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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.

    PubMed

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

    2012-12-14

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

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

    SciTech Connect

    Shimada, Rintaro; Hamaguchi, Hiro-o

    2014-05-28

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

  3. Dipole-dipole interaction in random electromagnetic fields

    E-print Network

    Sukhov, Sergey; Dogariu, Aristide

    2013-01-01

    We demonstrate that a non-vanishing interaction force exists between pairs of induced dipoles in random, statistically stationary electromagnetic field. This new type of optical binding force leads to long-range interaction between dipolar particles even when placed in spatially incoherent fields. We also discuss several unique features of dipole-dipole interaction in spatially incoherent Gaussian fields.

  4. Dipole-dipole interaction between rubidium Rydberg atoms

    SciTech Connect

    Altiere, Emily; Fahey, Donald P.; Noel, Michael W.; Smith, Rachel J.; Carroll, Thomas J.

    2011-11-15

    Ultracold Rydberg atoms in a static electric field can exchange energy via the dipole-dipole interaction. The Stark effect shifts the energy levels of the atoms which tunes the energy exchange into resonance at specific values of the electric field (Foerster resonances). We excite rubidium atoms to Rydberg states by focusing either a 480 nm beam from a tunable dye laser or a pair of diode lasers into a magneto-optical trap. The trap lies at the center of a configuration of electrodes. We scan the electric field by controlling the voltage on the electrodes while measuring the fraction of atoms that interact. Dipole-dipole interaction spectra are presented for initially excited rubidium nd states for n=31 to 46 and for four different pairs of initially excited rubidium ns states. We also present the dipole-dipole interaction spectra for individual rubidium 32d (j, m{sub j}) fine structure levels that have been selectively excited. The data are compared to calculated spectra.

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

    PubMed

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

    2014-04-24

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

  6. Critical behavior of isotropic three-dimensional systems with dipole-dipole interactions

    SciTech Connect

    Belim, S. M.

    2013-06-15

    The critical behavior of Heisenberg magnets with dipole-dipole interactions near the line of second-order phase transitions directly in three-dimensional space is investigated in terms of a field-theoretic approach. The dependences of critical exponents on the dipole-dipole interaction parameter are derived. Comparison with experimental facts is made.

  7. Modeling of band shapes in the low-temperature molecular liquid spectra affected by resonance dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Andrianov, D. S.; Cherevatova, A. N.; Kolomiitsova, T. D.; Shchepkin, D. N.

    2009-10-01

    The band shape theory of the vibrational transitions accompanied by an excitation of a strongly IR-active fundamental is elaborated for low-temperature molecular liquids with an account for strong intermolecular resonance dipole-dipole interactions. The developed model of a liquid uses the regular (fcc structure) crystal whose structure is then destroyed by introducing random, normally distributed displacements of particle positions, by assigning arbitrary molecular orientations as well as a varied number of randomly distributed vacancies. This model was applied to several molecular liquids (CF,SiF,SF,CFCl,andCFBr), those having triply degenerate modes were studied more in detail.

  8. Effective dipole-dipole interactions in multilayered dipolar Bose-Einstein condensates

    E-print Network

    Matthias Rosenkranz; Yongyong Cai; Weizhu Bao

    2012-01-30

    We propose a two-dimensional model for a multilayer stack of dipolar Bose-Einstein condensates formed by a strong optical lattice. We derive effective intra- and interlayer dipole-dipole interaction potentials and provide simple analytical approximations for a given number of lattice sites at arbitrary polarization. We find that the interlayer dipole-dipole interaction changes the transverse aspect ratio of the ground state in the central layers depending on its polarization and the number of lattice sites. The changing aspect ratio should be observable in time of flight images. Furthermore, we show that the interlayer dipole-dipole interaction reduces the excitation energy of local perturbations, affecting the development of a roton minimum.

  9. The Effect of Dipole-Dipole Interaction on Tripartite Entanglement in Different Cavities

    NASA Astrophysics Data System (ADS)

    Khan, Salman; Jan, Munsif

    2015-09-01

    The effect of dipole-dipole interaction, the initial relative phase and the coupling strength with the cavity on the dynamics of three two level atoms in the good and the bad cavity regime are investigated. It is found that the presence of strong dipole-dipole interaction not only ensures avoiding entanglement sudden death but also retains entanglement for long time. The choice of the phase in the initial state is crucial to the operational regime of the cavity. Under specific conditions, the entanglement can be frozen in time to its initial values through strong dipole-dipole interaction. This trait of tripartite entanglement may prove helpful in engineering multiparticle entanglement for the practical realization of quantum technology.

  10. Resonant dipole-dipole interaction in confined and strong-coupling dielectric geometries

    NASA Astrophysics Data System (ADS)

    El-Ganainy, Ramy; John, Sajeev

    2013-08-01

    Using the electromagnetic response function of an electric dipole located within a dielectric geometry, we derive the mathematical equivalence between the classical response and quantum mechanical resonant dipole-dipole interaction between two quantum objects (atoms, quantum dots, etc). Cooperative spontaneous emission likewise emerges from this equivalence. We introduce a practical numerical technique using finite difference time domain for calculating both dipole-dipole interaction and collective spontaneous emission in confined dielectric structures, where strong light-matter coupling might arise. This method is capable of obtaining resonant dipole-dipole interaction over a wide range of frequencies in a single run. Our method recaptures the results of quantum mechanical second order perturbation theory for weak light-matter coupling. In strong coupling situations such as near a photonic band edge, second order Rayleigh-Schrödinger perturbation theory leads to divergences, and instead Brillouin-Wigner perturbation theory is required. This is equivalent to the use of a variational wavefunction to describe the exciton transfer between initial and final states. We introduce a system of coupled classical oscillators, that describes resonant dipole-dipole interaction and vacuum Rabi splitting in the strong-coupling regime, and that provides an effective numerical scheme based on the finite difference time domain method. This includes the effects of quantum entanglement and the correlation of quantum fluctuations. We discuss the crossover to Forster energy transfer when quantum correlations between the dipoles are damped by strong environmental interactions.

  11. 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…

  12. Dipole-dipole interactions in optical lattices do not follow an inverse cube power law

    NASA Astrophysics Data System (ADS)

    Wall, M. L.; Carr, L. D.

    2013-12-01

    We study the effective dipole-dipole interactions in ultracold quantum gases on optical lattices as a function of asymmetry in confinement along the principal axes of the lattice. In particular, we study the matrix elements of the dipole-dipole interaction in the basis of lowest band Wannier functions which serve as a set of low-energy states for many-body physics on the lattice. We demonstrate that, for shallow lattices in quasi-reduced dimensional scenarios, the effective interaction between dipoles in an optical lattice is non-algebraic in the inter-particle separation at short to medium distance on the lattice scale and has a long-range power-law tail, in contrast to the pure power-law behavior of the dipole-dipole interaction in free space. The modifications to the free-space interaction can be sizable; we identify differences of up to 36% from the free-space interaction at the nearest-neighbor distance in quasi-one-dimensional arrangements. The interaction difference depends essentially on asymmetry in confinement, due to the d-wave anisotropy of the dipole-dipole interaction. Our results do not depend on statistics, applying to both dipolar Bose-Einstein condensates and degenerate Fermi gases. Using matrix product state simulations, we demonstrate that use of the correct lattice dipolar interaction leads to significant deviations from many-body predictions using the free-space interaction. Our results are relevant to up and coming experiments with ultracold heteronuclear molecules, Rydberg atoms and strongly magnetic atoms in optical lattices.

  13. Population Dynamics in Cold Gases Resulting from the Long-Range Dipole-Dipole Interaction

    E-print Network

    A. Mandilara; V. M. Akulin; P. Pillet

    2009-06-24

    We consider the effect of the long range dipole-dipole interaction on the excitation exchange dynamics of cold two-level atomic gase in the conditions where the size of the atomic cloud is large as compared to the wavelength of the dipole transition. We show that this interaction results in population redistribution across the atomic cloud and in specific spectra of the spontaneous photons emitted at different angles with respect to the direction of atomic polarization.

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

    SciTech Connect

    Ezawa, Motohiko

    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.

  15. Dipole-dipole interaction-induced spin-orbit coupling of polar molecules in optical lattices

    NASA Astrophysics Data System (ADS)

    Wall, M. L.; Syzranov, S. V.; Rey, A. M.

    2014-05-01

    Long-range dipole-dipole interactions between polar molecules in an optical lattice enable rotational excitations to move through the lattice even when the molecules themselves cannot, as has been directly observed in recent experiments [Yan et al., Nature 501, 521-525 (2013)]. We study the dynamics of rotational excitations in a 2D lattice of (bosonic or fermionic) polar molecules in the presence of electric dipole-dipole interactions which exchange rotational ``spin'' angular momentum projection with orbital angular momentum, forming a cold molecule analog of the Einstein-de Haas effect. In particular, we present analytic results for the statics and dynamics of a dilute gas of rotational excitations in a unit-filed lattice. Prospects for observing such processes in near-term polar molecule experiments are discussed.

  16. Simulations of the angular dependence of the dipole-dipole interaction among Rydberg atoms

    E-print Network

    Bigelow, Jacob L; Peleg, Matan; Sanford, Veronica L; Carroll, Thomas J

    2015-01-01

    The dipole-dipole interaction between two Rydberg atoms depends on the relative orientation of the atoms and on the change in the magnetic quantum number. We simulate the effect of this anisotropy on the energy transport in a many atom system with a homogeneous applied electric field. We consider two experimentally feasible geometries and find that the effects should be measurable in current generation imaging experiments.

  17. Impact of interparticle dipole-dipole interactions on optical nonlinearity of nanocomposites

    E-print Network

    Panov, Andrey V

    2013-01-01

    In this paper, effect of dipole-dipole interactions on nonlinear optical properties of the system of randomly located semiconductor nanoparticles embedded in bulk dielectric matrix is investigated. This effect results from the nonzero variance of the net dipole field in an ensemble. The analytical expressions describing the contribution of the dipole-dipole coupling to nonlinear dielectric susceptibility are obtained. The derived relationships are applicable over the full range of nanoparticle volume fractions. The factors entering into the contribution and depending on configuration of the dipoles are calculated for several cases. It is shown that for the different arrangements of dipole alignments the relative change of this contribution does not exceed 1/3.

  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; Koenderink, A. F.; Hernandez, J. V.; Robicheaux, F.

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

    NASA Astrophysics Data System (ADS)

    Baudin, Emmanuel

    2014-08-01

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

  1. On mechanisms of BEC stability and fermions instability for electric dipolar quantum gases with the exchange part of dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Andreev, Pavel

    2015-05-01

    In spite of the long-range nature of the dipole-dipole interaction, the self-consistent field part of the dipole-dipole interaction in BECs equals to zero. Hence the dipole-dipole interaction is related to the exchange part of the dipole-dipole interaction in BECs. However the exchange part of the dipole-dipole interaction in BECs coincides with the result of the formal application of the self-consistent field to dipolar BECs. Considering the electric dipole-dipole interaction in accordance with the Maxwell equations we obtain the positive and stable contribution of dipoles in the Bogoliubov spectrum. We obtain a different picture at the study of dipolar degenerate fermions, where there are both parts of the dipole-dipole interaction. The self-consistent field part gives the anisotropic positive contribution and the exchange part gives the negative isotropic contribution. The sing of the full contribution of dipoles depends on the direction of wave propagation. Hence the dipolar part of the spectrum of fermions brings the instability at large enough dipole moment, when the dipolar part overcomes the Fermi pressure. Strong dependence of the electric dipole-dipole interaction on the spin polarization is described as well.

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

    NASA Astrophysics Data System (ADS)

    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.

  3. 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

  4. Spatially Resolved Observation of Dipole-Dipole Interaction between Rydberg Atoms C. S. E. van Ditzhuijzen,1

    E-print Network

    Amsterdam, Universiteit van

    Ditzhuijzen,1 A. F. Koenderink,2 J. V. Herna´ndez,3 F. Robicheaux,3 L. D. Noordam,1 and H. B. van Linden van den Heuvell1,* 1 Van der Waals­Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018 XESpatially Resolved Observation of Dipole-Dipole Interaction between Rydberg Atoms C. S. E. van

  5. 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

  6. Quantum synchronization of ultracold atoms with dipole-dipole interactions in an optical lattice

    NASA Astrophysics Data System (ADS)

    Zhu, Bihui; Restrepo, Juan; Rey, Ana Maria; Holland, Murray

    2014-05-01

    Ultracold atoms confined in an optical lattice have been utilized as a powerful platform to study versatile many-body physics both experimentally and theoretically. A recent research focus has been the novel phenomena that would emerge with long-range interactions, which become especially important for atomic clocks where ultrahigh precision can amplify these effects. We develop theoretical models treating the two-level atoms as oscillators and study the synchronization of phases among a large ensemble of atoms coupled by dipole-dipole interactions, where the effect of geometry becomes relevant. We investigate the onset of synchronization and the related phase diagram, and further discuss the parameter regime for potential experimental observation using ultracold atoms such as Strontium. By applying different numerical methods, eg., quantum trajectories and truncated Wigner approximations to compare with the mean-field results, we also explore the underlying role of quantum fluctuations. We acknowledge funding from NIST, JILA-NSF-PFC-1125844, NSF-PIF, ARO, ARO-DARPA-OLE, and AFOSR.

