructures, potentially improving the detection of tumors without the need for contrast agents and providing a higher sensitivity and selectivity to magnetic susceptibility distributions in functional MRI brain studies. PMID:10931595

  9. Enhanced sensitivity to molecular diffusion with intermolecular double-quantum coherences: implications and potential applications.

    PubMed

    Zhong, J; Chen, Z; Kwok, E; Kennedy, S

    2001-01-01

    Apparent molecular self-diffusion rates for (1)H intermolecular double-quantum coherences (iDQCs) were measured in solvents covering a wide range of intrinsic diffusion coefficients at 1.5, 9.4 and 14T, and water iDQC diffusion-weighted images were obtained at 1.5T in human brains and at 9.4T in rat brains. Conventional single quantum coherence (SQC) measurements were also made in the same samples. Experimental results indicate that iDQCs are approximately twice as sensitive to diffusion as SQC. A general theoretical expression was derived, and a model was proposed to explain the phenomenon. Potential applications in DWI and brain fMRI were also discussed. PMID:11295344

  10. Accurate measurements of small J coupling constants under inhomogeneous fields via intermolecular multiple-quantum coherences.

    PubMed

    Lin, Yanqin; Chen, Zhong; Cai, Shuhui; Zhong, Jianhui

    2008-02-01

    Two new NMR pulse sequences, based on intermolecular multiple-quantum coherences (iMQCs), were developed to obtain apparent J coupling constants with a scaling factor from one to infinity relative to the conventional J coupling constants. Here the apparent J coupling constants were defined as apparent peak separations in unit of Hz in a reconstructed spectrum for a coupled spin system. Except for the adjustable scaling factor for apparent J coupling constants, the sequences hold the advantage of high acquisition efficiency, and retain the spectral information such as chemical shifts, multiplet patterns, and relative peak areas under inhomogeneous fields. For spin systems with small scalar coupling constants, well-resolved J-spectra can be achieved by selecting a proper scaling factor. Theoretical predictions are in good agreement with simulation results and experimental observations. PMID:18078770

  11. Flat pancake distant dipolar fields for enhancement of intermolecular multiple-quantum coherence signals.

    PubMed

    Cai, Congbo; Lin, Yulan; Cai, Shuhui; Sun, Huijun; Zhong, Jianhui; Chen, Zhong

    2012-03-01

    Intermolecular multiple-quantum coherences (iMQCs) originated from distant dipolar field (DDF) possess some appealing unique properties for magnetic resonance imaging (MRI). DDF is usually induced with continuous wave (i.e., sine- or square-wave) magnetization modulation in the whole sample. In this article, a spatially localized and enhanced DDF was optimally tailored in a thin slice with an adiabatic inversion pulse. Evidence was provided to show that careful tailoring of the spatially localized DDF can generate highly efficient iMQC signals, with more than two-fold enhancement compared to the conventional sine-wave magnetization modulation method, and 1.5 times of that with the square-wave modulation under the similar condition. Theoretical predictions, simulation results, and experimental verifications agree well with each other. Practical implementation of this approach for efficient iMQC MRI was explored. PMID:22401448

  12. Intermolecular double-quantum coherence MR microimaging of pig tail with unique image contrast.

    PubMed

    Hou, T; Chen, Z; Hwang, D W; Zhong, J H; Hwang, L P

    2004-05-01

    Image contrast in intermolecular double-quantum coherence (iDQC) imaging of a pig tail was investigated on a 7.05-T microimaging scanner. In addition to TR (repetition time) and TE (echo time), the time interval tau between radio frequency pulses during iDQC evolution and the areas under the iDQC-encode gradients in the iDQC imaging sequence were also used to manipulate image contrast. When suitable imaging parameters were selected, images with unique contrast, such as those with certain regions of the sample highlighted, were obtained without using contrast agents. The effects of iDQC-encode gradient on image contrast were studied quantitatively, and the unique contrast imposed by the related diffusion weighting was also shown. Experimental results demonstrated that the iDQC images have contrast fundamentally different from the conventional single-quantum coherence images. PMID:15120174

  13. Enhancement of magnetization transfer effects by inter-molecular multiple quantum filtered NMR.

    PubMed

    Eliav, Uzi; Navon, Gil

    2008-01-01

    There are a number of methods that give MRI contrasts based on changes of the water M(z) magnetization as a result of magnetization transfer to macromolecules. In the present work we report that a combination of these methods with inter-molecular multiple quantum coherences (iMQC) gives enhanced effects. For the magnetization transfer contrast (MTC) method an effect of (M(z)/M(0)) becomes (M(z)/M(0))(l) where l is the rank of the tensors constituting the iMQC. A similar trend was found upon combining iMQC with the Goldman-Shen experiment. It is pointed out that the method is general for all magnetization transfer methods, including the nuclear Overhauser effect. PMID:17936657

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

    NASA Technical Reports Server (NTRS)

    Green, Sheldon

    1990-01-01

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

  15. Azide-water intermolecular coupling measured by 2-color 2D IR spectroscopy

    NASA Astrophysics Data System (ADS)

    Borek, J. A.; Perakis, F.; Hamm, P.

    2013-03-01

    We present 2-color two-dimensional infrared spectroscopy of intermolecular coupling between azide ions and their solvation shell water molecules. The cross-peak between azide asymmetric stretch vibration and the OD-stretch vibration is a result of low- probability uphill population transfer. Narrow bleach/excited state absorption peak shows selectivity to solvation shell water molecules only and the characteristics of the cross-peak suggest that the solvation shell hydrogen bond potential has similar anharmonic properties as the hydrogen bond in ice Ih. Population and depopulation of the excited state of the OD-stretch vibration happen on 150 fs and 1.7 ps timescales, respectively, with early manifesting heating effects that limit the selectivity to population times up to 1 ps.

  16. Intermolecular Association Provides Specific Optical and NMR Signatures for Serotonin at Intravesicular Concentrations

    PubMed Central

    Nag, Suman; Balaji, J.; Madhu, P. K.; Maiti, S.

    2008-01-01

    Neurotransmitter vesicles contain biomolecules at extraordinarily high concentrations (hundreds of millimoles/liter). Such concentrations can drive intermolecular associations, which may affect vesicular osmolarity and neuronal signaling. Here we investigate whether aqueous serotonin (a monoamine neurotransmitter) forms oligomers at intravesicular concentrations and whether these oligomers have specific spectroscopic signatures that can potentially be used for monitoring neuronal storage and release. We report that, as serotonin concentration is increased from 60 ?M to 600 mM, the normalized fluorescence spectrum of serotonin displays a growing long-wavelength tail, with an isoemissive point at 376 nm. The fluorescence decay is monoexponential with a lifetime of 4 ns at low concentrations but is multiexponential with an average lifetime of 0.41 ns at 600 mM. A 600 mM serotonin solution has 30% less osmolarity than expected for monomeric serotonin, indicating oligomer formation. The proton NMR chemical shifts move upfield by as much as 0.3 ppm at 600 mM compared to those at 10 mM, indicating a stacking of the serotonin indole moieties. However, no intermolecular crosspeak is evident in the two-dimensional NMR rotating frame Overhauser effect spectroscopy spectrum even at 600 mM, suggesting that oligomeric structures are possibly weakly coupled. The appearance of a single peak for each proton suggests that the rate of interconversion between the monomeric and the oligomeric structures is faster than 240 Hz. A stopped-flow kinetic experiment also confirms that the rate of dissociation is faster than 100 ms. We conclude that serotonin forms oligomers at intravesicular concentrations but becomes monomeric quickly on dilution. NMR signatures of the oligomers provide potential contrast agents for monitoring the activity of serotonergic neurons in vivo. PMID:18234835

  17. Intermolecular coupling between loop 38-52 and the C-terminus in actin filaments.

    PubMed Central

    Kim, E; Reisler, E

    1996-01-01

    The recently reported structural connectivity in F-actin between the DNase I binding loop on actin (residues 38-52) and the C-terminus region was investigated by fluorescence and proteolytic digestion methods. The binding of copper to Cys-374 on F- but not G-actin quenched the fluorescence of dansyl ethylenediamine (DED) attached to Gin-41 by more than 50%. The blocking of copper binding to DED-actin by N-ethylmaleimide labeling of Cys-374 on actin abolished the fluorescence quenching. The quenching of DED-actin fluorescence was restored in copolymers (1:9) of N-ethylmaleimide-DED-actin with unlabeled actin. The quenching of DED-actin fluorescence by copper was also abolished in copolymers (1:4) of DED-actin and N-ethylmaleimide-actin. These results show intermolecular coupling between loop 38-52 and the C-terminus in F-actin. Consistent with this, the rate of subtilisin cleavage of actin at loop 38-52 was increased by the bound copper by more than 10-fold in F-actin but not in G-actin. Neither acto-myosin subfragment-1 (S1) ATPase activity nor the tryptic digestion of G-actin and F-actin at the Lys-61 and Lys-69 sites were affected by the bound copper. These observations suggest that copper binding to Cys-374 does not induce extensive changes in actin structure and that the perturbation of loop 38-52 environment results from changes in the intermolecular contacts in F-actin. PMID:8889166