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

    NASA Astrophysics Data System (ADS)

    Aver'yanov, E. M.

    2014-07-01

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

  8. 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.

  9. 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.

  10. Modeling Barkhausen Noise in magnetic glasses with dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Dubey, Awadhesh K.; Hentschel, H. George E.; Jaiswal, Prabhat K.; Mondal, Chandana; Procaccia, Itamar; Gupta, Bhaskar Sen

    2015-10-01

    Long-ranged dipole-dipole interactions in magnetic glasses give rise to magnetic domains having labyrinthine patterns on the scale of about 1 micron. Barkhausen Noise then results from the movement of domain boundaries which is modeled by the motion of elastic membranes with random pinning. Here we propose that on the nanoscale new sources of Barkhausen Noise can arise. We propose an atomistic model of magnetic glasses in which we measure the Barkhausen Noise which results from the creation of new domains and the movement of domain boundaries on the nanoscale. The statistics of the Barkhausen Noise found in our simulations is in striking disagreement with the expectations in the literature. In fact we find exponential statistics without any power law, stressing the fact that Barkhausen Noise can belong to very different universality classes. In the present model the essence of the phenomenon is the fact that the spin response Green's function is decaying too rapidly for having sufficiently large magnetic jumps. A theory is offered in excellent agreement with the measured data without any free parameter.

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

    NASA Astrophysics Data System (ADS)

    Ota, Satoshi; Yamada, Tsutomu; Takemura, Yasushi

    2015-05-01

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

  12. 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.

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

    E-print Network

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

    2015-01-12

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

  14. Measurement of the angular dependence of the dipole-dipole interaction between two individual Rydberg atoms at a Förster resonance

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    We measure the angular dependence of the resonant dipole-dipole interaction between two individual Rydberg atoms with controlled relative positions. By applying a combination of static electric and magnetic fields on the atoms, we demonstrate the possibility to isolate a single interaction channel at a Förster resonance, that shows a well-defined angular dependence. We first identify spectroscopically the Förster resonance of choice and we then perform a direct measurement of the interaction strength between the two atoms as a function of the angle between the internuclear axis and the quantization axis. Our results show good agreement with the angular dependence ?(1 -3 cos2? ) expected for this resonance. Understanding in detail the angular dependence of resonant interactions is important in view of using Förster resonances for quantum state engineering with Rydberg atoms.

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

    PubMed

    Saalwächter, Kay

    2014-08-14

    A recent implementation of a double-quantum (DQ) recoupling solid-state NMR experiment, dubbed DQ-DRENAR, provides a quantitative measure of homonuclear dipole-dipole coupling constants in multispin-1/2 systems. It was claimed to be more robust than another, previously known experiment relying on the recording of point-by-point normalized DQ build-up curves. Focusing on the POST-C7 and BaBa-xy16 DQ pulse sequences, I here present an in-depth comparison of both approaches based upon spin-dynamics simulations, stressing that they are based upon very similar principles and that they are largely equivalent when no imperfections are present. With imperfections, it is found that DQ-DRENAR/POST-C7 does not fully compensate for additional signal dephasing related to chemical shifts (CS) and their anisotropy (CSA), which over-compensates the intrinsic CS(A)-related efficiency loss of the DQ Hamiltonian and leads to an apparent cancellation effect. The simulations further show that the CS(A)-related dephasing in DQ-DRENAR can be removed by another phase cycle step or an improved super-cycled wideband version. Only the latter, or the normalized DQ build-up, are unaffected by CS(A)-related signal loss and yield clean pure dipolar-coupling information subject to unavoidable, pulse sequence specific performance reduction related to higher-order corrections of the dipolar DQ Hamiltonian. The intrinsically super-cycled BaBa-xy16 is shown to exhibit virtually no CS(A) related imperfection terms, but its dipolar performance is somewhat more challenged by CS(A) effects than POST-C7, which can however be compensated when applied at very fast MAS (>50 kHz). Practically, DQ-DRENAR uses a clever phase cycle separation to achieve a significantly shorter experimental time, which can also be beneficially employed in normalized DQ build-up experiments. PMID:25134563

  16. Effect of the dipole-dipole interaction of particles in an active medium on the character of superradiation

    SciTech Connect

    Berezovsky, V. V.; Men'shikov, L. I.; Oberg, S.; Latham, C. D.

    2008-07-15

    The motion of a system of interacting nonlinear charged oscillators is investigated numerically. Because of nonlinearity, the total collective electric field gives rise to a phasing effect-correlations in the phases of the oscillators. The consequence is superradiation-the enhanced spontaneous short-term emission of the energy stored in the oscillators. It is shown that the oscillations of the oscillators become stochastic because of the dipole-dipole interaction between them and their nearest neighbors. As a result, as the density of the oscillators increases, distant collective correlations are suppressed, superradiation ceases to be generated, and radiation is shielded in the medium. The phenomena considered in the present paper can play an important role in cyclotron emission from a plasma and thus should be taken into account in emission calculations. The process whereby the energy of the transverse electron motion in electron cooling devices decreases is analyzed as an example. This process occurs as a result of the development of cyclotron maser instability and has the nature of superradiation. The onset of correlations between individual electrons moving in their Larmor circles is the initial, linear stage of instability developing in the plasma. Superradiation is the final, nonlinear instability stage.

  17. 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.

  18. Effects of magnetic dipole-dipole interaction and rotation of (DyPr)CoFeB microparticles on the magnetic properties of their ensembles

    NASA Astrophysics Data System (ADS)

    Kablov, E. N.; Ospennikova, O. G.; Piskorskii, V. P.; Korolev, D. V.; Kunitsyna, E. I.; Talantsev, A. D.; Morgunov, R. B.

    2015-11-01

    The differences in the hysteresis loops of the (DyPr)CoFeB ferrimagnetic alloy powders dispersed in a polymer and eicosane, in a free form, and in sintered samples, have been analyzed. It has been shown that the differences are determined by changes in the dipole-dipole interaction between microparticles upon their dissolution, as well as are determined by the mechanical rotation of the particles and the degree of pinning of their easy axes.

  19. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H···O=C and C-H···O=C hydrogen-bonded complexes.

    PubMed

    Li, Shu-Shi; Huang, Cui-Ying; Hao, Jiao-Jiao; Wang, Chang-Sheng

    2014-03-01

    In this article, a polarizable dipole-dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen-bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N-H, C=O, and C-H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole-dipole interaction model to a series of hydrogen-bonded complexes containing the N-H···O=C and C-H···O=C hydrogen bonds, such as simple amide-amide dimers, base-base dimers, peptide-base dimers, and ?-sheet models. We find that a simple two-term function, only containing the permanent dipole-dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6-31G(d) method, whereas the high-quality counterpoise-corrected (CP-corrected) MP2/aug-cc-pVTZ interaction energies for the hydrogen-bonded complexes can be well-reproduced by a four-term function which involves the permanent dipole-dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole-dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen-bonded complexes are further discussed. PMID:24497309

  20. 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).

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

    E-print Network

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

    2007-11-02

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

  2. Intermolecular-interaction effects on quantum-phase and information-entropy dynamics of dimers interacting with a single-mode coherent field

    NASA Astrophysics Data System (ADS)

    Nakano, Masayoshi; Yamaguchi, Kizashi

    2000-07-01

    Using a numerically exact approach to the dynamics of a molecule-photon field-coupled system, we investigate the quantum-phase and the information-entropy dynamics of molecular dimers interacting with a single-mode coherent photon field. The intermolecular interaction between monomers is treated by the dipole-dipole interaction. The influence of the dipole-dipole interaction on the feature of the collapse-revival behavior of dimer population is revealed from the viewpoint of the photon-phase dynamics and the entanglement between dimer and photon.

  3. Measurement of the Angular Dependence of the Dipole-Dipole Interaction Between Two Individual Rydberg Atoms at a F\\"orster Resonance

    E-print Network

    Ravets, Sylvain; Barredo, Daniel; Lahaye, Thierry; Browaeys, Antoine

    2015-01-01

    We measure the angular dependence of the resonant dipole-dipole interaction between two individual Rydberg atoms with controlled relative positions. By applying a combination of static electric and magnetic fields on the atoms, we demonstrate the possibility to isolate a single interaction channel at a F\\"orster resonance, that shows a well-defined angular dependence. We first identify spectroscopically the F\\"orster resonance of choice and we then perform a direct measurement of the interaction strength between the two atoms as a function of the angle between the internuclear axis and the quantization axis. Our results show good agreement with the expected angular dependence $\\propto(1-3\\cos^2\\theta)$, and represent an important step towards quantum state engineering in two-dimensional arrays of individual Rydberg atoms.

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

    E-print Network

    Yavuz, Deniz

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

  5. Trapping and chaining self-assembly of colloidal polystyrene particles over a floating electrode by using combined induced-charge electroosmosis and attractive dipole-dipole interactions.

    PubMed

    Liu, Weiyu; Shao, Jinyou; Jia, Yankai; Tao, Ye; Ding, Yucheng; Jiang, Hongyuan; Ren, Yukun

    2015-10-14

    We propose a novel low-frequency strategy to trap 10 ?m colloidal polystyrene (PS) particles of small buoyancy velocity on the surface of a floating electrode, on the basis of combined induced-charge electroosmotic (ICEO) flow and dipole-dipole chaining phenomenon. For field frequencies of 5-50 Hz, much lower than the reciprocal RC time scale, double-layer polarization makes electric field lines pass around the 'insulating' surface of the ideally polarizable floating electrode. Once the long-range ICEO convective micro-vortexes transport particles quickly from the bulk fluid to the electrode surface, neighbouring particles aligned along the local horizontal electric field attract one another by attractive dipolar interactions, and form arrays of particle chains that are almost parallel with the applied electric field. Most importantly, this low-frequency trapping method takes advantage of the dielectrophoretic (DEP) particle-particle interaction to enhance the downward buoyancy force of this dipolar chaining assembly structure, in order to overcome the upward ICEO fluidic drag and realize stable particle trapping around the flow stagnation region. For the sake of comparison, the field frequency is further raised far above the DC limit. At the intermediate frequencies of 200 Hz-2 kHz, this trapping method fails to work, since the normal electric field component emanates from the conducting electrode surface. Besides, at high field frequencies (>3 kHz), particles can be once again effectively trapped at the electrode center, though with a compact (3 kHz) or disordered (10 kHz) 2D packing state on the electrode surface and mainly governed by the short-range negative DEP force field, resulting in requiring a much longer trapping time. To gain a better interpretation of the various particle behaviours observed in experiments, we develop a theoretical framework that takes into account both Maxwell-Wagner interfacial charge relaxation at the particle/electrolyte interface and the field-induced double-layer polarization at the electrode/electrolyte interface, and apply it to quantify the particle-particle electrokinetic interactions. With this simple geometrical configuration of a floating electrode, our results provide a new way to realize trapping of colloidal particles with a small buoyancy velocity under the combined action of ICEO flow and an attractive dipole-dipole interaction. PMID:26332897

  6. Measurement of homonuclear magnetic dipole-dipole interactions in multiple 1/2-spin systems using constant-time DQ-DRENAR NMR.

    PubMed

    Ren, Jinjun; Eckert, Hellmut

    2015-11-01

    A new pulse sequence entitled DQ-DRENAR (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. As described in the present manuscript, the efficiency and performance of this sequence can be significantly improved, if the measurement is done in the constant-time mode. We describe both the theoretical analysis of this method and its experimental validation of a number of crystalline model compounds, considering both symmetry-based and back-to-back (BABA) DQ-coherence excitation schemes. Based on the combination of theoretical analysis and experimental results we discuss the effect of experimental parameters such as the chemical shift anisotropy (CSA), the spinning rate, and the radio frequency field inhomogeneity upon its performance. Our results indicate that constant-time (CT-) DRENAR is a method of high efficiency and accuracy for compounds with multiple homonuclear spin systems with particular promise for the analysis of stronger-coupled and short T2 spin systems. PMID:26397219

  7. DQ-DRENAR with back-to-back (BABA) excitation: Measuring homonuclear dipole-dipole interactions in multiple spin-1/2 systems.