  18. This journal is c the Owner Societies 2011 Phys. Chem. Chem. Phys. Cite this: DOI: 10.1039/c1cp21175g

    E-print Network

    Kotochigova, Svetlana

    21175g Anisotropy in the interaction of ultracold dysprosium Svetlana Kotochigova* and Alexander Petrovw dipole­dipole, and electric quadrupole­quadrupole forces between two dysprosium atoms. Each dysprosium

  19. Synthesis and Properties of Zwitterionic Nonlinear Optical Chromophores with Large

    E-print Network

    Wenseleers, Wim

    - ficients, lower dielectric constants, and good processibility.2 To obtain a large EO response, chromophores of poor solubility and strong dipole-dipole interactions. For example, DEMI was reported to have a high µ

  20. 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

  1. PHYSICAL REVIEW B 83, 245307 (2011) Optical evidence for intermolecular coupling in mixed films of pentacene and perfluoropentacene

    E-print Network

    Schreiber, Frank

    2011-01-01

    PHYSICAL REVIEW B 83, 245307 (2011) Optical evidence for intermolecular coupling in mixed films; published 20 June 2011) We present optical absorption spectra of mixed films of pentacene (PEN is influenced by changes in the volume ratio of the two components. By comparison with the pure film spectra

  2. A new ab initio intermolecular potential energy surface and predicted rotational spectra of the Kr-H2O complex

    NASA Astrophysics Data System (ADS)

    Lei, Jinping; Zhou, Yanzi; Xie, Daiqian; Zhu, Hua

    2012-12-01

    We report a new three-dimensional ab initio intermolecular potential energy surface for the Kr-H2O complex with the H2O 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 Å 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-H2O 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.

  3. Highly enantioselective and anti-diastereoselective catalytic intermolecular glyoxylate-ene reactions: effect of the geometrical isomers of alkenes.

    PubMed

    Zhang, Xiang; Wang, Min; Ding, Ran; Xu, Yun-He; Loh, Teck-Peng

    2015-06-01

    An efficient method for the synthesis of homoallylic alcohols with high enantioselectivities and anti-diastereoselectivities via an In(III)-catalyzed intermolecular glyoxylate-ene reaction has been developed. The geometrical isomers of alkenes were shown to have different reactivities. Only the isomers of the alkenes having a proton ?-cis to the substituent reacted in this catalytic system. PMID:25965690

  4. Intermolecular distances of carboxylated TEMPO derivatives on TiO2 evaluated by spin-probe ESR.

    PubMed

    Kano, Yuta; Kushimoto, Kohei; Komaguchi, Kenji; Ooyama, Yousuke; Imae, Ichiro; Ohshita, Joji; Harima, Yutaka

    2012-12-14

    Nearest-neighbor intermolecular distances of molecules adsorbed on the surface of nanocrystalline TiO(2) particles were evaluated by the electron spin resonance (ESR) technique with molecules having a nitroxide radical and a carboxyl group as a spin probe to clarify their aggregation behaviors on TiO(2) and the influence of coadsorbates. PMID:23099428

  5. 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

  6. 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.

  7. Controlling Er-Tm interaction in Er and Tm codoped silicon-rich silicon oxide using nanometer-scale spatial separation for efficient, broadband infrared luminescence

    SciTech Connect

    Seo, Se-Young; Shin, Jung H. [Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), 373-1 Guseong-dong, Yuseong-gu, Daejon (Korea, Republic of)

    2004-11-01

    The effect of nanometer-scale spatial separation between Er{sup 3+} and Tm{sup 3+} ions in Er and Tm codoped silicon-rich silicon oxide (SRSO) films is investigated. Er and Tm codoped SRSO films, which consist of nanocluster Si (nc-Si) embedded inside SiO{sub 2} matrix, were fabricated with electron cyclotron resonance-plasma enhanced chemical vapor deposition of SiH{sub 4} and O{sub 2} with concurrent sputtering of Er and Tm metal targets. Spatial separation between Er{sup 3+} and Tm{sup 3+} ions was achieved by depositing alternating layers of Er- and Tm-doped layers of varying thickness while keeping the total film thickness the same. The films display broadband infrared photoluminescence (PL) from 1.5 to 2.0 {mu}m under a single source excitation due to simultaneous excitation of Er{sup 3+} and Tm{sup 3+} ions by nc-Si. Increasing the layer thickness from 0 to 72 nm increases the Er{sup 3+} PL intensity nearly 50-fold while the Tm{sup 3+} PL intensity is unaffected. The data are well-explained by a model assuming a dipole-dipole interaction between excited Er{sup 3+} and Tm{sup 3+} ions, and suggest that by nanoscale engineering, efficient, ultrabroadband infrared luminescence can be obtained in an optically homogeneous material using a single light source.

  8. Investigation of chromophore-chromophore interaction by electro-optic measurements, linear dichroism, x-ray scattering, and density-functional calculations.

    PubMed

    Apitz, D; Bertram, R P; Benter, N; Hieringer, W; Andreasen, J W; Nielsen, M M; Johansen, P M; Buse, K

    2005-09-01

    Free-beam interferometry and angle-resolved absorption spectra are used to investigate the linear electro-optic coefficients and the linear dichroism in photoaddressable bis-azo copolymer thin films. From the first- and second order parameters deduced, the chromophore orientation distribution is calculated and displayed for several poling temperatures and chromophore concentrations. The influence of dipole-dipole interaction on the overall polymer dynamics is discussed. The first order parameter, and therefore the Pockels effect, peaks for a poling temperature of around 10 degrees C above the glass transition. The decrease of the Pockels effect above this temperature region is triggered by a head-to-tail chromophore orientation, i.e., a transition to a microcrystalline phase, increasing the second order parameter. Comparison of the experimentally observed absorption spectra and those obtained by density-functional calculations support the picture of differently aligned bis-azo dye molecules in a trans,trans configuration. Complementary wide-angle x-ray scattering is recorded to confirm the various kinds of ordering in samples poled at different temperatures. PMID:16241595

  9. Investigation of chromophore-chromophore interaction by electro-optic measurements, linear dichroism, x-ray scattering, and density-functional calculations

    SciTech Connect

    Apitz, D. [Optics and Plasma Research Department, Risoe National Laboratory, 4000 Roskilde (Denmark); Institute of Physics, University of Bonn, 53115 Bonn (Germany); Bertram, R.P.; Benter, N.; Buse, K. [Institute of Physics, University of Bonn, 53115 Bonn (Germany); Hieringer, W. [Department of Physical and Theoretical Chemistry, Friedrich-Alexander-University Erlangen-Nuremberg, 91058 Erlangen (Germany); Andreasen, J.W.; Nielsen, M.M. [Danish Polymer Center, Risoe National Laboratory, 4000 Roskilde (Denmark); Johansen, P.M. [SIMAC - Svendborg International Maritime Academy, 5700 Svendborg (Denmark)

    2005-09-01

    Free-beam interferometry and angle-resolved absorption spectra are used to investigate the linear electro-optic coefficients and the linear dichroism in photoaddressable bis-azo copolymer thin films. From the first- and second order parameters deduced, the chromophore orientation distribution is calculated and displayed for several poling temperatures and chromophore concentrations. The influence of dipole-dipole interaction on the overall polymer dynamics is discussed. The first order parameter, and therefore the Pockels effect, peaks for a poling temperature of around 10 deg. C above the glass transition. The decrease of the Pockels effect above this temperature region is triggered by a head-to-tail chromophore orientation, i.e., a transition to a microcrystalline phase, increasing the second order parameter. Comparison of the experimentally observed absorption spectra and those obtained by density-functional calculations support the picture of differently aligned bis-azo dye molecules in a trans,trans configuration. Complementary wide-angle x-ray scattering is recorded to confirm the various kinds of ordering in samples poled at different temperatures.

  10. 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.

  11. Supramolecular assemblies of dimolybdenum transoids built by Mo2-enhanced perfluorophenyl-perfluorophenyl synthons.

    PubMed

    Han, Li Juan; Fan, Li Yan; Meng, Miao; Wang, Xuefeng; Liu, Chun Y

    2011-12-28

    Two supramolecular assemblies were developed by the dimmolybdenum paddlewheel complex trans-Mo(2)(DAniF)(2)(O(2)CC(6)F(5))(2) (1) (ancillary ligand DAniF = N,N'-di-(p-anisyl)formamidinate) through intermolecular offset face to face C(6)F(5)···C(6)F(5) interactions. The two networks are different because of the presence and absence of tetrahydrofuran (THF) axial coordination to the Mo(2) units, but feature commonly short interplanar distances between the two paired perfluorophenyl groups, that is, 3.30 Å and 3.23 Å, respectively, which are similar to the shortest intermolecular C···F contacts between two atoms in meta and ortho positions. Consistently, as indicated by the Mulliken population analysis, the dipole moments for the meta and ortho C-F bonds are considerably enlarged because the pentafluorobenzoate groups are bonded to the dimetal unit. In comparison, X-ray structural and theoretical analyses were also made for the parent molecule pentafluorobenzoic acid. The resultant data show that charge distribution on the perfluorophenyl group has a major influence on the C(6)F(5)···C(6)F(5) binding mode. Therefore, it is evidenced that the dimetal unit plays a role in further polarizing the highly polarized C-F bonds and the intermolecular perfluorophenyl-perfluorophenyl interactions are dominated by the C···F dipole-dipole interaction, rather than aromatic-aromatic ?-? stacking. PMID:22041689

  12. Metallacyclic yttrium alkyl and hydrido complexes: synthesis, structures and catalytic activity in intermolecular olefin hydrophosphination and hydroamination.

    PubMed

    Kissel, Alexander A; Mahrova, Tatyana V; Lyubov, Dmitry M; Cherkasov, Anton V; Fukin, Georgy K; Trifonov, Alexander A; Del Rosal, Iker; Maron, Laurent

    2015-07-21

    Metallacyclic neutral and ionic yttrium alkyl complexes coordinated by a dianionic ene-diamido ligand ([2,6-iPr2C6H3NC(Me)[double bond, length as m-dash]C(Me)NC6H3iPr2-2,6] = L(1)) [L(1)]Y(CH2SiMe3)(THF)2 (2), {[L(1)]Y(CH2SiMe3)2}(-){Li(THF)4}(+) (3), [L(1)]Y(OEt2)(?-Me)2Li(TMEDA) (4) were synthesized using a salt-metathesis approach starting from the related chloro complex [L(1)]Y(THF)2(?-Cl)2Li(THF)2 (1) in 70, 85 and 72% yields respectively. The reactions of 2 with H2 or PhSiH3 afford the dimeric hydride {[L(1)]Y(THF)(?-H)}2(?-THF) (5) containing two ?-bridging hydrido and one ?-bridging THF ligands (91 and 85% yields). The X-ray studies of complexes 2, 3 and 5 revealed ?(2)-coordination of the C[double bond, length as m-dash]C fragment of an ene-diamido ligand to a Y cation. DFT calculations were carried out to give an insight into the metal-ligand bonding and especially the interaction between the metal and the ene-diamido ligand. The observed bonding of the ene-diamido fragment is found to reflect the acidity of the metal center in the complex that is partially overcome by a better donation from the double bond (better overlap with an empty d orbital at the yttrium center). The treatment of complex 4 with DME resulted in the C-O bond cleavage of DME and afforded a three nuclear methoxide oxide complex [{[L(1)]Y}3(?(2)-OMe)3(?(3)-O)](2-)[Li(DME)3](+)2 (6). Complexes 2, 3, 5 and 7 proved to be efficient precatalysts for the intermolecular hydrophosphination of styrene, 4-vinylpyridine, and 1-nonene with PhPH2 and Ph2PH as well as hydroamination of styrene and pyrrolidine. PMID:25710900

  13. Pressure waves generated by metastable intermolecular composites in an aqueous environment

    NASA Astrophysics Data System (ADS)

    Maines, Geoff; Radulescu, Matei; Bacciochini, Antoine; Jodoin, Bertrand; Lee, Julian

    2013-06-01

    In the present study, pressure waves generated by a metastable intermolecular composite (MIC) have been measured experimentally in an aqueous environment. 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 aluminum and copper(II)oxide particles were evaluated. Two types of samples were constructed; a mixture of micron-sized raw powders, and ball milled powders with a lamellated nanostructure. A planetary mill was used to refine reactant powders from micron- to nano-scale dimensions. Manual compaction and cold spray deposition techniques were used to consolidate powders in various densities. The dynamics of the pressure wave and high pressure gas bubble were monitored via pressure data and high-speed Schlieren visualization. The effects of reactant particle size and sample density have been evaluated quantitatively and compared with equilibrium calculations. Dynamics of the pressure wave were correlated with the amount of gas released and the rate of burning of the sample material. In the present study, pressure waves generated by a metastable intermolecular composite (MIC) have been measured experimentally in an aqueous environment. 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 aluminum and copper(II)oxide particles were evaluated. Two types of samples were constructed; a mixture of micron-sized raw powders, and ball milled powders with a lamellated nanostructure. A planetary mill was used to refine reactant powders from micron- to nano-scale dimensions. Manual compaction and cold spray deposition techniques were used to consolidate powders in various densities. The dynamics of the pressure wave and high pressure gas bubble were monitored via pressure data and high-speed Schlieren visualization. The effects of reactant particle size and sample density have been evaluated quantitatively and compared with equilibrium calculations. Dynamics of the pressure wave were correlated with the amount of gas released and the rate of burning of the sample material. Work supported by DRDC Suffield (Dr. Julian J. Lee).

  14. 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.

  15. Formation of an intermolecular charge-transfer compound in UHV codeposited tetramethoxypyrene and tetracyanoquinodimethane

    NASA Astrophysics Data System (ADS)

    Medjanik, K.; Perkert, S.; Naghavi, S.; Rudloff, M.; Solovyeva, V.; Chercka, D.; Huth, M.; Nepijko, S. A.; Methfessel, T.; Felser, C.; Baumgarten, M.; Müllen, K.; Elmers, H. J.; Schönhense, G.

    2010-12-01

    Ultrahigh vacuum (UHV)-deposited films of the mixed phase of tetramethoxypyrene and tetracyanoquinodimethane (TMP1-TCNQ1) on gold have been studied using ultraviolet photoelectron spectroscopy (UPS), x-ray diffraction (XRD), infrared (IR) spectroscopy, and scanning tunneling spectroscopy (STS). The formation of an intermolecular charge-transfer (CT) compound is evident from the appearance of new reflexes in XRD ( d1=0.894nm and d2=0.677nm ). A softening of the CN stretching vibration (redshift by 7cm-1 ) of TCNQ is visible in the IR spectra, being indicative of a CT on the order of 0.3e from TMP to TCNQ in the complex. Characteristic shifts in the electronic level positions occur in UPS and STS that are in reasonable agreement with the prediction of density-functional theory (DFT) calculations (GAUSSIAN03 with hybrid functional B3LYP). STS reveals a highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap of the CT complex of about 1.25 eV being much smaller than the gaps (>3.0eV) of the pure moieties. The electron-injection and hole-injection barriers are 0.3 eV and 0.5 eV, respectively. Systematic differences in the positions of the HOMOs determined by UPS and STS are discussed in terms of the different information content of the two methods.

  16. Enantioselective Imidation of Sulfides via Enzyme-Catalyzed Intermolecular Nitrogen-Atom Transfer

    PubMed Central

    2015-01-01

    Engineering enzymes with novel reaction modes promises to expand the applications of biocatalysis in chemical synthesis and will enhance our understanding of how enzymes acquire new functions. The insertion of nitrogen-containing functional groups into unactivated C–H bonds is not catalyzed by known enzymes but was recently demonstrated using engineered variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium. Here, we extend this novel P450-catalyzed reaction to include intermolecular insertion of nitrogen into thioethers to form sulfimides. An examination of the reactivity of different P450BM3 variants toward a range of substrates demonstrates that electronic properties of the substrates are important in this novel enzyme-catalyzed reaction. Moreover, amino acid substitutions have a large effect on the rate and stereoselectivity of sulfimidation, demonstrating that the protein plays a key role in determining reactivity and selectivity. These results provide a stepping stone for engineering more complex nitrogen-atom-transfer reactions in P450 enzymes and developing a more comprehensive biocatalytic repertoire. PMID:24901646

  17. Theoretical formalism and experimental verification of line shapes of NMR intermolecular multiple-quantum coherence spectra.