    PubMed

    Ren, Jinjun; Eckert, Hellmut

    2015-10-01

    A new pulse sequence entitled DQ-DRENAR, (Double-Quantum based Dipolar Recoupling Effects Nuclear Alignment Reduction) was recently described for the quantitative measurement of magnetic dipole-dipole interactions in homonuclear spin-1/2 systems involving multiple nuclei. The double quantum coherences were created via a windowless symmetry-based pulse sequence (POST-C7). The present contribution evaluates the performance of the "Back-to-Back" excitation pulse scheme BABA-xy16 in such DRENAR experiments. Using SIMPSON simulations, special attention is given to finite pulse length effects, dipolar truncation, and chemical shift anisotropy interference. Experimental results on model compounds demonstrate good stability up to long mixing times (>10ms) as well as high accuracy. As its dipolar coupling efficiency is relatively high (the dipolar coupling scaling factor is 4.24 times as high as that of POST-C7), DQ-DRENAR-BABA-xy16 is most appropriate for the measurement of relatively weak dipolar coupling strengths (<400Hz). Different from POST-C7, for which the spinning rate is limited to 1/7 of the nutation frequency, DQ-DRENAR-BABA-xy16 experiments can take full advantage of ultrafast MAS experiments. PMID:26483328

  8. 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…

  9. An isotopic mass effect on the intermolecular potential

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  10. 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.

  11. Electron paramagnetic resonance investigation of photosynthetic reaction centers from Rhodobacter sphaeroides R-26 in which Fe2+ was replaced by Cu2+. Determination of hyperfine interactions and exchange and dipole-dipole interactions between Cu2+ and QA-.

    PubMed Central

    Calvo, R; Passeggi, M C; Isaacson, R A; Okamura, M Y; Feher, G

    1990-01-01

    We report electron paramagnetic resonance (EPR) experiments in frozen solutions of unreduced and reduced photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides R-26 in which Fe2+ has been chemically replaced by the isotope 65Cu2+. Samples in which the primary quinone acceptor QA is unreduced (Cu2+QA:RCs) give a powder EPR spectrum typical for Cu2+ having axial symmetry, corresponding to a d(x2 - y2) ground state orbital, with g values g parallel = 2.314 +/- 0.001 and g perpendicular = 2.060 +/- 0.003. The spectrum shows a hyperfine structure for the nuclear spin of copper (65I = 3/2) with A parallel = (-167 +/- 1) x 10(-4) cm-1 and /A perpendicular/ = (16 +/- 2) x 10(-4) cm-1, and hyperfine couplings with three nitrogen ligands. This has been verified in samples containing the naturally occurring 14N isotope (l = 1), and in samples where the nitrogen ligands to copper were replaced by the isotope 15N (l = 1/2). We introduce a model for the electronic structure at the position of the metal ion which reflects the recently determined three-dimensional structure of the RCs of Rb. sphaeroides (Allen, J. P., G. Feher, T. O. Yeates, H. Komiya, and D. C. Rees. 1987. Proc. Natl. Acad. Sci. USA. 84:5730: Allen, J. P., G. Feher, T. O. Yeates, H. Komiya, and D. C. Rees. 1988. Proc. Natl. Acad. Sci. USA, 85:8487) as well as our EPR results. In this model the copper ion is octahedrally coordinated to three nitrogens from histidine residues and to one carboxylate oxygen from a glutamic acid, forming a distorted square in the plane of the d(x2 = y2) ground state orbital. It is also bound to a nitrogen of another histidine and to the other carboxylate oxygen of the same glutamic acid residue, in a direction approximately normal to this plane. The EPR spectrum changes drastically when the quinone acceptor QA is chemically reduced (Cu2+QA-:RCs); the change is due to the exchange and dipole-dipole interactions between the Cu2+ and QA- spins. A model spin Hamiltonian proposed for this exchange coupled cooper-quinone spin dimer accounts well for the observed spectra. From a comparison of the EPR spectra of the Cu2+QA:RC and CU2+QA-:RC complexes we obtain the values /J0/ = (0.30 +/- 0.02) K for the isotropic exchange coupling, and /d/ = (0.010 +/- 0.002) K for the projection of the dipole-dipole interaction tensor on the symmetry axis of the copper spin. From the EPR experiments only the relative signs of J0 and d can be deduced; it was determined that they have the same sign. The magnitude of the exchange coupling calculated for Cu2+QA-:RC is similar to that observed for the Fe2+QA-:RC complex (J0 = -0.43K). The exchange coupling is discussed in terms of the superexchange paths connecting the Cu2+ ion and the quinone radical using the structural data for the RCs of Rb. sphaeroides. From the value of the dipole-dipole interaction, d, we determined R approximately 8.4 A for the weighted distance between the metal ion and the quinone in reduced RCs, which is to be compared with 10 A obtained from x-ray analysis of unreduced RCs. This points to a shortening of the Cu2+ -QA- distance upon reduction of the quinone, as has been proposed by Allen et al. (1988). PMID:2166597

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

    NASA Astrophysics Data System (ADS)

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

    2013-08-01

    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)4] layers to form a solid of formula unit T(ImD)2[Ni(CN)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)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.

  13. Constraints on exotic dipole-dipole couplings between electrons at the micron scale

    NASA Astrophysics Data System (ADS)

    Kotler, Shlomi; Ozeri, Roee; Jackson Kimball, Derek

    2015-05-01

    Until recently, the magnetic dipole-dipole coupling between electrons had not been directly observed experimentally. This is because at the atomic scale dipole-dipole coupling is dominated by the exchange interaction and at larger distances the dipole-dipole coupling is overwhelmed by ambient magnetic field noise. In spite of these challenges, the magnetic dipole-dipole interaction between two electron spins separated by 2.4 microns was recently measured using the valence electrons of trapped Strontium ions [S. Kotler, N. Akerman, N. Navon, Y. Glickman, and R. Ozeri, Nature 510, 376 (2014)]. We have used this measurement to directly constrain exotic dipole-dipole interactions between electrons at the micron scale. For light bosons (mass 0.1 eV), we find that coupling constants describing pseudoscalar and axial-vector mediated interactions must be | gPegPe/4 ??c | <= 1 . 5 × 10-3 and | gAegAe/4 ??c | <= 1 . 2 × 10-17 , respectively, at the 90% confidence level. These bounds significantly improve on previous constraints in this mass range: for example, the constraints on axial-vector interactions are six orders of magnitude stronger than electron-positron constraints based on positronium spectroscopy. Supported by the National Science Foundation, I-Core: the Israeli excellence center, and the European Research Council.

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

    PubMed

    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. PMID:25871184

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

    SciTech Connect

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

    2013-08-15

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

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2006-01-01

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

  18. Dipole -dipole interaction between cold Rydberg atoms

    E-print Network

    Amsterdam, Universiteit van

    reported in this thesis was carried out at the group "Quantum Gases & Quantum Information", Van der Waals de graad van doctor aan de Universiteit van Amsterdam, op gezag van de Rector Magnificus prof. dr. D. Kouwenhoven dr. E. J. D. Vredenbregt prof. dr. M. S. Golden dr. T. W. Hijmans dr. R. J. C. Spreeuw Faculteit

  19. Higher-order dipole-polarizabilities and intermolecular interaction potential of P 4 clusters obtained from collision-induced light scattering measurements

    NASA Astrophysics Data System (ADS)

    Hohm, Uwe

    1999-09-01

    Collision-induced light scattering spectra of phosphorus vapour measured at 1000 K and density 132 mol m -3 are used to deduce a Lennard-Jones type (15-6) intermolecular interaction potential U( R), the dipole-quadrupole polarizability A, and dipole-octopole polarizability E of P 4 clusters. Using a recent experimental value of the dipole-dipole polarizability ?0=14.42×10 -30 m 3 at ?=514.5 nm, the experimentally recorded depolarized interaction-induced Raman spectra are best fitted with ?=4.4×10 -10 m, ?/ k=700 K, A=(6±2)×10 -40 m 4, and | E|=(127±17)×10 -50 m 5. The analysis is hampered by the existence of the ?3- ?2 vibrational combination band at 98 cm -1.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

    We investigate the exact dynamics of trace distance discord (TDD) 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 TDD 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 TDD. It is interesting to find that the freezing TDD 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 (EWL) states and investigate the differences between TDD and entanglement. The influences of initial state and the dipole-dipole coupling of the two qubits on the dynamics of nonclassical correlations are explored.

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

    PubMed

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

    2015-10-26

    Intermolecular S···O interactions are very common and are important in biological systems, but until recently, the presence of these contacts in protein-ligand systems largely depended on serendipitous discovery instead of rational design. Here we provide insight into the phenomenon of intermolecular S···O contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the S···O interactions and to determine their energy dependence on their geometric parameters. Protein Data Bank mining is performed to systematically determine the occurrence and geometry of intermolecular S···O interactions, and several representative examples are discussed. Three typical cases are investigated using a combined quantum mechanics/molecular mechanics approach to demonstrate the potential of these interactions in improving binding affinities and physiochemical properties. Overall, our work elucidates the structures and energy features of intermolecular S···O interactions and addresses their use in molecular design. PMID:26393532

  2. Spectral manifestation of intermolecular interaction in phthalimide and isatin dimers

    NASA Astrophysics Data System (ADS)

    Él'Kin, M. D.; Shal'Nova, T. A.; Smirnov, A. P.

    2010-03-01

    A theoretical analysis of vibrational spectra of phthalimide and isatin is carried out by the DFT/b3LYP method. The influence of intermolecular interaction in dimers of the compounds is estimated. It is shown that one can reliably interpret vibrational spectra of conjugated cyclic compounds, construct structural-dynamic models for dimers of such compounds, and predict a mechanism for intermolecular interaction based on nonempirical quantum calculations of the adiabatic potential.

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

    SciTech Connect

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

    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.

  4. 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.

  5. 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…

  6. Collision-induced spectroscopy with long-range intermolecular interactions: A diagrammatic representation and the invariant form of the induced properties

    SciTech Connect

    Kouzov, A. P.; Chrysos, M.; Rachet, F.; Egorova, N. I.

    2006-07-15

    Collision-induced properties of two interacting molecules a and b are derived by means of a general diagrammatic method involving M molecule-molecule and N photon-molecule couplings. The method is an extension of previous graphical treatments of nonlinear optics because it exhaustively determines interaction-induced polarization mechanisms in a trustworthy and handy fashion. Here we focus on long-range intermolecular interactions. Retardation effects are neglected. A fully quantum-mechanical treatment of the molecules is made whereas second quantization for the electromagnetic field, in the nonrelativistic approximation, is implicitly applied. The collision-induced absorption, Raman, and hyper-Raman processes are viewed and studied, through guiding examples, as specific cases N=1, 2, and 3, respectively. In Raman (N=2), the standard first-order (M=1) dipole-induced dipole term of the incremental polarizability, {delta}{alpha}, is the result of a coupling of the two photons with distinct molecules, a and b, which perturb each other via a dipole-dipole mechanism. Rather, when the two photons interact with the same molecule, a or b, the (N=2, M=1) graphs predict the occurrence of a nonlinear polarization mechanism. The latter is expected to contribute substantially to the collision-induced Raman bands by certain molecular gases.

  7. Studies of pilocarpine:carbomer intermolecular interactions.

    PubMed

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

    2012-05-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the ? bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5KF211CJ1).

  9. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

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

    2015-01-01

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

  10. Quantitative analysis of intermolecular interactions in orthorhombic rubrene.

    PubMed

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

    2015-09-01

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

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

    PubMed Central

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

    2015-01-01

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

  12. 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

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

    NASA Astrophysics Data System (ADS)

    Kannemann, Felix; Becke, Axel

    2010-03-01

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

  14. Constraints on Exotic Dipole-Dipole Couplings between Electrons at the Micrometer Scale.

    PubMed

    Kotler, Shlomi; Ozeri, Roee; Kimball, Derek F Jackson

    2015-08-21

    New constraints on exotic dipole-dipole interactions between electrons at the micrometer scale are established, based on a recent measurement of the magnetic interaction between two trapped 88Sr(+) ions. For light bosons (mass?0.1??eV) we obtain a 90% confidence interval for an axial-vector-mediated interaction strength of |g(A)(e)g(A)(e)/4??c|?1.2×10(-17). Assuming CPT invariance, this constraint is compared to that on anomalous electron-positron interactions, derived from positronium hyperfine spectroscopy. We find that the electron-electron constraint is 6 orders of magnitude more stringent than the electron-positron counterpart. Bounds on pseudoscalar-mediated interaction as well as on torsion gravity are also derived and compared with previous work performed at different length scales. Our constraints benefit from the high controllability of the experimental system which contained only two trapped particles. It therefore suggests a useful new platform for exotic particle searches, complementing other experimental efforts. PMID:26340180

  15. Constraints on Exotic Dipole-Dipole Couplings between Electrons at the Micrometer Scale

    NASA Astrophysics Data System (ADS)

    Kotler, Shlomi; Ozeri, Roee; Kimball, Derek F. Jackson

    2015-08-01

    New constraints on exotic dipole-dipole interactions between electrons at the micrometer scale are established, based on a recent measurement of the magnetic interaction between two trapped 88Sr+ ions. For light bosons (mass?0.1 eV ) we obtain a 90% confidence interval for an axial-vector-mediated interaction strength of |gAegAe/4 ? ?c | ?1.2 ×10-17 . Assuming C P T invariance, this constraint is compared to that on anomalous electron-positron interactions, derived from positronium hyperfine spectroscopy. We find that the electron-electron constraint is 6 orders of magnitude more stringent than the electron-positron counterpart. Bounds on pseudoscalar-mediated interaction as well as on torsion gravity are also derived and compared with previous work performed at different length scales. Our constraints benefit from the high controllability of the experimental system which contained only two trapped particles. It therefore suggests a useful new platform for exotic particle searches, complementing other experimental efforts.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    E-print Network

    2013-07-10

    Jul 10, 2013 ... PHYSICAL REVIEW A 88, 013616 (2013). Effective ... role both in today's technology and in fundamental physical theories. Technological examples are aplenty in the magneto- electronic industries, e.g., hard disks or magnetic sensors. One ..... Magnetostriction causes the dipolar BEC to expand along the.