    PubMed

    Zheng, Bingwen; Chen, Zhong; Cai, Shuhui; Zhong, Jianhui; Ye, Chaohui

    2005-08-15

    Although the theories and potential applications of intermolecular multiple-quantum coherences (iMQCs) have been under active investigations for over a decade, discussion of iMQC NMR signal formation was mainly confined in the time domain. In this paper, a full line-shape theory was developed to describe iMQC signals in the frequency domain. Relevant features of the line shape, such as peak height, linewidth, and phase, were investigated in detail. Predictions based on the theory agree well with experimental and simulated results. Since radiation-damping effects always couple with iMQCs in highly polarized liquid-state NMR systems, and strongly radiation-damped signals have many spectral characteristics similar to those of iMQCs, a detailed comparison was also made between them from different spectral aspects. With detailed comparison of peak height, linewidth, and phase, this work demonstrates that the iMQC and radiation-damping phenomena result from two completely different physical mechanisms despite that both present similar signal features and coexist in highly polarized liquid-state NMR systems. PMID:16229580

  18. Brain PP2A is modified by thiol-disulfide exchange and intermolecular disulfide formation.

    PubMed

    Foley, Timothy D; Kintner, Marissa E

    2005-05-20

    The regulation of protein phosphatase 2A (PP2A) activity by thiol-disulfide exchange and resulting formation of an intermolecular disulfide was examined following exposure of a rat brain soluble fraction to a biotinylated derivative of the model disulfide HPDP (HPDP-biotin) which would be expected to label reactive protein thiols with a disulfide-linked biotin. The results show that a low concentration (500 microM) of HPDP-biotin produced substantial inhibition of PP2A activity and promoted the binding of the catalytic subunit of PP2A to an immobilized avidin-affinity column. Both the inhibition of PP2A activity and the binding of PP2A to the avidin column were reversed by treatment with the disulfide reducing agent dithiothreitol (DTT). Furthermore, the specific activity of PP2A was up to 7-fold higher in the DTT-eluted fractions from the avidin-affinity column than in the soluble fraction. These findings demonstrate directly that PP2A is susceptible to reversible inhibitory modification by thiol-disulfide exchange and provide mechanistic support for the emerging view that PP2A is an oxidant-sensitive protein phosphatase. PMID:15823574

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

    PubMed

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

    2015-02-12

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

  20. Intermolecular contacts influencing the conformational and geometric features of the pharmaceutically preferred mebendazole polymorph C.

    PubMed

    Martins, Felipe T; Neves, Person P; Ellena, Javier; Camí, Gerardo E; Brusau, Elena V; Narda, Griselda E

    2009-07-01

    Mebendazole (MBZ) is a common benzimidazole anthelmintic that exists in three different polymorphic forms, A, B, and C. Polymorph C is the pharmaceutically preferred form due to its adequated aqueous solubility. No single crystal structure determinations depicting the nature of the crystal packing and molecular conformation and geometry have been performed on this compound. The crystal structure of mebendazole form C is resolved for the first time. Mebendazole form C crystallizes in the triclinic centrosymmetric space group and this drug is practically planar, since the least-squares methyl benzimidazolylcarbamate plane is much fitted on the forming atoms. However, the benzoyl group is twisted by 31(1) degrees from the benzimidazole ring, likewise the torsional angle between the benzene and carbonyl moieties is 27(1) degrees. The formerly described bends and other interesting intramolecular geometry features were viewed as consequence of the intermolecular contacts occurring within mebendazole C structure. Among these features, a conjugation decreasing through the imine nitrogen atom of the benzimidazole core and a further resonance path crossing the carbamate one were described. At last, the X-ray powder diffractogram of a form C rich mebendazole mixture was overlaid to the calculated one with the mebendazole crystal structure. PMID:18855910

  1. Enantioselective imidation of sulfides via enzyme-catalyzed intermolecular nitrogen-atom transfer.

    PubMed

    Farwell, Christopher C; McIntosh, John A; Hyster, Todd K; Wang, Z Jane; Arnold, Frances H

    2014-06-18

    Engineering enzymes with novel reaction modes promises to expand the applications of biocatalysis in chemical synthesis and will enhance our understanding of how enzymes acquire new functions. The insertion of nitrogen-containing functional groups into unactivated C-H bonds is not catalyzed by known enzymes but was recently demonstrated using engineered variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium. Here, we extend this novel P450-catalyzed reaction to include intermolecular insertion of nitrogen into thioethers to form sulfimides. An examination of the reactivity of different P450BM3 variants toward a range of substrates demonstrates that electronic properties of the substrates are important in this novel enzyme-catalyzed reaction. Moreover, amino acid substitutions have a large effect on the rate and stereoselectivity of sulfimidation, demonstrating that the protein plays a key role in determining reactivity and selectivity. These results provide a stepping stone for engineering more complex nitrogen-atom-transfer reactions in P450 enzymes and developing a more comprehensive biocatalytic repertoire. PMID:24901646

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed Central

    Cie?lik, Marcin; Derewenda, Zygmunt S.

    2009-01-01

    The integrity and X-ray diffraction quality of protein crystals depend on the three-dimensional order of relatively weak but reproducible intermolecular contacts. Despite their importance, relatively little attention has been paid to the chemical and physical nature of these contacts, which are often regarded as stochastic and thus not different from randomly selected protein surface patches. Here, logistic regression was used to analyze crystal contacts in a database of 821 unambiguously monomeric proteins with structures determined to 2.5?Å resolution or better. It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces, which are typically small and hydrophobic, have been underestimated with respect to their contact-forming potential by earlier area-based calculations. For any given solvent-exposed surface, small and hydrophobic residues are more likely to be involved in crystal contacts than large and charged amino acids. Side-chain entropy is the single physicochemical property that is most negatively correlated with the involvement of amino acids in crystal contacts. It is also shown that crystal contacts with larger buried surfaces containing eight or more amino acids have cores that are depleted of polar amino acids. PMID:19390155

  4. Report on dipole-dipole resistivity and technology transfer at the Ahuachapan Geothermal field Ahuachapan, El Salvador

    SciTech Connect

    Fink, J.B. (Geophynque International, Tucson, AZ (United States))

    1988-08-01

    The Ahuachapan Geothermal Field (AGF) is a 90 megawatt geothermal-sourced powerplant operated by the Comision Ejecutiva Hidroelectrica del Rio Lempa (CEL) of El Salvador. During the period November 1987 through May 1988 a deep resistivity survey and technology transfer was performed at the AGF at the request of Los Alamos National Laboratory (LANL) as part of a United States Agency for International Development (USAID) project. The resistivity surveying is ongoing at the time of this report under the supervision of CEL personnel. LANL and contract personnel were present at the site during performance of the initial surveying for the purpose of technology transfer. This report presents the results and interpretation of the two initial resistivity survey lines performed on site during and shortly after the technology transfer period.

  5. Skeletal rearrangement of o-propargylic formaldoximes by a gold-catalyzed cyclization/intermolecular methylene transfer sequence.

    PubMed

    Nakamura, Itaru; Gima, Shinya; Kudo, Yu; Terada, Masahiro

    2015-06-01

    Skeletal rearrangement of O-propargylic formaldoximes, in the presence of gold catalysts, afforded 4-methylene-2-isoxazolines in good to excellent yields by an intermolecular methylene transfer. In addition, the cascade reaction with maleimide in the presence of a gold catalyst afforded isoxazole derivatives by cyclization/methylene transfer and a subsequent ene reaction, whereas that using a copper catalyst gave oxazepines through a 2,3-rearrangement. PMID:25932619

  6. Visible-light induced isoindoles formation to trigger intermolecular diels-alder reactions in the presence of air.

    PubMed

    Lin, Chao; Zhen, Le; Cheng, Yong; Du, Hong-Jin; Zhao, Hui; Wen, Xiaoan; Kong, Ling-Yi; Xu, Qing-Long; Sun, Hongbin

    2015-06-01

    Visible-light induced isoindole formation triggered an intermolecular Diels-Alder reaction with dienophiles such as acetylenedicarboxylate and maleimides in the presence of air. The reaction resulted in excellent diastereoselctivity and high yields under mild reaction conditions. This protocol provides an atom-economical, transition-metal-free (TM-free) and straightforward approach to structurally diverse bridged-ring heterocycles from easily accessible molecules. PMID:25973634

  7. Intermolecular vibrational modes and orientational dynamics of cooperative hydrogen-bonding dimer of 7-azaindole in solution

    NASA Astrophysics Data System (ADS)

    Kato, Tatsuya; Shirota, Hideaki

    2011-04-01

    We observed the low-frequency Raman-active intermolecular vibrational modes of 7-azaindole in CCl4 by femtosecond Raman-induced Kerr effect spectroscopy. To understand the dynamical aspects and vibrational modes of 7-azaindole in the solution, the ultrafast dynamics of 1-benzofuran in CCl4 was also examined as a reference and ab initio quantum chemistry calculations were performed for 7-azaindole and 1-benzofuran. The cooperative hydrogen-bonding vibrational bands of 7-azaindole dimer in CCl4 appeared at 89 cm-1 and 105 cm-1 represent the overlap of stagger and wheeling modes and the intermolecular stretching mode, respectively. They are almost independent of the concentration in the solution. We further found from the low-frequency differential Kerr spectra of the solutions with neat CCl4 that the intermolecular motion in the low frequency region below 20 cm-1 was less active in the case of 7-azaindole/CCl4 than in the case of 1-benzofuran/CCl4. The slow orientational relaxation time in 7-azaindole/CCl4 is ˜3.5 times that in 1-benzofuran/CCl4 because of the nature of the dimerization of 7-azaindole.

  8. Non-canonical Interactions in a Kissing Loop Complex: The Dimerization Initiation Site of HIV-1

    E-print Network

    Westhof, Eric

    Non-canonical Interactions in a Kissing Loop Complex: The Dimerization Initiation Site of HIV-1. Two RNA monomers form a kissing loop complex via intermolecular interactions of the six nucleotide of the kissing helix and are in- corporated into a three-dimensional model of the kissing loop dimer. In addition

  9. Diabatic intermolecular potentials and bound states of open-shell atom-molecule dimers: Application to the F(2P)-H2 complex

    NASA Astrophysics Data System (ADS)

    Zeimen, W. B.; K?os, J.; Groenenboom, G. C.; van der Avoird, A.

    2003-04-01

    We present a general derivation of the expansion of diabatic intermolecular potentials for an open-shell atom interacting with a closed-shell molecule and the multipolar expansion of these potentials in the long range. It is outlined how to compute bound states of the open-shell atom-molecule complex from the set of asymptotically degenerate diabatic potentials in a body-fixed basis of rovibrational wave functions with the inclusion of spin-orbit coupling. This method is applied to produce all the bound energy levels of the F(2P)-H2 van der Waals complex with recent diabatic potentials obtained from ab initio calculations by K?os et al. [Int. J. Quantum Chem. 90, 1038 (2002)]. The binding energy D0 is 14.6 cm-1 for the para-H2 complex and 19.3 cm-1 for the ortho-H2 complex. The para-H2-F complex does not possess any bound states for rotational quantum numbers J larger than 9/2, the ortho-H2-F complex has a maximum J of 11/2.

  10. Ion–ion interaction in room temperature ionic liquid 1-ethyl-3-methylimidazolium tetrafluoroborate studied by large angle X-ray scattering experiment and molecular dynamics simulations

    Microsoft Academic Search

    Ryo Kanzaki; Takushi Mitsugi; Shuhei Fukuda; Kenta Fujii; Munetaka Takeuchi; Yasufumi Soejima; Toshiyuki Takamuku; Toshio Yamaguchi; Yasuhiro Umebayashi; Shin-ichi Ishiguro

    2009-01-01

    Large angle X-ray scattering (LAXS) experiment for 1-ethyl-3-methylimidazolium tetrafluoroborate [EMI+][BF4?] ionic liquid was carried out at 298 K, to reveal the closest ion–ion interaction in the ionic liquid. The intra-molecular atom–atom correlations based on the molecular geometries in crystals were subtracted from the total pair correlation function to yield the inter-molecular pair correlation function. In the inter-molecular pair correlation function, peaks

  11. 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

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

    PubMed

    Krylov, Igor B; Vil', Vera A; Terent'ev, Alexander O

    2015-01-01

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

  13. Molecular and ionic diffusion in aqueous - deep eutectic solvent mixtures: Probing inter-molecular interactions using PFG NMR

    E-print Network

    D'Agostino, Carmine; Gladden, Lynn F.; Mantle, Mick D.; Abbott, Andrew P.; Ahmed, Essa I.; Al-Murshedi, Azhar Y. m.; Harris, Robert C.

    2015-06-02

    Pulsed field gradient (PFG) NMR has been used to probe self-diffusion of molecular and ionic species in aqueous mixtures of choline chloride (ChCl) based deep eutectic solvents (DESs), in order to elucidate the effect of water on motion and inter...

  14. Tuning Intermolecular Interactions: A Study of the Structural and Vibrational Properties of p-Hexaphenyl under Pressure

    E-print Network

    Glaser, Rainer

    neighboring phenyl rings as a function of the torsional angle is "W"-shaped. The libration of the phenyl rings the arrangement of the phenyl rings within one molecule and the arrangement of the molecules with respect

  15. Coherent two-dimensional Raman scattering: Frequency-domain measurement of the intra- and intermolecular vibrational interactions

    NASA Astrophysics Data System (ADS)

    Cho, Minhaeng; Okumura, Ko; Tanimura, Yoshitaka

    1998-01-01

    A new experiment of frequency-domain coherent two-dimensional Raman scattering is theoretically proposed. By using three fields whose wave vectors and frequencies are independently controlled, one can measure the nonlinear Raman responses in either gas or condensed phases. The connection to the time-domain femtosecond two-dimensional Raman spectroscopy is completely established. By considering several limiting cases in detail, it is found that from the coherent 2D Raman scattering spectrum one can obtain quantitative information on the anharmonicity, anharmonic mode coupling, and polarizability coupling.

  16. An in vitro network of intermolecular interactions between viral RNA segments of an avian H5N2

    E-print Network

    Paris-Sud XI, Université de

    ). They are responsible for the majority of seasonal flu cases and for occasional flu pandemics that can have high case in the waterfowl than in the human population (9). A human IAV pandemic can arise when a flu strain jumps from changes: it is thought that such a process gave rise to the `Spanish flu' in 1918. Alternatively, when

  17. Relationship between molecular weight of poly(ethylene)glycol and intermolecular interaction of Taka-amylase A monomers

    Microsoft Academic Search

    Kazuo Onuma; Naoki Furubayashi; Fujiko Shibata; Yoshiko Kobayashi; Sachiko Kaito; Yuki Ohnishi; Koji Inaka

    2010-01-01

    Dynamic and static light scattering investigations of Taka-amylase A (TAA) protein monomers were done using solutions containing poly(ethylene)glycol (PEG) with molecular weights of 1500, 4000, 8000, and 20000. The anomalies observed in a previous study using a weight of 8000, in which the hydrodynamic TAA monomer radius at a zero protein concentration and the molecular weight of the monomers decreased

  18. Competition between H···? and H···O interactions in furan heterodimers.

    PubMed

    Sánchez-García, Elsa; Jansen, Georg

    2012-06-14

    Here the interactions of furan with HZ (Z = CCH, CCF, CN, Cl, and F) are studied using a variety of electron correlation methods (MP2, CCSD(T), DFT-SAPT) and correlation-consistent triple- and quadruple-? basis sets including complete basis set (CBS) extrapolation. For Fu-HF all methods agree that a n-type structure with a hydrogen bridge between the oxygen lone-pair of furan and the hydrogen atom of HF is the global minimum structure. It is found to be significantly more stable than a ?-type structure where the hydrogen atom of HF points toward the ? system of furan. For the other four dimers MP2 and DFT-SAPT predict the ?-type structure to be somewhat more stable, while CCSD(T) favors the n-type structure as the global minimum for Fu-HCl and predicts both structures as nearly isoenergetic for Fu-HCCH and Fu-HCCF. From a geometrical point of view, the Fu-HCN dimer structures are more related to those of the Fu-HCl complex than to Fu-HCCH. The different behavior of HCCF and HF upon complexation with furan evidence the effect of the presence of a ? system in the aggregation of fluorine derivatives. It is shown that aggregates of furan cannot be understood by means of dipole-dipole and electrostatic analysis only. Yet, through a combined and detailed analysis of DFT-SAPT energy contributions and resonance effects on the molecular charge distributions a consistent explanation of the aggregation of furan with both ? electron rich molecules and halogen hydrides is provided. PMID:22650151