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

    PubMed

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

    2016-01-01

    The recent ?-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. © 2015 Wiley Periodicals, Inc. PMID:26010349

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

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

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

    SciTech Connect

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

    1993-07-01

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

  1. 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)....

  2. Electric dipole polarizabilities and C6 dipole-dipole dispersion coefficients for sodium clusters and C60.

    PubMed

    Jiemchooroj, Auayporn; Norman, Patrick; Sernelius, Bo E

    2006-09-28

    The frequency-dependent polarizabilities of closed-shell sodium clusters containing up to 20 atoms have been calculated using the linear complex polarization propagator approach in conjunction with Hartree-Fock and Kohn-Sham density functional theories. In combination with polarizabilities for C(60) from a previous work [J. Chem. Phys. 123, 124312 (2005)], the C(6) dipole-dipole dispersion coefficients for the metal-cluster-to-cluster and cluster-to-buckminster-fullerene interactions are obtained via the Casimir-Polder relation [Phys. Rev. 73, 360 (1948)]. The B3PW91 results for the polarizability of the sodium dimer and tetramer are benchmarked against coupled cluster calculations. The error bars of the reported theoretical results for the C(6) coefficients are estimated to be 5%, and the results are well within the error bars of the experiment. PMID:17014173

  3. Electric dipole polarizabilities and C6 dipole-dipole dispersion coefficients for sodium clusters and C60

    NASA Astrophysics Data System (ADS)

    Jiemchooroj, Auayporn; Norman, Patrick; Sernelius, Bo E.

    2006-09-01

    The frequency-dependent polarizabilities of closed-shell sodium clusters containing up to 20 atoms have been calculated using the linear complex polarization propagator approach in conjunction with Hartree-Fock and Kohn-Sham density functional theories. In combination with polarizabilities for C60 from a previous work [J. Chem. Phys. 123, 124312 (2005)], the C6 dipole-dipole dispersion coefficients for the metal-cluster-to-cluster and cluster-to-buckminster-fullerene interactions are obtained via the Casimir-Polder relation [Phys. Rev. 73, 360 (1948)]. The B3PW91 results for the polarizability of the sodium dimer and tetramer are benchmarked against coupled cluster calculations. The error bars of the reported theoretical results for the C6 coefficients are estimated to be 5%, and the results are well within the error bars of the experiment.

  4. Influence of silver nanoparticles on relaxation processes and efficiency of dipoledipole energy transfer between dye molecules in polymethylmethacrylate films

    NASA Astrophysics Data System (ADS)

    Bryukhanov, V. V.; Konstantinova, E. I.; Borkunov, R. Yu; Tsarkov, M. V.; Slezhkin, V. A.

    2015-10-01

    The fluorescence and phosphorescence of dyes in thin polymethylmethacrylate (PMMA) films in the presence of ablated silver nanoparticles has been investigated in a wide temperature range by methods of femtosecond and picosecond laser photoexcitation. The fluorescence and phosphorescence times, as well as spectral and kinetic characteristics of rhodamine 6G (R6G) molecules in PMMA films are measured in a temperature range of 80 – 330 K. The temperature quenching activation energy of the fluorescence of R6G molecules in the presence of ablated silver nanoparticles is found. The vibrational relaxation rate of R6G in PMMA films is estimated, the efficiency of the dipoledipole electron energy transfer between R6G and brilliant green molecules (enhanced by plasmonic interaction with ablated silver nanoparticles) is analysed, and the constants of this energy transfer are determined.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  6. Remarks on the static dipole-dipole potential at large distances

    NASA Astrophysics Data System (ADS)

    Giordano, Matteo; Meggiolaro, Enrico

    2015-11-01

    We determine the large-distance behavior of the static dipole-dipole potential for a wide class of gauge theories on nonperturbative grounds, exploiting only general properties of the theory. In the case of QCD, we recover the known results in the regime of small dipole sizes and discuss recent nonperturbative calculations. Moreover, we discuss the case of pure-gauge theories and compare our prediction with the available lattice results.

  7. Isomerization and intermolecular solutesolvent interactions of ethyl isocyanate: Ultrafast infrared vibrational echoes and linear

    E-print Network

    Fayer, Michael D.

    Isomerization and intermolecular solute­solvent interactions of ethyl isocyanate: Ultrafast induced gauche­trans isomerization and direct solute­solvent interactions of the solute, ethyl isocyanate isomerization. To describe the observations, a model is presented that involves both intramolecular dynamics

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

    PubMed Central

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

    2013-01-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  10. Direction-dependent Intermolecular Interactions: Catechol on TiO2(110)-11

    E-print Network

    Diebold, Ulrike

    Direction-dependent Intermolecular Interactions: Catechol on TiO2(110)-1×1 Shao-Chun Li and Ulrike of a submonolayer of catechol (C6H6O2) on the rutile TiO2(110)-1×1 surface has been investigated by Scanning Tunneling Microscopy (STM). The catechol molecules are preferentially adsorbed on the surface 5-fold

  11. Dipole, dipole-quadrupole, and dipole-octopole polarizability of adamantane, C10H16, from refractive index measurements, depolarized collision-induced light scattering, conventional ab initio and density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Maroulis, G.; Xenides, D.; Hohm, U.; Loose, A.

    2001-11-01

    Refractive index (RI) measurements, depolarized collision-induced light (CILS) scattering and ab initio quantum chemical calculations are used to determine the dipole (?), dipole-quadrupole (A), and dipole-octopole polarizability (E) of adamantane, C10H16. For this molecule of symmetry group Td the three polarizabilities can be represented by a single scalar quantity. From experiment we obtain for the static dipole polarizability at T?400-500 K 107.5±1.1 e2a02Eh-1, and for the higher polarizabilities |A|=102.0±7.8 e2a03Eh-1, and |E|=720±80 e2a04Eh-1. We have performed conventional ab initio and density functional theory calculations with specifically designed basis sets. A very large [4s3p3d1f/3s2p1d] basis set consisting of 574 basis functions is thought to provide near-Hartree-Fock values for ?,A and E: ?=101.72 e2a02Eh-1, A=-6.5 e2a03Eh-1, and E=-71.0 e2a04Eh-1. Our final theoretical estimates for these properties are ?=107.5±1.0 e2a02Eh-1, A=-8.0±1.5 e2a03Eh-1, and E=-76.5±5.5 e2a04Eh-1. Very strong electron correlation effects are found for both the first (?) and second (?) hyperpolarizability. Our estimate for ???xyz and the mean ?¯ are 41.4±5.6 e3a03Eh-2 and (25±2)×103 e4a04Eh-3, respectively. For the octopole and hexadecapole moments we propose ?=-4.4±0.2 ea03 and ?=-100.8±5.5 ea04. The basis sets constructed in this work should provide reliable computational tools for the study of intermolecular interactions of adamantane.

  12. Ab initio investigation of intermolecular interactions in solid benzene

    E-print Network

    O. Bludsky; M. Rubes; P. Soldan

    2008-01-04

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

  13. Cation-? interactions: accurate intermolecular potential from symmetry-adapted perturbation theory.

    PubMed

    Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd

    2013-09-01

    Symmetry-adapted perturbation theory (SAPT) is used to decompose the total intermolecular interaction energy between the ammonium cation and a benzene molecule into four physically motivated individual contributions: electrostatics, exchange, dispersion, and induction. Based on this rigorous decomposition, it is shown unambiguously that both the electrostatic and the induction energy components contribute almost equally to the attractive forces stabilizing the dimer with a nonnegligible contribution coming from the dispersion term. A polarizable potential model for the interaction of ammonium cation with benzene is parametrized by fitting these four energy components separately using the functional forms of the AMOEBA force field augmented with the missing charge penetration energy term calculated as a sum over pairwise electrostatic energies between spherical atoms. It is shown that the proposed model is able to produce accurate intermolecular interaction energies as compared to ab initio results, thus avoiding error compensation to a large extent. PMID:23924321

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

    SciTech Connect

    Han, Heekyung; Wardlaw, David M.; Frolov, Alexei M.

    2014-05-28

    We examine the effect of decoherence and intermolecular interactions (chiral discrimination energies) on the chiral stability and the distinguishability of initially pure versus mixed states in an open chiral system. Under a two-level approximation for a system, intermolecular interactions are introduced by a mean-field theory, and interaction between a system and an environment is modeled by a continuous measurement of a population difference between the two chiral states. The resultant equations are explored for various parameters, with emphasis on the combined effects of the initial condition of the system, the chiral discrimination energies, and the decoherence in determining: the distinguishability as measured by a population difference between the initially pure and mixed states, and the decoherence process; the chiral stability as measured by the purity decay; and the stationary state of the system at times long relative to the time scales of the system dynamics and of the environmental effects.

  15. Mass Spectrometry Tools for Analysis of Intermolecular Interactions

    PubMed Central

    Auclair, Jared R.; Somasundaran, Mohan; Green, Karin M.; Evans, James E.; Schiffer, Celia A.; Ringe, Dagmar; Petsko, Gregory A.; Agar, Jeffrey N.

    2015-01-01

    The small quantities of protein required for mass spectrometry (MS) make it a powerful tool to detect binding (protein–protein, protein–small molecule, etc.) of proteins that are difficult to express in large quantities, as is the case for many intrinsically disordered proteins. Chemical cross-linking, proteolysis, and MS analysis, combined, are a powerful tool for the identification of binding domains. Here, we present a traditional approach to determine protein–protein interaction binding sites using heavy water (18O) as a label. This technique is relatively inexpensive and can be performed on any mass spectrometer without specialized software. PMID:22821539

  16. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    SciTech Connect

    Alocci, Davide; Bernini, Andrea; Niccolai, Neri; SienaBioGrafix Srl, via A. Fiorentina 1, 53100 Siena

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  18. Revealing Intermolecular Interaction and Surface Restructuring of an Aromatic Thiol Assembling on Au(111) by Tip-Enhanced Raman Spectroscopy.

    PubMed

    Wang, Xiang; Zhong, Jin-Hui; Zhang, Meng; Liu, Zheng; Wu, De-Yin; Ren, Bin

    2016-01-01

    Controlling the packing structure and revealing the intermolecular interaction of self-assembled monolayers (SAMs) on solid surfaces are crucial for manipulating its properties. We utilized tip-enhanced Raman spectroscopy (TERS) to address the challenge in probing the subtle change of the intermolecular interaction during the assembly of a pyridine-terminated aromatic thiol on the single crystal Au(111) surface that cannot produce enhanced Raman signal, together with electrochemical methods to study the charge transfer properties of SAM. We observed that the aromatic C?C bond stretching vibration can be a marker to monitor the strength of the intermolecular interaction of SAMs, because this Raman peak is very sensitive to the intermolecular ?-? stacking. Our results indicate that the SAM experiences a surface restructuring after the formation of a densely packed monolayer. We propose that the intermolecular electrostatic repulsion governs the restructuring when the packing density is high. The correlated TERS and electrochemical studies also suggest that the intermolecular interaction may have some impact on the charge transfer properties of SAM. This study provides a molecular-level insight into understanding and exploiting the intermolecular interactions toward better control over the assembling process and tuning the electrical properties of aromatic thiols. PMID:26633597

  19. Critical examination of the supermolecule density functional theory calculations of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Cybulski, S?awomir M.; Seversen, Christopher E.

    2005-01-01

    The results of calculations employing twelve different combinations of exchange and correlation functionals are compared with results of ab initio calculations for two different configurations of the water dimer and three different configurations of the thymine-adenine complex. None of the density functional theory (DFT) treatments could properly reproduce the results of coupled-cluster calculations for all configurations examined. The DFT approaches perform well when the interaction energy is dominated by the electrostatic component and the dispersion energy is less important. Two mechanisms that compensate for the missing dispersion component were identified. The first one is the decrease of the magnitude of the intermolecular exchange-repulsion and the second one is the increase of the magnitude of the attractive deformation energy. For some functionals both effects are observed together, but for some other ones only the second effect occurs. The three correlation functionals that were examined were found to make only very small contributions to the deformation energy. The examination of angular and distance dependence of the interactions shows that the currently available DFT approaches are not suitable for developing intermolecular potential energy surfaces. They could however be used to find global minima on potential energy surfaces governed by intermolecular electrostatic interactions. Additional single point ab initio calculations are recommended as the means of validating optimized structures.

  20. 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.

  1. Competition between intermolecular and substrate interactions in a multicomponent lattice gas model

    NASA Astrophysics Data System (ADS)

    Liu, Qiang; Weeks, John

    2008-03-01

    Recent experiments have shown that acridine-9-carboxylic acid (ACA) molecules form a dense phase consisting of chain-like structures on Ag(111) with alternating orientations along the chain direction that permit the formation of strong hydrogen bonds. Despite the anisotropy in intermolecular interactions that leads to chain formation, molecular boundaries along and normal to the chair direction have very similar thermodynamic properties and fluctuations. We introduce a multicomponent lattice gas model where molecules with different orientations are treated as different species with different intermolecular interactions as well as different interactions with the substrate. This a generalization of the familiar Blume-Emery-Griffiths model of a binary lattice gas but in a region of parameter space not usually explored. We argue that the novel domain shapes, boundary fluctuations and phase densities seen in experiment arise from a competition between favorable anisotropic pair interactions in the chain phase and less favorable substrate interactions due to the different orientations. Detailed results of Monte Carlo simulations of this model and analytic work using mean field and pair approximation theories will be presented.

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

    PubMed

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

    2015-10-01

    The recognition properties of heteroditopic hemicryptophane hosts towards anions, cations, and neutral pairs, combining both cation-? and anion-? interaction sites, were investigated to probe the complexity of interfering weak intermolecular interactions. It is suggested from NMR experiments, and supported by CASSCF/CASPT2 calculations, that the binding constants of anions can be modulated by a factor of up to 100 by varying the fluorination sites on the electron-poor aromatic rings. Interestingly, this subtle chemical modification can also reverse the sign of cooperativity in ion-pair recognition. Wavefunction calculations highlight how short- and long-range interactions interfere in this recognition process, suggesting that a disruption of anion-? interactions can occur in the presence of a co-bound cation. Such molecules can be viewed as prototypes for examining complex processes controlled by the competition of weak interactions. PMID:26401973

  3. Intermolecular Tl···H-C anagostic interactions in luminescent pyridyl functionalized thallium(I) dithiocarbamates.

    PubMed

    Kumar, Vinod; Singh, Vikram; Gupta, Ajit N; Drew, Michael G B; Singh, Nanhai

    2015-01-28

    Crystal structures of novel pyridyl functionalised [Tl(L)]? (L = (N-benzyl-N-methylpyridyl) dithiocarbamate(L1) 1, bis(N-methylpyridyl) dithiocarbamate(L2) 2, (N-methyl(1,4-benzodioxane-6-yl)-N-methylpyridyl)dithiocarbamate(L3) 3, (N-ferrocenyl-N-methylpyridyl) dithiocarbamate(L4) 4) complexes revealed rare intermolecular C-H···Tl anagostic and C-S···Tl interactions forming a six-membered chelate ring about the metal center, which have been assessed by DFT calculations. The strong thallophilic bonding is responsible for the strong luminescent characteristics of the complexes in the solid phase. PMID:25461980

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

    PubMed

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

    2015-12-01

    Vibrational circular dichroism spectra (VCD) in the mid-IR region and electronic circular dichroism (ECD) spectra for three carnitine derivatives in the form of hydrochloride salts were recorded in deuterated methanol solutions. Density Functional Theory calculations help one to understand the significance of the observed VCD bands. VCD and ECD spectra are informative about the absolute configuration of the molecule, but VCD data reveal also some conformational aspects in the N,N,N-trimethyl moiety and inform us about intermolecular interactions gained from the carbonyl stretching region for the acyl substituted carnitines. Chirality 27:907-913, 2015. © 2015 Wiley Periodicals, Inc. PMID:26447810

  5. Improving intermolecular interactions in DFTB3 using extended polarization from chemical-potential equalization.

    PubMed

    Christensen, Anders S; Elstner, Marcus; Cui, Qiang

    2015-08-28

    Semi-empirical quantum mechanical methods traditionally expand the electron density in a minimal, valence-only electron basis set. The minimal-basis approximation causes molecular polarization to be underestimated, and hence intermolecular interaction energies are also underestimated, especially for intermolecular interactions involving charged species. In this work, the third-order self-consistent charge density functional tight-binding method (DFTB3) is augmented with an auxiliary response density using the chemical-potential equalization (CPE) method and an empirical dispersion correction (D3). The parameters in the CPE and D3 models are fitted to high-level CCSD(T) reference interaction energies for a broad range of chemical species, as well as dipole moments calculated at the DFT level; the impact of including polarizabilities of molecules in the parameterization is also considered. Parameters for the elements H, C, N, O, and S are presented. The Root Mean Square Deviation (RMSD) interaction energy is improved from 6.07 kcal/mol to 1.49 kcal/mol for interactions with one charged species, whereas the RMSD is improved from 5.60 kcal/mol to 1.73 for a set of 9 salt bridges, compared to uncorrected DFTB3. For large water clusters and complexes that are dominated by dispersion interactions, the already satisfactory performance of the DFTB3-D3 model is retained; polarizabilities of neutral molecules are also notably improved. Overall, the CPE extension of DFTB3-D3 provides a more balanced description of different types of non-covalent interactions than Neglect of Diatomic Differential Overlap type of semi-empirical methods (e.g., PM6-D3H4) and PBE-D3 with modest basis sets. PMID:26328834

  6. Characterizing and circumventing intermolecular electrostatic interactions in highly electro-optic polymers

    SciTech Connect

    Harper, A.W.; Zhu, J.; He, M.; Dalton, L.R.; Garner, S.M.; Steier, W.H.

    1998-07-01

    In general, polymers possessing non-resonant electro-optic activities exceeding 20 pm/V require chromophores with strong electron withdrawing groups (cyanovinyls, carbon acid moieties, etc.) as well as highly polarizable bridges. Although much progress has been made on designing and preparing materials with molecular electro-optic activities, their incorporation into polymers to show comparable large bulk electro-optic activities has been met with little success. The authors report here the nature of the difficulty of the translation of microscopic to macroscopic electro-optic activity. The optimization of molecular activity increases intermolecular electrostatic interactions between chromophores, and these interactions impede induction of polar ascentric order in the polymers. Theoretical analysis of the problem is presented, as well as one example of a material that is designed to circumvent these interactions. The resulting material possesses electro-optic coefficients as high as 29 pm/V and optical losses as low as 1.5 dB/cm.

  7. Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines.

    PubMed

    Dou, Wei-Dong; Huang, Shu-Ping; Lee, Chun-Sing

    2015-10-01

    Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure ?-? interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc and CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface. PMID:26450327

  8. Interfacial and intermolecular interactions determining the rotational orientation of C60 adsorbed on Au(111)

    NASA Astrophysics Data System (ADS)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

    Close-packed monolayers of fullerenes on metallic substrates are very rich systems with respect to their rotational degrees of freedom and possible interactions with different adsorption sites or next neighbours. In this connection, we report in detail on the (2?3 × 2?3)R30°-superstructure of C60 with respect to the Au(111)-surface. We use molecular orbital imaging in systematic UHV-STM studies to reveal the delicate balance of interfacial and intermolecular interactions in this system. Thus, bright C60-molecules in 5:6-top and 6:6-top geometries are observed depending on the respective next neighbours. Moreover, tiny changes in the appearance of the unoccupied molecular orbitals of dim C60-molecules in hex-vac positions are identified which are caused by the respective interaction with the facets surrounding the Au-vacancy.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    SciTech Connect

    Giordano, Matteo; Meggiolaro, Enrico

    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.

  11. A Colloidal Description of Intermolecular Interactions Driving Fibril-Fibril Aggregation of a Model Amphiphilic Peptide.

    PubMed

    Owczarz, Marta; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

    2015-07-14

    We apply a kinetic analysis platform to study the intermolecular interactions underlying the colloidal stability of dispersions of charged amyloid fibrils consisting of a model amphiphilic peptide (RADA 16-I). In contrast to the aggregation mechanisms observed in the large majority of proteins and peptides, where several elementary reactions involving both monomers and fibrils are present simultaneously, the system selected in this work allows the specific investigation of the fibril-fibril aggregation process. We examine the intermolecular interactions driving the aggregation reaction at pH 2.0 by changing the buffer composition in terms of salt concentration, type of ion as well as type and concentration of organic solvent. The aggregation kinetics are followed by dynamic light scattering, and the experimental data are simulated by Smoluchowski population balance equations, which allow to estimate the energy barrier between two colliding fibrils in terms of the Fuchs stability ratio (W). When normalized on a dimensionless time weighted on the Fuchs stability ratio, the aggregation profiles under a broad range of conditions collapse on a single master curve, indicating that the buffer composition modifies the aggregation kinetics without affecting the aggregation mechanism. Our results show that the aggregation process does not occur under diffusion-limited conditions. Rather, the reaction rate is limited by the presence of an activation energy barrier that is largely dominated by electrostatic repulsive interactions. Such interactions could be reduced by increasing the concentration of salt, which induces charge screening, or the concentration of organic solvent, which affects the dielectric constant. It is remarkable that the dependence of the activation energy on the ionic strength can be described quantitatively in terms of charge screening effects in the frame of the DLVO theory, although specific anion and cation effects are also observed. While anion effects are mainly related to the binding to the positive groups of the fibril surface and to the resulting decrease of the surface charge, cation effects are more complex and involve additional solvation forces. PMID:26125620

  12. Solvent scales used to study the intermolecular interactions in binary solutions of two p-aryl-pyridazinium methylids.

    PubMed

    Babusca, Daniela; Dorohoi, Dana Ortansa

    2016-01-01

    The visible electronic absorption band with intramolecular charge transfer of two pyridazinium ylids having common carbanion and different heterocycles is recorded in solutions and its position is correlated to parameters of some empirical scales of solvents. The nature of the intermolecular interactions in pyridazinium ylid solutions is discussed and the supply of each type of interaction is established based on solvatochromic study. PMID:26208269

  13. Generalized Intermolecular Interaction Tensor Applied to Long-Range Interactions in Hydrogen and Coinage Metal (Cu, Ag, and Au) Clusters.

    PubMed

    Hatz, Richard; Korpinen, Markus; Hänninen, Vesa; Halonen, Lauri

    2015-12-01

    We present a novel formulation for the intermolecular interaction tensor, which is used to describe the long-range electrostatic, induction, and dispersion interactions. Our formulation is based on concepts drawn from combinatorial analysis and Clifford calculus and enables us to present the interaction tensor in a form that is simple to use and suitable for both numerical and symbolic analyses. We apply the derived formulas to calculate the long-range interaction coefficients in hydrogen and coinage metal (Cu, Ag, and Au) clusters. The electronic structure calculations are performed at the CCSD(T) level, with triple-? and quadruple-? basis sets. The multipole moments and dispersion coefficients are obtained as fits to the derived interaction formulas. The most important interaction parameters are obtained accurately and are in good agreement with other results. PMID:26501212

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

    NASA Astrophysics Data System (ADS)

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-01

    Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N6) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N5) computational cost.

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

    NASA Astrophysics Data System (ADS)

    Kröger, Ingo; Stadtmüller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-01

    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.

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

    SciTech Connect

    Yogesha, S.D.; SHarff, A.; Bricogne, G.; Izard, .T.

    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.

  17. Structural aspects of two ?-dihydrazones displaying a complete survey of intermolecular interactions.

    PubMed

    Bustos, Carlos; Alvarez-Thon, Luis; Baggio, Ricardo

    2015-12-01

    The compounds (2'E,2'E)-2,2'-(propane-1,2-diylidene)bis[1-(2-nitrophenyl)hydrazine], C15H14N6O4, (I), and (2Z,3Z)-ethyl 3-[2-(2-nitrophenyl)hydrazinylidene]-2-[2-(4-nitrophenyl)hydrazinylidene]butanoate tetrahydrofuran hemisolvate, C18H18N6O6·0.5C4H8O, (II), are puzzling outliers deviating from a general synthetic route aimed at the preparation of substituted pyrazoles. Possible reasons for this outcome, which is exceptional in an otherwise firmly established synthetic procedure, are analyzed. Compound (I) is unsolvated, while compound (II) crystallizes with a tetrahydrofuran solvent molecule lying on an inversion centre. The ethoxycarbonyl chain of (II), in turn, appears disordered into two equally populated (50%) moieties. In both structures, a plethora of different commonly occurring weak intermolecular interactions [viz. ?(phenyl)...?(phenyl), ?(C=N)...?(C=N), ?(phenyl)...?(C=N), N-H...O and C-H...O] appear responsible for the crystal stability. Much less common are the short O(nitro)...O(nitro) contacts which are observed in the structure of (I), an example of unusual `electron donor-acceptor' (EDA) interactions. PMID:26632840

  18. Vibrational dynamics, intermolecular interactions, and compound formation in GeH4-H2 under pressure

    NASA Astrophysics Data System (ADS)

    Strobel, Timothy A.; Chen, Xiao-Jia; Somayazulu, Maddury; Hemley, Russell J.