  19. The origin of the anomeric effect: probing the impacts of stereoelectronic interactions.

    PubMed

    Hasanzadeh, Neda; Nori-Shargh, Davood; Farzipour, Mahdieh; Ahmadi, Bahareh

    2015-07-01

    To gain further insight on the origin of the anomeric effect [stabilization energies associated with electron delocalization (SE), electrostatic models associated with the dipole-dipole interactions (EM) and Pauli exchange-type repulsions (PETR)], the correlations between SE, EM, PETR, bond-orders, donor and acceptor orbital energies and occupancies, structural parameters and configurational behavior of 2,3-difluoro-1,4-oxathiane (1), 2,3-dichloro-1,4-oxathiane (2), and 2,3-dibromo-1,4-oxathiane (3) as well as 2,5-difluoro-1,4-oxathiane (4), 2,5-dichloro-1,4-oxathiane (5), and 2,5-dibromo-1,4-oxathiane (6) were investigated by means of the complete basis set (CBS-4), hybrid density functional theory method (B3LYP/6-311+G**) and natural bond orbital (NBO) interpretations. The differences in the total energies among four possible configurations of compounds 1-6 do not correlate with the differences in their corresponding SE, EM or PETR values but can be controlled by their cooperative or uncooperative impacts. The results obtained showed that the SE has a determining impact on the structural properties of compounds 1-6 but fails to account solely for the variations of the energy differences between the configurations in compounds 1-6. The SE and PETR components are in favor of the (ax,ax) forms (the most stable configuration) going from compound 1 to compound 3 but the EM has the opposite impact; therefore, these factors have counterintuitive impacts on the configurational properties of compounds 1-3. Because there are no significant dipole moment values for the (ax,ax) and (eq,eq) forms of compounds 4-6, the energy differences between these forms can result from the conflict between the SE and PETR components. Therefore, the conclusions published previously in the literature about the origin of the anomeric effect should be reexamined. PMID:26022618

  20. Formation of dendrite crystals in poly(ethylene oxide) interacting with bioresourceful tannin

    Microsoft Academic Search

    Kai Cheng Yen; E. M. Woo

    2009-01-01

    A dendritic morphology, induced by miscibility with strong intermolecular interaction between poly(ethylene oxide) (PEO) and\\u000a bioresourceful tannin [tannic acid (TA)]. Mechanism was investigated by differential scanning calorimetry (DSC), Fourier-transform\\u000a infrared spectroscopy, wide-angle X-ray diffraction, and polarized optical microscopy. The cell crystallography preference\\u000a in correlation to the intermolecular interaction in the dendrites in PEO\\/TA (70\\/30) blend was analyzed. Dendritic morphology\\u000a was

  1. 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.

  2. Theoretical Studies of Intra- and Inter Magnetic Interactions in TMAO(1,3,5,7 - Tetramethyl - 2, 6- Diazaadamantane N, N? - Dioxyl)

    Microsoft Academic Search

    Takashi Kawakami; Akifumi Oda; Sadamu Takeda; Wasuke Mori; Kizashi Yamaguchi

    1999-01-01

    Ferromagnetic properties of TMAO organic crystal, especially ?-form crystal, are studied theoretically. There are two nitroxide groups, that is, both intramolecular magnetic interaction in one molecule and inter-molecular interaction between two molecules are expected in contrast to many organic ferromagnetic crystalline species that have been reported by other groups. Obtained Jab values for intra- and inter- molecular interactions are positive

  3. Organozirconium complexes as catalysts for Markovnikov-selective intermolecular hydrothiolation of terminal alkynes: scope and mechanism.

    PubMed

    Weiss, Charles J; Marks, Tobin J

    2010-08-01

    The efficient and selective organozirconium(IV)-mediated, intermolecular hydrothiolation of terminal alkynes by aliphatic, benzylic, and aromatic thiols using CGCZrMe(2) (CGC = Me(2)SiCp'' NCMe(3), Cp'' = C(5)Me(4)), Cp*ZrBn(3) (Cp* = C(5)Me(5), Bn = benzyl), Cp*ZrCl(2)NMe(2), Cp*(2)ZrMe(2), and Zr(NMe(2))(4) precatalysts is reported. These transformations are shown to be highly Markovnikov-selective, with selectivities up to 99%, and typically in greater than 90% yields. The reaction has been demonstrated on the preparative scale with 72% isolated yield and 99% Markovnikov selectivity. A mixture of anti-Markovnikov products is occasionally observed as a result of a known, non-organometallic, radical mechanism, which can be suppressed by addition of a radical inhibitor. Kinetic investigations show that the CGCZrMe(2)-mediated reaction between 1-pentanethiol and 1-hexyne is first-order in catalyst concentration, first-order in alkyne concentration, and also first-order in thiol at lower concentrations but transitions to zero-order at concentrations > 0.3 M. Deuterium labeling of the alkyne yields k(H)/k(D) = 1.3(0.1), along with evidence of thiol-mediated protonolytic detachment of product from the Zr center. Activation parameters for CGCZrMe(2)-mediated 1-pentanethiol hydrothiolation of 1-hexyne measured over the temperature range of 50-80 degrees C are DeltaH(double dagger) = +18.1(1.2) kcal/mol and DeltaS(double dagger) = -20.9(2.5) e.u. for [alkyne] and [thiol] at 0.2 M. These and other findings are consistent with turnover-limiting alkyne insertion into the Zr-SR bond, followed by a thiol-induced Zr-C protonolysis. Observed zirconium-thiolate dimers in the reaction medium suggest instances of dimeric catalyst resting states and possible aggregated, hydrothiolation-active species. PMID:20617838

  4. High-resolution MR spectroscopy via intermolecular double-quantum coherences in inhomogeneous B0 and B1 fields.

    PubMed

    Lin, Yanqin; Cai, Congbo; Cai, Shuhui; Zhong, Jianhui; Chen, Zhong

    2011-06-01

    Inhomogeneity in static field B0 and/or RF field B1 is inevitable under some circumstances. In this work, a method based on intermolecular double-quantum coherences is employed for high-resolution 1D MR spectroscopy via 2D acquisition under such a condition. High-resolution information on chemical shifts, multiplet patterns, J coupling constants and relative peak areas can be retained in the resulting 1D projected spectra, as shown with results from a narrow-bore NMR spectrometer and a whole-body clinical scanner. PMID:21531101

  5. Intermolecular nitrogen transfer in the enzymic conversion of glutamate to delta-aminolevulinic acid by extracts of Chlorella vulgaris.

    PubMed

    Mayer, S M; Gawlita, E; Avissar, Y J; Anderson, V E; Beale, S I

    1993-03-01

    delta-Aminolevulinic acid (ALA), the universal biosynthetic precursor of tetrapyrrole pigments, is synthesized from glutamate in plants, algae, and many bacteria via a three-step process that begins with activation by ligation of glutamate to tRNA(Glu), followed by reduction to glutamate-1-semialdehyde (GSA) and conversion of GSA to ALA. The GSA aminotransferase step requires no substrate other than GSA. A previous study examined whether the aminotransferase reaction proceeds via intramolecular or intermolecular N transfer and concluded that the reaction catalyzed by Chlamydomonas extracts occurs via intermolecular N transfer (Y.-H.L. Mau and W.-Y. Wang [1988] Plant Physiol 86: 793-797). However, in that study the possibility was not excluded that the result was a consequence of N exchange among product ALA molecules during the incubation, rather than intermolecular N transfer during the conversion of GSA to ALA. Therefore, this question was reexamined in another species and with additional controls. A gel-filtered extract of Chlorella vulgaris cells was incubated with ATP, Mg2+, NADPH, tRNA, and a mixture of L-glutamate molecules, one-half of which were labeled with 15N and the other half with 13C at C-1. The ALA product was purified, derivatized, and analyzed by gas chromatography-mass spectrometry. A significant fraction of the ALA molecules was heavy by two mass units, indicating incorporation of both 15N and 13C. These results show that the N and C atoms of each ALA molecule were derived from different glutamate molecules. Control experiments indicated that the results could not be attributed to exchange of N atoms between glutamate or ALA molecules during the incubation. These results confirm the earlier conclusion that GSA is converted to ALA via intermolecular N transfer and extend the results to another species. The labeling results, combined with the results of kinetic and inhibitor studies, support a model for the GSA aminotransferase reaction in which a single molecule of GSA is converted to ALA via an enzyme-bound 4,5-diaminovaleric acid intermediate. PMID:7906043

  6. Effect of persistence length on binding of DNA to polyions and overcharging of their intermolecular complexes in aqueous and in 1-methyl-3-octyl imidazolium chloride ionic liquid solutions.