    2010-10-01

    Optical microscopy, spectroscopic and x-ray diffraction studies at high-pressure are used to investigate intermolecular interactions in binary mixtures of germane (GeH4)+hydrogen (H2). The measurements reveal the formation of a new molecular compound, with the approximate stoichiometry GeH4(H2)2, when the constituents are compressed above 7.5 GPa. Raman and infrared spectroscopic measurements show multiple H2 vibrons substantially softened from bulk solid hydrogen. With increasing pressure, the frequencies of several Raman and infrared H2 vibrons decrease, indicating anomalous attractive interaction for closed-shell, nonpolar molecules. Synchrotron powder x-ray diffraction measurements show that the compound has a structure based on face-centered cubic (fcc) with GeH4 molecules occupying fcc sites and H2 molecules likely distributed between Oh and Td sites. Above ca. 17 GPa, GeH4 molecules in the compound become unstable with respect to decomposition products (Ge+H2), however, the compound can be preserved metastably to ca. 27 GPa for time-scales of the order of several hours.

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

    PubMed

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

    2014-09-01

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

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

    SciTech Connect

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

    2013-11-21

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

  1. Vibrational dynamics, intermolecular interactions, and compound formation in GeH4–H2 under pressure

    SciTech Connect

    Strobel, Timothy A.; Chen, Xiao-Jia; Somayazulu, Maddury; Hemley, Russell J.

    2010-01-01

    Optical microscopy, spectroscopic and x-ray diffraction studies at high-pressure are used to investigate intermolecular interactions in binary mixtures of germane (GeH{sub 4} )+hydrogen (H{sub 2} ) . The measurements reveal the formation of a new molecular compound, with the approximate stoichiometry GeH{sub 4} (H{sub 2} ){sub 2} , when the constituents are compressed above 7.5 GPa. Raman and infrared spectroscopic measurements show multiple H{sub 2} vibrons substantially softened from bulk solid hydrogen. With increasing pressure, the frequencies of several Raman and infrared H{sub 2} vibrons decrease, indicating anomalous attractive interaction for closed-shell, nonpolar molecules. Synchrotron powder x-ray diffraction measurements show that the compound has a structure based on face-centered cubic (fcc) with GeH{sub 4} molecules occupying fcc sites and H{sub 2} molecules likely distributed between O{sub h} and T{sub d} sites. Above ca. 17 GPa, GeH{sub 4} molecules in the compound become unstable with respect to decomposition products (Ge+H{sub 2} ) , however, the compound can be preserved metastably to ca. 27 GPa for time-scales of the order of several hours.

  2. Cyano-Functionalized Triarylamines on Coinage Metal Surfaces: Interplay of Intermolecular and Molecule-Substrate Interactions.

    PubMed

    Müller, Kathrin; Moreno-López, Juan Carlos; Gottardi, Stefano; Meinhardt, Ute; Yildirim, Handan; Kara, Abdelkader; Kivala, Milan; Stöhr, Meike

    2016-01-11

    The self-assembly of cyano-functionalized triarylamine derivatives on Cu(111), Ag(111) and Au(111) was studied by means of scanning tunnelling microscopy, low-energy electron diffraction, X-ray photoelectron spectroscopy and density functional theory calculations. Different bonding motifs, such as antiparallel dipolar coupling, hydrogen bonding and metal coordination, were observed. Whereas on Ag(111) only one hexagonally close-packed pattern stabilized by hydrogen bonding is observed, on Au(111) two different partially porous phases are present at submonolayer coverage, stabilized by dipolar coupling, hydrogen bonding and metal coordination. In contrast to the self-assembly on Ag(111) and Au(111), for which large islands are formed, on Cu(111), only small patches of hexagonally close-packed networks stabilized by metal coordination and areas of disordered molecules are found. The significant variety in the molecular self-assembly of the cyano-functionalized triarylamine derivatives on these coinage metal surfaces is explained by differences in molecular mobility and the subtle interplay between intermolecular and molecule-substrate interactions. PMID:26636437

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

    SciTech Connect

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

    2012-02-07

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

  4. 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.

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

    SciTech Connect

    Azar, Richard Julian Head-Gordon, Martin

    2015-05-28

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

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

    PubMed

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

    2015-07-15

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

  7. 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...

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

    SciTech Connect

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

    2014-08-14

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

  9. Intermolecular interactions in aqueous solutions of gallic acid at 296-306 K according to spectrofluorimetry and densimetry data

    NASA Astrophysics Data System (ADS)

    Grigoryan, K. R.; Sargsyan, L. S.

    2015-12-01

    Features of intermolecular interactions in aqueous solutions of gallic acid (GA) are studied by means of densimetry and fluorescence spectroscopy (intrinsic fluorescence, 2D spectra, and excitation/ emission matrix fluorescence spectra, 3D) at 296.15, 301.15, and 306.15 K in the concentration range of 5.88 × 10-4-5.88 × 10-2 mol L-1. It is shown by analyzing the concentration and temperature dependences of the apparent molar volumes and fluorescence parameters of GA that the equilibrium between nonassociated and associated species in the solution and the hydration of these species undergo changes.

  10. Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions.

    PubMed

    Ch?ci?ska, Lilianna; Grabowsky, Simon; Ma?ecka, Magdalena; Rybarczyk-Pirek, Agnieszka J; Jó?wiak, Andrzej; Paulmann, Carsten; Luger, Peter

    2011-12-01

    A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C-H···C(?), C,N(?)···C,N(?) and H···H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment. PMID:22101546

  11. The effects of intra- and inter-molecular interactions on the photophysics of platinum(II) complexes

    NASA Astrophysics Data System (ADS)

    Hight, Lauren M.

    Square planar platinum(II) complexes have been the subject of intense study for several years due to their many unique properties and potential applications. Exploiting the emission of these complexes allows for a wide range of applications as spectroscopic probes and anticancer reagents. Manipulation of both intra-molecular and inter-molecular interactions allows one to tune the photophysical properties of compounds with great precision. Chapter one of this thesis will introduce the critical role of platinum(II) in medicinal chemistry and basic photophysics of platinum(II) complexes. Chapter two describes the synthesis and studies of a series of novel expanded framework polypyridine platinum(II) complexes that employ a little-explored method of intra-molecular modification. The majority of the compounds exhibit improved photophysics over the parent compound [Pt(trpy)Cl]+. Chapter three summarizes a body of work conducted by McMillin group members over the past several years and describes the synthesis and characterization of the missing members of the series. These complexes involving 4'-substituted trpy ligands, exhibit very impressive photophysics and utilize a well-recognized approach to intra-molecular modification. Chapter four describes the solid state photophysical properties of compounds synthesized by the Lu group. These compounds provide excellent examples of classic intermolecular interaction in Pt(II) compounds and MMLCT emission.

  12. Formation of intermolecular crosslinks by the actinocin derivatives with DNA in interaction under conditions of semidilute solution

    NASA Astrophysics Data System (ADS)

    Osinnikova, D. N.; Moroshkina, E. B.

    2014-12-01

    Interaction of native calf thymus DNA (ctDNA) with the actinocin derivatives containing protonated diethylamino groups, dimethylamino groups and unsubstituted amino groups and having different length of the alkyl chain have been studied by the method of viscometry. An anomalous hydrodynamic behavior of solutions of DNA with very low amount of ligands prepared under conditions of semidilute solution was revealed. We assumed that such an anomalous behavior of solutions of DNA complexes with actinocin derivatives associated with the formation of intermolecular crosslinks while the preparation of the complex was in terms of overlapping of macromolecular coils in solution. Comparative study of the hydrodynamic behavior of the DNA complexes with various actinocin structures lead us to the conclusion of the formation of crosslinks by the compounds containing protonated diethylamino groups.

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

    PubMed Central

    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

  14. 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

  15. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    SciTech Connect

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

    1988-10-26

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

  18. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    NASA Astrophysics Data System (ADS)

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

  19. Au nanoparticle scaffolds modulating intermolecular interactions among the conjugated azobenzenes chemisorbed on curved surfaces: tuning the kinetics of cis-trans isomerisation

    NASA Astrophysics Data System (ADS)

    Raimondo, Corinna; Kenens, Bart; Reinders, Federica; Mayor, Marcel; Uji-I, Hiroshi; Samorì, Paolo

    2015-08-01

    ?-? Intermolecular interactions among adjacent conjugated azobenzenes chemisorbed on (non-)flat Au surfaces can be tuned by varying the curvature of the Au nanoparticles. Here we show that such interactions rule the thermal cis-trans isomerization kinetics, towards a better control on the azobenzene bistability for its optimal integration as a responsive material.?-? Intermolecular interactions among adjacent conjugated azobenzenes chemisorbed on (non-)flat Au surfaces can be tuned by varying the curvature of the Au nanoparticles. Here we show that such interactions rule the thermal cis-trans isomerization kinetics, towards a better control on the azobenzene bistability for its optimal integration as a responsive material. Electronic supplementary information (ESI) available: Physico-chemical characterization of the different sizes of nanoparticles, UV-Vis, Surface Enhanced Raman Spectroscopy (SERS), materials and methods. See DOI: 10.1039/c5nr03688g

  20. 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

  1. The role of intermolecular interactions in the prediction of the phase equilibria of carbon dioxide hydrates.

    PubMed

    Costandy, Joseph; Michalis, Vasileios K; Tsimpanogiannis, Ioannis N; Stubos, Athanassios K; Economou, Ioannis G

    2015-09-01

    The direct phase coexistence methodology was used to predict the three-phase equilibrium conditions of carbon dioxide hydrates. Molecular dynamics simulations were performed in the isobaric-isothermal ensemble for the determination of the three-phase coexistence temperature (T3) of the carbon dioxide-water system, at pressures in the range of 200-5000 bar. The relative importance of the water-water and water-guest interactions in the prediction of T3 is investigated. The water-water interactions were modeled through the use of TIP4P/Ice and TIP4P/2005 force fields. The TraPPE force field was used for carbon dioxide, and the water-guest interactions were probed through the modification of the cross-interaction Lennard-Jones energy parameter between the oxygens of the unlike molecules. It was found that when using the classic Lorentz-Berthelot combining rules, both models fail to predict T3 accurately. In order to rectify this problem, the water-guest interaction parameters were optimized, based on the solubility of carbon dioxide in water. In this case, it is shown that the prediction of T3 is limited only by the accuracy of the water model in predicting the melting temperature of ice. PMID:26342376

  2. The role of intermolecular interactions in the prediction of the phase equilibria of carbon dioxide hydrates

    NASA Astrophysics Data System (ADS)

    Costandy, Joseph; Michalis, Vasileios K.; Tsimpanogiannis, Ioannis N.; Stubos, Athanassios K.; Economou, Ioannis G.

    2015-09-01

    The direct phase coexistence methodology was used to predict the three-phase equilibrium conditions of carbon dioxide hydrates. Molecular dynamics simulations were performed in the isobaric-isothermal ensemble for the determination of the three-phase coexistence temperature (T3) of the carbon dioxide-water system, at pressures in the range of 200-5000 bar. The relative importance of the water-water and water-guest interactions in the prediction of T3 is investigated. The water-water interactions were modeled through the use of TIP4P/Ice and TIP4P/2005 force fields. The TraPPE force field was used for carbon dioxide, and the water-guest interactions were probed through the modification of the cross-interaction Lennard-Jones energy parameter between the oxygens of the unlike molecules. It was found that when using the classic Lorentz-Berthelot combining rules, both models fail to predict T3 accurately. In order to rectify this problem, the water-guest interaction parameters were optimized, based on the solubility of carbon dioxide in water. In this case, it is shown that the prediction of T3 is limited only by the accuracy of the water model in predicting the melting temperature of ice.

  3. Synthesis and description of intermolecular interactions in new sulfonamide derivatives of tranexamic acid

    NASA Astrophysics Data System (ADS)

    Ashfaq, Muhammad; Arshad, Muhammad Nadeem; Danish, Muhammad; Asiri, Abdullah M.; Khatoon, Sadia; Mustafa, Ghulam; Zolotarev, Pavel N.; Butt, Rabia Ayub; ?ahin, Onur

    2016-01-01

    Tranexamic acid (4-aminomethyl-cyclohexanecarboxylic acid) was reacted with sulfonyl chlorides to produce structurally related four sulfonamide derivatives using simple and environmental friendly method to check out their three-dimensional behavior and van der Walls interactions. The molecules were crystallized in different possibilities, as it is/after alkylation at its O and N atoms/along with a co-molecule. All molecules were crystallized in monoclinic crystal system with space group P21/n, P21/c and P21/a. X-ray studies reveal that the molecules stabilized themselves by different kinds of hydrogen bonding interactions. The molecules are getting connected through O-H⋯O hydrogen bonds to form inversion dimers which are further connected through N-H⋯O interactions. The molecules in which N and O atoms were alkylated showed non-classical interaction and generated centro-symmetric R22(24) ring motif. The co-crystallized host and guest molecules are connected to each other via O-H⋯O interactions to generate different ring motifs. By means of the ToposPro software an analysis of the topologies of underlying nets that correspond to molecular packings and hydrogen-bonded networks in structures under consideration was carried out.

  4. Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4?-bipy and methyl benzoates

    NASA Astrophysics Data System (ADS)

    Xin-Jian, Wu; Yi-Ping, Chen; Ze-Min, Xia; Su-Zhi, Ge; Feng, Chai; Ling-Yan, Zhao; Jian-Zhong, Chen

    2013-03-01

    Two manganese complexes containing 4,4'-bipyridine and methyl benzoate as ligands have been prepared and crystallized by solvent evaporation method in DMF. The single crystal X-ray crystallographic analyses reveal that the complexes crystallize in monoclinic system. Crystal of 1 [Mn2(4,4'-bipy)2 (o-MBA)4]n has space group of P21/c with unit cell parameters of a = 17.508 (Å), b = 11.6229 (Å), c = 27.983 (Å), ? = 128.123°, V = 4.4797 nm3, empirical formula: C52H44Mn2N4O8, Mr = 962.79, Z = 4, Dc = 1.428 g/cm3, ? = 0.625 mm-1, and F(000) = 1992. The crystal of 2 [Mn (4,4'-bipy)(m-MBA)2]n belongs to space group C2/c with a = 16.079 (Å), b = 11.652 (Å), c = 24.887 (Å), ? = 92.02°, V = 4.660 nm3, empirical formula: C26H22MnN2O4, Mr = 481.40, Z = 8, Dc = 1.372 g/cm3, ? = 1.179 mm-1, F(000) = 1992. The weak interactions in structures are observed from the X-ray crystallographic data. These include the Csbnd H⋯O hydrogen bonds, ?-? stacking and Csbnd H⋯? interactions found in 1. The different strength of intermolecular interaction in the structures is reflected on their different thermal stability of the two complexes measured by thermal gravimetric analysis and the 2D-IR correlation spectroscopy. The study of weak interactions is meaningful to provide supporting data for potential application in molecular biology.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    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.

  6. Intermolecular interactions in aniline benzene hetero-trimer and aniline homo-trimer ions

    NASA Astrophysics Data System (ADS)

    Ohashi, Kazuhiko; Inokuchi, Yoshiya; Nishi, Nobuyuki; Sekiya, Hiroshi

    2002-05-01

    The charge distribution and binding features of aniline-benzene hetero-trimer and aniline homo-trimer ions are investigated by vibrational spectroscopy and by near-infrared photodissociation and spontaneous unimolecular dissociation of mass-selected cluster ions. The absence of the charge resonance absorption indicates the charge localization in the trimer ions. Substantial red-shifts and enhanced intensities of the vibrational transitions suggest strong perturbations to the NH oscillators. The trimer ions are stabilized by the hydrogen-bonding interaction through the NH 2 group of the charged aniline with the neutral molecules rather than the charge-delocalization interaction among the component molecules.

  7. 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)

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

    E-print Network

    Glaser, Rainer

    Interactions between Iodomethane and Chloropicrin Rainer Glaser* and Kaitlan Prugger Department of Chemistry fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry and season.15 Field volatility studies17 showed that CH3I concentrations would reach about 1 ppmv

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

    SciTech Connect

    Fitzwater, S.

    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.

  10. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: the hydration of Cf³?.

    PubMed

    Galbis, Elsa; Hernández-Cobos, Jorge; Pappalardo, Rafael R; Sánchez Marcos, Enrique

    2014-06-01

    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(H2O)n](m+)(H2O)? 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 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R(Cf-O) in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R(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. PMID:24907987

  11. Investigation of intermolecular interactions in finasteride drug crystals in view of X-ray and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Bojarska, Joanna; Maniukiewicz, Waldemar

    2015-11-01

    The N,N-dimethylformamide (DMF) solvate hemihydrate (1) of finasteride, has been structurally characterized by single-crystal X-ray diffraction at 100 K and compared with previously reported finasteride crystalline forms. In addition, in order to resolve ambiguity concerning H-bond interactions, the crystal structure of finasteride hemihydrate, (2), originally reported by Schultheiss et al. in 2009, has been redetermined with higher precision. The (1) and (2) pseudopolymorphs of finasteride crystallize as orthorhombic in chiral P212121 space group with two very similar host molecules in the asymmetric unit. The conformation of fused 6-membered rings are screw-boat, chair and chair for both molecules, while 5-membered rings assume chair in (1), and half-chair in (2). There is a fairly close resemblance of the molecular geometry for all analyzed compounds, arising due to the rigid host molecule. Inter- and intramolecular host-host, host-guest strong O-H⋯O, N-H⋯O hydrogen bonds and weak C-H⋯O interactions form 3D net conferring stability to the crystal packing. Finasterides can be classified as synthon pseudopolymorphs. Isostructural solvates crystallizing in the orthorhombic space group P212121, with Z? = 2, exhibit R22(8) C22(15) network, monoclinic solvate (Z? = 1) possess D11(2), while both orthorhombic and monoclinic polymorphs have C(4) motifs, respectively. The structural similarities and subtle differences have been interpreted in view of the 3D Hirshfeld surface analysis and associated 2D fingerprint plots, which enabled detailed qualitative and quantitative insight into the intermolecular interactions. The 97-100% of Hirshfeld surface areas are due to H···H, O···H/H⋯O, C···H/H⋯C and N⋯H/H⋯N contacts. Furthermore, the electrostatic potential has been mapped over the Hirshfeld surfaces to decode the electrostatic complementarities, which exist in the crystal packing.

  12. 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

  13. 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

  14. 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

  15. Conductance switching in a molecular device: The role of side groups and intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Taylor, Jeremy; Brandbyge, Mads; Stokbro, Kurt

    2003-09-01

    We report first-principles studies of electronic transport in monolayers of Tour wires functionalized with different side groups. An analysis of the scattering states and transmission eigenchannels suggests that the functionalization does not strongly affect the resonances responsible for current flow through the monolayer. However, functionalization has a significant effect on the interactions within the monolayer, so that monolayers with NO2 side groups exhibit local minima associated with twisted conformations of the molecules. We use our results to interpret observations of negative differential resistance and molecular memory in monolayers of NO2 functionalized molecules in terms of a twisting of the central ring induced by an applied bias potential.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  17. Appropriate description of intermolecular interactions in the methane hydrates: an assessment of DFT methods.

    PubMed

    Liu, Yuan; Zhao, Jijun; Li, Fengyu; Chen, Zhongfang

    2013-01-15

    Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates (MHs). Using high-level ab initio MP2 and CCSD(T) results as the reference, we carefully assessed the performance of a variety of exchange-correlation functionals and various basis sets in describing the noncovalent interactions in MH. The functionals under investigation include the conventional GGA, meta-GGA, and hybrid functionals (PBE, PW91, TPSS, TPSSh, B3LYP, and X3LYP), long-range corrected functionals (?B97X, ?B97, LC-?PBE, CAM-B3LYP, and LC-TPSS), the newly developed Minnesota class functionals (M06-L, M06-HF, M06, and M06-2X), and the dispersion-corrected density functional theory (DFT) (DFT-D) methods (B97-D, ?B97X-D, PBE-TS, PBE-Grimme, and PW91-OBS). We found that the conventional functionals are not suitable for MH, notably, the widely used B3LYP functional even predicts repulsive interaction between CH(4) and (H(2)O)(6) cluster. M06-2X is the best among the M06-Class functionals. The ?B97X-D outperforms the other DFT-D methods and is recommended for accurate first-principles calculations of MH. B97-D is also acceptable as a compromise of computational cost and precision. Considering both accuracy and efficiency, B97-D, ?B97X-D, and M06-2X functional with 6-311++G(2d,2p) basis set without basis set superposition error (BSSE) correction are recommended. Though a fairly large basis set (e.g., aug-cc-pVTZ) and BSSE correction are necessary for a reliable MP2 calculation, DFT methods are less sensitive to the basis set and BSSE correction if the basis set is sufficient (e.g., 6-311++G(2d,2p)). These assessments provide useful guidance for choosing appropriate methodology of first-principles simulation of MH and related systems. © 2012 Wiley Periodicals, Inc. PMID:22949382

  18. 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

  19. 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

  20. Intermolecular interactions of proton transfer compounds: synthesis, crystal structure and Hirshfeld surface analysis.

    PubMed

    Direm, Amani; Altomare, Angela; Moliterni, Anna; Benali-Cherif, Nourredine

    2015-08-01

    Three new proton transfer compounds, [2-ammonio-5-methylcarboxybenzene perchlorate (1), (C8H10NO2(+)·ClO4(-)), 4-(ammoniomethyl)carboxybenzene nitrate (2), (C8H10NO2(+)·NO3(-)), and 4-(ammoniomethyl)carboxybenzene perchlorate (3), (C8H10NO2(+)·ClO4(-))], have been synthesized, their IR modes of vibrations have been assigned and their crystal structures studied by means of single-crystal X-ray diffraction. Their asymmetric units consist of one cation and one anion for both compounds (1) and (2). However, the crystal structure of compound (3) is based on a pair of cations and a pair of anions in its asymmetric unit. The three-dimensional Hirshfeld surface analysis and the two-dimensional fingerprint maps revealed that the three structures are dominated by H...O/O...H and H...H contacts. The strongest hydrogen-bonding interactions are associated with O-H...O and N-H...O constituting the highest fraction of approximately 50%, followed by those of the H...H type contributing 20%. Other close contacts are also present, including weak C...H/H...C contacts (with about 10%). PMID:26208623

  1. 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

  2. Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid ?-Peptides.

    PubMed

    Lemkul, Justin A; Huang, Jing; MacKerell, Alexander D

    2015-12-24

    Amyloid-forming proteins undergo a structural transition from ?-helical to disordered conformations and, ultimately, cross-? fibrils. The unfolding and aggregation of the amyloid ?-peptide (A?) have been implicated in the development and progression of Alzheimer's disease (AD) and cerebral amyloid angiopathy (CAA). However, the events underlying the initial structural transition leading to the disease state remain unclear. Although most cases are sporadic, several genetic variants exist that alter the electrostatic properties of A? and lead to more rapid unfolding and more severe phenotypes. In the present study, the enhanced unfolding is shown to be due to the mutated side chains altering the local peptide-bond dipole moments leading to local destabilization of the ?-helix, as determined from polarizable molecular dynamics (MD) simulations of wild-type (WT) A? fragments and several common mutations. The local perturbation of the helix then leads to progressive unwinding of the ?-helix in a cooperative fashion due to decreases in adjacent (i ± 1) and hydrogen-bonded (i + 4) peptide-bond dipole moments. Side-chain dynamics, subsequent variations in dipole moments, and ultimately the response in the peptide-bond dipole moments are all modulated by solvent dielectric properties based on simulations in water versus ethanol. The polarizable simulation results, along with simulations using the additive CHARMM36 force field, further indicate that cooperativity due to the alignment of peptide bonds leading to enhanced dipole moments is a fundamental force in stabilizing ?-helices. PMID:26629591

  3. Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid ?-Peptides

    PubMed Central

    2015-01-01

    Amyloid-forming proteins undergo a structural transition from ?-helical to disordered conformations and, ultimately, cross-? fibrils. The unfolding and aggregation of the amyloid ?-peptide (A?) have been implicated in the development and progression of Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA). However, the events underlying the initial structural transition leading to the disease state remain unclear. Although most cases are sporadic, several genetic variants exist that alter the electrostatic properties of A? and lead to more rapid unfolding and more severe phenotypes. In the present study, the enhanced unfolding is shown to be due to the mutated side chains altering the local peptide-bond dipole moments leading to local destabilization of the ?-helix, as determined from polarizable molecular dynamics (MD) simulations of wild-type (WT) A? fragments and several common mutations. The local perturbation of the helix then leads to progressive unwinding of the ?-helix in a cooperative fashion due to decreases in adjacent (i ± 1) and hydrogen-bonded (i + 4) peptide-bond dipole moments. Side-chain dynamics, subsequent variations in dipole moments, and ultimately the response in the peptide-bond dipole moments are all modulated by solvent dielectric properties based on simulations in water versus ethanol. The polarizable simulation results, along with simulations using the additive CHARMM36 force field, further indicate that cooperativity due to the alignment of peptide bonds leading to enhanced dipole moments is a fundamental force in stabilizing ?-helices. PMID:26629591

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

    In the present work, a detailed spectroscopic analysis of 4-(benzyloxy)benzaldehyde thiosemicarbazone (3) has been carried out using 1H NMR, 13C NMR, UV-Visible and FT-IR spectroscopic techniques. The quantum chemical calculations have been carried out using DFT level of theory, B3LYP functional and 6-31G(d,p) basis set. The calculated thermodynamic parameters show that the formation of 3 is an exothermic and spontaneous reaction at 25 °C. The vibrational analysis indicates the formation of dimer in the solid state by intermolecular hydrogen bonding (Nsbnd H⋯Sdbnd C) and the binding energy of dimer is calculated to be 11.2 kcal/mol, using DFT calculation. NBO analysis is carried out to investigate the charge transfer in various intra and intermolecular interactions involved in dimer. Topological parameters at bond critical points (BCPs) are calculated to analyze the strength and nature of various intra and intermolecular interactions in dimer by Bader's 'Atoms in molecules' AIM theory in detail. The local reactivity descriptors such as Fukui functions (fk+, fk-), local softnesses (sk+, sk-) and electrophilicity indices (?k+, ?k-) analysis are performed to determine the reactive sites within molecule. Non linear optical (NLO) behavior of title compound is investigated by the computed value of first hyperpolarizability (?0).