    PubMed

    Rawat, Kamla; Pathak, Jyotsana; Bohidar, H B

    2013-08-01

    The effect of persistence length on the intermolecular binding of DNA (200 bp, persistence length l(p) = 50 nm, polyanion) with three proteins, gelatin B (GB) (l(p) = 2 nm, polyampholyte chain), bovine serum albumin (BSA) (l(p) = 7 nm, polyampholyte colloid), gelatin A (GA) (l(p) = 10 nm, polyampholyte chain), and a polysaccharide chitosan (l(p) = 17 nm, polycation), was investigated in aqueous and in 1-methyl-3-octyl imidazolium chloride ionic liquid ([C8mim][Cl]) solutions. In DNA-GB and DNA-BSA solutions complexation primarily arises from surface patch binding whereas DNA-chitosan and DNA-GA binding was predominantly governed by electrostatic forces. These occurred at well defined pH values: (i) at pHc associative interactions ensued and soluble complexes were formed, (ii) at pH? soluble complexes coalesced to give rise to liquid-liquid phase separation (coacervation) and (iii) at pH(prep) formation of large insoluble complexes drove the solution towards liquid-solid phase separation. A universal phase diagram encapsulating the aforesaid interactions can be made using the persistence length of polyion as an independent variable. DNA formed overcharged intermolecular complexes with all these polyions when the polyion concentration was more than the concentration required to produce charge neutralized complexes (disproportionate binding). In IL solutions maximum binding occurred when 0.075 < [IL] < 0.10% (w/v) and the effect of overcharging was substantially screened. The extent of overcharge was a monotonous increasing function of the polyion persistence length. Results clearly revealed that DNA-polyion binding was hierarchical in polyion concentration and persistence length. Overcharging of the DNA-polyion complex was found to be ubiquitous for the polyions used in the present study. PMID:23775068

  7. Intermolecular magnetic couplings in the dinuclear copper(II) complex mu-chloro-mu-[2,5-bis(2-pyridyl)-1,3,4-thiadiazole] aqua chlorocopper(II) dichlorocopper(II): synthesis, crystal structure, and EPR and magnetic characterization.

    PubMed

    Bentiss, Fouad; Lagrenée, Michel; Mentré, Olivier; Conflant, Pierre; Vezin, Hervé; Wignacourt, Jean Pierre; Holt, Elizabeth M

    2004-03-22

    Mu-chloro-mu-[2,5-bis(2-pyridyl)-1,3,4-thiadiazole] aqua chlorocopper(II) dichlorocopper(II) is the first characterized dimeric complex of a transition metal and this hetero ligand [C(12)H(10)Cl(4)Cu(2)N(4)OS; triclinic; space group P; a = 9.296(3) A, b = 9.933(3) A, c = 10.412(3) A; alpha = 79.054(5) degrees, beta = 82.478(6) degrees, gamma = 67.099(5) degrees; Z = 2 at room temperature]. The Cu(II) ions are bridged by the N-N thiadiazole bond and a chloride ion [Cu1-Cu2 = 3.7800(8) A]. Thermogravimetric analysis shows this structure to be stable at temperatures up to 348 K. At higher temperatures, the successive loss of a water molecule and one chloride of the dimeric unit is identified. From room temperature to 125 K, half of the Cu(2+) ions are progressively engaged in intermolecular dinuclear antiferromagnetic exchanges, while the other half remain paramagnetic. At lower temperatures, both susceptibility and electron paramagnetic resonance measurements show the paramagnetic-only couplings of this half of the Cu(2+) ions, involving a singlet ground state for interacting Cu(2+). This unusual behavior has been satisfactorily explained on the basis of intermolecular Cu-Cu interactions (J = -180 cm(-1)), involving the magnetic d(z)2 orbital perpendicular to the molecular plane, on which are seen the conjugate effects of the bridging chloride and the planar thiadiazole. It is noteworthy that the behavior of the title compound is original, compared to the systematic in-plane intramolecular antiferromagnetic coupling of other thiadiazole-containing binuclear complexes. PMID:15018505

  8. Density functional theory calculations on dipeptide–gallic acid interaction

    Microsoft Academic Search

    B. Madhan; R Parthasarathi; V Subramanian; J Raghava Rao; Balachandran Unni Nair; T Ramasami

    2003-01-01

    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

  9. Investigations on the intrinsic viscosity of poly(vinyl chloride)(PVC) affected by polymer–polymer interactions in solution

    Microsoft Academic Search

    Yang Haiyang; Zhu Pingping; Li Guofeng; Wu Peng; Ren Feng

    1999-01-01

    The concentration-dependent intermolecular interactions between poly(vinyl chloride) (PVC) and various polymers selected to form polymer solvent were thoroughly investigated by the method of polymer solvent. It has been found that these interactions depended upon both the polymer selected to form the polymer solvent and the concentration of the selected polymer in polymer solvent. If polystyrene (PS), an incompatible polymer with

  10. Interactions of egg yolk phosphatidylcholine with cholesteryl polyethoxy neoglycolipids containing N-acetyl- D-glucosamine

    NASA Astrophysics Data System (ADS)

    Kemoun, Rachida; Gelhausen, Micaèle; Besson, Françoise; Lafont, Dominique; Buchet, René; Boullanger, Paul; Roux, Bernard

    1999-03-01

    Series of neoglycolipids containing cholesteryl and N-acetyl- D-glucosaminyl groups were synthesized with various ethoxy linkers. Their self aggregations and intermolecular interactions, without and with egg yolk phosphatidylcholine (EYPC), were characterized in dry and hydrated states, by using infrared spectroscopy. The neoglycolipids in the dry state formed intermolecular hydrogen bonds between the C?O and N-H or O-H groups of N-acetyl- D-glucosamine (GlcNAc). In the presence of EYPC, these intermolecular interactions were broken and new hydrogen bonds, involving the phosphate group of EYPC and N-H or O-H groups of GlcNAc of neoglycolipid, were formed. The presence of water molecules altered these intermolecular hydrogen bonds. The C?O groups of EYPC were not affected by the presence of neoglycolipids, either in hydrated or in dry states, indicating that the GlcNAc polar groups interacted mostly with EYPC phosphate residues. The phase transition-temperature of mixtures of EYPC containing either cholesterol or neoglycolipid were similar, indicating that the cholesteryl group of the neoglycolipid interacted in the same manner as cholesterol with hydrocarbon chains of EYPC. Some structural models of molecular interactions of neoglycolipids were discussed in relation with the molecular recognition of wheat germ agglutinin.

  11. About the nature of intermolecular three-body forces in ionic systems: The case of protonated hydrates

    NASA Astrophysics Data System (ADS)

    Kelterbaum, R.; Turki, N.; Rahmouni, A.; Kochanski, E.

    1994-01-01

    The three-body intermolecular energy is computed for the water/oxonium ion/water system from ab initio self-consistent-field (SCF) calculations and 170 geometrical configurations. It is decomposed into two parts: ?E1stnonadd is obtained at the first iteration of the calculation and ?Edelocnonadd is due to the following iterations till convergency. The nonadditive three-body energy, Eindnonadd, is computed from the perturbation theory. It is shown that all these energy components can be either attractive or repulsive according to the geometry. Edelocnonadd is often seriously different of Eindnonadd, a nonadditive ``induction-exchange'' term being sometimes as large as Eindnonadd. In most cases, this ``induction-exchange'' term is much larger than E1stnonadd, with the same sign. This suggests that these two terms can be approximated by a same expression, but because of the sign, more than one exponential term should be used. An approximation of Eindnonadd is discussed with a particular attention to the range of the validity according to the intermolecular distances.

  12. Intermolecular packing and alignment in an ordered beta-hairpin antimicrobial peptide aggregate from 2D solid-state NMR.

    PubMed

    Tang, Ming; Waring, Alan J; Hong, Mei

    2005-10-12

    The aggregation and packing of a membrane-disruptive beta-hairpin antimicrobial peptide, protegrin-1 (PG-1), in the solid state are investigated to understand its oligomerization and hydrogen-bonding propensity. Incubation of PG-1 in phosphate buffer saline produced well-ordered nanometer-scale aggregates, as indicated by 13C and 15N NMR line widths, chemical shifts, and electron microscopy. Two-dimensional 13C and 1H spin diffusion experiments using C-terminus strand and N-terminus strand labeled peptides indicate that the beta-hairpin molecules in these ordered aggregates are oriented parallel to each other with like strands lining the intermolecular interface. In comparison, disordered and lyophilized peptide samples are randomly packed with both parallel and antiparallel alignments. The PG-1 aggregates show significant immobilization of the Phe ring near the beta-turn, further supporting the structural ordering. The intermolecular packing of PG-1 found in the solid state is consistent with its oligomerization in lipid bilayers. This solid-state aggregation approach may be useful for determining the quaternary structure of peptides in general and for gaining insights into the oligomerization of antimicrobial peptides in lipid bilayers in particular. PMID:16201813

  13. Intermolecular charge flux as the origin of infrared intensity enhancement upon halogen-bond formation of the peptide group

    NASA Astrophysics Data System (ADS)

    Torii, Hajime

    2010-07-01

    The changes in the vibrational properties of the peptide group upon formation of O⋯X and N⋯X halogen bonds are studied theoretically. Calculations are carried out for complexes of N-methylacetamide (NMA), a well known model molecule of the peptide group, with halogen-containing molecules. For comparison, calculations are also carried out for some NMA-water hydrogen-bonding complexes. It is shown that the infrared (IR) intensity of the amide I mode of the peptide group is enhanced significantly (up to about 520 km mol-1 or 2.6 times) upon C?O⋯X halogen-bond formation, in spite of rather modest magnitudes of the intermolecular electric field and of the changes in the C?O bond length and in the amide I vibrational frequency as compared with the cases of the C?O⋯H(D) hydrogen bonding. From the analysis of the changes in the dipole derivative and in the electronic structure, it is shown that this IR intensity enhancement arises from the intermolecular charge flux. For the N⋯X halogen bonding complexes, some characteristic changes in the vibrational properties are seen, among which the IR intensity enhancement of the ND out-of-plane wagging mode is most notable. The reason why such large IR intensity enhancements are seen for these particular vibrational modes is examined.

  14. 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

  15. Quantitative description of interactions between linear organic chromophores

    NASA Astrophysics Data System (ADS)

    Denis, Jean-Christophe; Schumacher, Stefan; Galbraith, Ian

    2012-12-01

    To model intermolecular excitation transfer between organic chromophores in the framework of Förster theory, the interaction matrix element is needed for all relative orientations and separations of chromophores. Simulations of extended multi-chromophoric systems thus require a fast but reliable approximation scheme to calculate these dipole interactions. By means of a comparative study of the dipole approximation with quantum chemistry, we demonstrate that the usual line-dipole theory, while suitable for short molecules, breaks down for longer molecules with inter-molecular separations similar to or smaller than the length of the interacting chromophores; a limit that is typically found in conjugated polymer thin films. As a remedy, we propose an improved way of distributing the sub-dipole moments within a line which provides results in very good agreement with the quantum chemistry, and is still simple enough to be used in large scale simulations.

  16. ATOMIC AND MOLECULAR PHYSICS: Apparent diffusion behaviour of intermolecular double-quantum coherence modulated by a distant dipolar field in solution NMR

    NASA Astrophysics Data System (ADS)

    Shen, Gui-Ping; Cai, Cong-Bo; Cai, Shu-Hui; Chen, Zhong

    2009-11-01

    A modified correlated spectroscopy (COSY) revamped with asymmetric Z-gradient echo detection sequence was designed to investigate the influence of diffusion behaviour on intermolecular double-quantum coherence signal attenuation during the pre-acquisition period. Theoretical formulas were deduced and experimental measurements and simulations were performed. It is found that the diffusion behaviour of intermolecular double-quantum coherence in the pre-acquisition period may be different from that of conventional single-quantum coherence, depending on the relative orientation of diffusion weighting gradients to coherence selection gradients. When the orientation of the diffusion weighting gradients is parallel or anti-parallel to the orientation of the coherence selection gradients, the diffusion is modulated by the distant dipolar field. This study is helpful for understanding the signal properties in intermolecular double-quantum coherence magnetic resonance imaging.

  17. 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

  18. {pi}-{pi} Interactions and magnetic properties in a series of hybrid inorganic-organic crystals

    SciTech Connect

    Gonzalez, M.; Lemus-Santana, A.A. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada, Unidad Legaria, Instituto Politecnico Nacional, Mexico, D. F. (Mexico); Rodriguez-Hernandez, J. [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada, Unidad Legaria, Instituto Politecnico Nacional, Mexico, D. F. (Mexico); Instituto de Ciencia y Tecnologia de Materiales, Universidad de La Habana (Cuba); Knobel, M. [Instituto de Fisica 'Gleb Wataghin', Universidade Estadual de Campinas, SP (Brazil); Reguera, E., E-mail: edilso.reguera@gmail.com [Centro de Investigacion en Ciencia Aplicada y Tecnologia Avanzada, Unidad Legaria, Instituto Politecnico Nacional, Mexico, D. F. (Mexico)

    2013-01-15

    The series of hybrid inorganic-organic solids T(Im){sub 2}[Ni(CN){sub 4}] with T=Fe, Co, Ni and Im=imidazole were prepared by soft chemical routes from aqueous solutions of the involved building units: imidazole, T{sup 2+} metal and the [Ni(CN){sub 4}]{sup 2-} anionic block. The obtained samples were characterized from infrared and UV-vis spectroscopies, and thermogravimetric, X-ray diffraction and magnetic measurements. Anhydrous solids which crystallize with a monoclinic unit cell, in the I2/a space group with four formula units per cell (Z=4) were obtained. Their crystal structure was solved ab initio from the recorded X-ray powder patterns and then refined by the Rietveld method. The metal T is found with octahedral coordination to four N ends of CN groups and two imidazole molecules while the inner Ni atom preserves its planar coordination. The system of layers remains stacked in an ordered 3D structure through dipole-dipole and {pi}-{pi} interactions between imidazole rings from neighboring layers. In this way, a pillared structure is achieved without requiring the coordination of both nitrogen atoms from imidazole ring. The recorded magnetic data indicate the occurrence of a predominant ferromagnetic interaction at low temperature for Co and Ni but not for Fe. Such magnetic ordering is more favorable for Ni with transition temperature of 14.67 K, which was ascribed to the relatively high polarizing power for this metal. Within the considered T metals, to nickel the highest electron-withdrawing ability corresponds and this leads to an increase for the metal-ligand electron clouds overlapping and to a stronger {pi}-{pi} attractive interaction, two factors that result into a higher magnetic ordering temperature. - Graphical Abstract: Magnetic ordering through the {pi}-{pi} interaction between the imidazole rings. Highlights: Black-Right-Pointing-Pointer Hybrid inorganic-organic solids. Black-Right-Pointing-Pointer Hybrid inorganic-organic molecular based magnets. Black-Right-Pointing-Pointer Ferromagnetic interaction through {pi}-{pi} stacking of imidazole rings. Black-Right-Pointing-Pointer Organic pillars formed through {pi}-{pi} stacking.

  19. The correlation energy in the random phase approximation: Intermolecular forces between closed-shell systems

    Microsoft Academic Search

    Attila Szabo; Neil S. Ostlund

    1977-01-01

    A new expression for the correlation energy within the random phase approximation (RPA) is presented. It has the following properties: it is (1) size consistent, (2) invariant to unitary transformations of degenerate orbitals, (3) correct to second order in perturbation theory, and (4) when applied to a supermolecule comprised of two interacting closed-shells, it describes the dispersive part of the

  20. Intermolecular forces between large molecules: the structure of anthracene stable dimers

    Microsoft Academic Search

    John M. Morris

    1974-01-01

    Calculations are reported concerning the structure of the anthracene stable dimer. It is shown that the use of an ‘exp-6’ atom-atom potential produces a structure which is definitely not that allowed by the experimental data : this is shown to be due to the absence of any simulation of permanent moment interactions in the atom-atom potentials. A number of conventional