  5. Synthesis, X-Ray Structure, Magnetic Properties, and a Study of Intra/Intermolecular Radical-Radical Interactions of a Triradical TEMPO Compound.

    PubMed

    Lloveras, Vega; Badetti, Elena; Wurst, Klaus; Vidal-Gancedo, José

    2015-10-01

    A novel triradical compound with a P=S core and three branches functionalized with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) radicals is synthesized and characterized by IR, (1) H?NMR, (31) P?NMR, and EPR spectroscopy and MALDI-TOF mass spectrometry, and its chemical structure is confirmed by X-ray diffraction analysis. The triradical shows neither spin exchange interactions between its radical units nor detectable dipolar interactions. This is consistent with the separation between the radical units found in its X-ray diffraction structure, and discounts the existence of intramolecular interactions. This conclusion is confirmed by an EPR concentration study. The concentration at which intermolecular interactions start to appear is determined (5×10(-3) ?m) and this concentration should be taken into account as a higher concentration limit when studies on intramolecular radical-radical interactions in polyradicals with similar structure are required. SQUID magnetometry analysis of the compound shows antiferromagnetic interactions between the spin carriers of different molecules; that is, antiferromagnetic intermolecular interactions. PMID:26489060

  6. Inter-molecular interactions in a 44 kDa interferon-receptor complex detected by asymmetric reverse-protonation and 2D NOESY†

    PubMed Central

    Nudelman, Ilona; Akabayov, Sabine R.; Schnur, Einat; Biron, Zohar; Levy, Rina; Xu, Yingqi; Yang, Daiwen; Anglister, Jacob

    2010-01-01

    Type I Interferons (IFNs) are a family of homologous helical cytokines initiating strong anti-viral and anti-proliferative activity. All type I IFNs bind to a common cell surface receptor consisting of two subunits, IFNAR1 and IFNAR2, associating upon binding of interferon. We studied inter-molecular interactions between IFNAR2-EC and IFN?2 using asymmetric reverse-protonation of the different complex components and 2D homonuclear NOESY. This new approach revealed with excellent signal-to-noise ratio 24 new intermolecular NOEs between the two molecules despite the low concentration of the complex (0.25 mM) and its high molecular weight (44 kDA). Sequential and side-chain assignment of IFNAR2-EC and IFN?2 in their binary complex helped assign the inter-molecular NOEs to the corresponding protons. A docking model of the IFNAR2-EC/IFN?2 complex was calculated based on the inter-molecular interactions found in the present study as well as four double mutant cycle constraints, previously observed NOEs between a single pair of residues and the NMR mapping of the binding sites on IFNAR2-EC and IFN?2. Our docking model doubles the buried surface area of the previous model and significantly increases the number of inter-molecular hydrogen bonds, salt bridges and Van der-Waals interactions. Furthermore, the current model reveals participation of several new regions in the binding site such as the N-terminus and A-helix of IFN?2 and the C-domain of IFNAR2-EC. As a result of these additions, the orientation of IFNAR2-EC relative to IFN?2 has changed by 30° in comparison with a previously calculated model that was based on NMR mapping of the binding sites and double mutant cycle constraints. In addition, the new model strongly supports the recently proposed allosteric changes in IFN?2 upon IFNAR1-EC binding to the binary IFN?2/IFNAR2-EC complex. PMID:20496919

  7. Phase transition broadening due to interfacial premelting: a new quantitative access to intermolecular interactions within submonolayer films at solid/vapor interfaces.

    PubMed

    Mutihac, Radu-Cristian; Riegler, Hans

    2010-05-01

    Investigations of submonolayer films show that phase transition broadening due to interfacial premelting is a general phenomenon. Its experimental observation and thermodynamic interpretation is particularly simple for molecules, which form solid monolayer domains of uniform thickness. This is demonstrated with submonolayer films of two classes of molecules: long chain alkanes and alcohols. The investigations yield quantitative data on the intermolecular interactions within the films at the interface between silica and air for molecular coverages extending over several orders of magnitude. At low surface coverages, we find for the two classes of substances a similar behavior. They behave like 2-dimensional gases. For higher coverages, when the molecules form closed films, the behavior is very different. This is explained by the different molecular organization within the films at higher coverages. The alkanes form a homogeneous, van der Waals-like liquid film with randomly oriented molecules. The alcohols are organized as a closed film with the OH groups oriented toward the silica surface. Thus, the OH group density at the silica/film interface changes with varying coverage. This leads to a change in the OH group hydration, which dominates the interactions between the alcohol molecules. The results demonstrate that the interface-induced premelting can be used as a new and quite universal tool to measure intermolecular interactions within molecularly thin films at solid/vapor interfaces. PMID:20420462

  8. Density matrix based microscopic theory of molecule metal-nanoparticle interactions: Linear absorbance and plasmon enhancement of intermolecular excitation energy transfer

    NASA Astrophysics Data System (ADS)

    Kyas, Gerold; May, Volkhard

    2011-01-01

    A microscopic theory of interacting molecule metal-nanoparticle (MNP) systems is presented and used to compute absorption spectra and the plasmon enhancement of intermolecular excitation energy transfer (EET). The approach is based on a nonperturbative consideration of the Coulomb coupling matrix elements responsible for EET between the molecules and the MNP. In this way, the need to determine the local fields induced by surface plasmon excitations of the MNP is removed, but the whole description is restricted to distances among the interacting species less than the wavelength of absorbed photons. Based on a density matrix theory, the approach accounts for the vibrational level structure of the molecules, intramolecular vibrational energy redistribution (IVR), and plasmon damping. Numerical results for linear absorbance spectra and EET dynamics are offered. In this respect the importance of energy dissipation in the MNP due to rapid surface plasmon decay is emphasized.

  9. Density matrix based microscopic theory of molecule metal-nanoparticle interactions: linear absorbance and plasmon enhancement of intermolecular excitation energy transfer.

    PubMed

    Kyas, Gerold; May, Volkhard

    2011-01-21

    A microscopic theory of interacting molecule metal-nanoparticle (MNP) systems is presented and used to compute absorption spectra and the plasmon enhancement of intermolecular excitation energy transfer (EET). The approach is based on a nonperturbative consideration of the Coulomb coupling matrix elements responsible for EET between the molecules and the MNP. In this way, the need to determine the local fields induced by surface plasmon excitations of the MNP is removed, but the whole description is restricted to distances among the interacting species less than the wavelength of absorbed photons. Based on a density matrix theory, the approach accounts for the vibrational level structure of the molecules, intramolecular vibrational energy redistribution (IVR), and plasmon damping. Numerical results for linear absorbance spectra and EET dynamics are offered. In this respect the importance of energy dissipation in the MNP due to rapid surface plasmon decay is emphasized. PMID:21261378

  10. Structural elucidation, density functional calculations and contribution of intermolecular interactions in cholest-4-en-3-one crystals: Insights from X-ray and Hirshfeld surface analysis

    NASA Astrophysics Data System (ADS)

    Khanam, Hena; Mashrai, Ashraf; Siddiqui, Nazish; Ahmad, Musheer; Alam, Mohammad Jane; Ahmad, Shabbir; Shamsuzzaman

    2015-03-01

    The foremost objective of the present work is systematic analysis of intermolecular interactions in crystal structure of cholest-4-en-3-one (2) molecule. It is accomplished by Hirshfeld surface analysis and fingerprint plot. Hirshfeld surface analysis has been used to visualize the fidelity of the crystal structure. This method permitted for the identification of individual types of intermolecular contacts and their impact on the complete packing. Molecules are linked by a combination of Cdbnd O---H, Csbnd H---H, and C---H contacts, which have clear signatures in the fingerprint plots. The theoretical study was attempted to predict the optimized geometry and computed spectra by the Density Functional Theory (DFT) using the B3LYP function with the 6-311++G(d,p) basis set. Atomic charges, MEP mapping, HOMO-LUMO, various thermodynamic and molecular properties have been reported. In addition thermal stability, optical, morphological, and microstructral properties of the title compound (2) have also been explored.

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

    NASA Astrophysics Data System (ADS)

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

    2005-02-01

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

  12. 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.

  13. 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

  14. 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

  15. Landau-Zener tunneling in the presence of weak intermolecular interactions in a crystal of Mn4 single-molecule magnets

    NASA Astrophysics Data System (ADS)

    Wernsdorfer, W.; Bhaduri, S.; Vinslava, A.; Christou, G.

    2005-12-01

    A Mn4 single-molecule magnet (SMM), with a well-isolated spin ground state of S=9/2 , is used as a model system to study Landau-Zener (LZ) tunneling in the presence of weak intermolecular dipolar and exchange interactions. The anisotropy constants D and B are measured with minor hysteresis loops. A transverse field is used to tune the tunnel splitting over a large range. Using the LZ and inverse LZ method, it is shown that these interactions play an important role in the tunnel rates. Three regions are identified: (i) at small transverse fields, tunneling is dominated by single tunnel transitions, (ii) at intermediate transverse fields, the measured tunnel rates are governed by reshuffling of internal fields, and (iii) at larger transverse fields, the magnetization reversal starts to be influenced by the direct relaxation process, and many-body tunnel events may occur. The hole digging method is used to study the next-nearest-neighbor interactions. At small external fields, it is shown that magnetic ordering occurs which does not quench tunneling. An applied transverse field can increase the ordering rate. Spin-spin cross-relaxations, mediated by dipolar and weak exchange interactions, are proposed to explain additional quantum steps.

  16. Synthesis, crystal structure and intermolecular magnetic interactions of a new N-TEMPO-3,5-di- tert-butylsalicylaldimine radical

    NASA Astrophysics Data System (ADS)

    Kasumov, Veli T.; Uçar, Ibrahim; Bulut, Ahmet; Yerli, Yusuf

    2011-10-01

    A new N-TEMPO-3,5-di- tert-butylsalicylaldimine radical ( 1) has been synthesized and characterized by single crystal X-ray diffraction, elemental analysis, IR, UV-vis, and EPR spectroscopy and temperature dependent magnetic susceptibility. X-ray diffraction revealed that H-atoms of ?-CH in TEMPO and CH 3 in salicylaldimine moieties, are located in close contact with the neighboring N-O radical group in crystal 1. The temperature dependence of the magnetic susceptibility ( ?m) of 1 has been fitted by the Curie-Weiss law with ? = -0.3 K within 10-300 K, suggesting the presence of a weak intermolecular antiferromagnetic interaction between radical centers at T < 10 K. It has been demonstrated that radical 1 possesses crystal structure involving co-existence of antiferromagnetic and ferromagnetic interactions through C-H⋯O-N rad contacts of ?-CH and tBu groups hydrogen atoms, in which the former path dominates over the latter.

  17. 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

  18. Crystal habits of cubic insulin from porcine pancreas and evaluation of intermolecular interactions by macrobond and EET analyses

    NASA Astrophysics Data System (ADS)

    Ootaki, Masanori; Endo, Shigeru; Sugawara, Yoko; Takahashi, Takuya

    2009-08-01

    Experimental and theoretical investigations of the crystal growth of cubic insulin from porcine pancreas were carried out. Three different crystal habits, cube, cube and dodecahedron, and rhombic dodecahedron forms, were obtained. Judging from the results of macroseeding, the most stable of these forms would be the rhombic dodecahedron surrounded by {1 1 0} faces. Molecular interactions in the crystal were evaluated by the macrobond analysis and electrostatic energy of transfer (EET) analysis. The calculated surface energy of {1 1 0} was lower than {1 0 0} by around 40%, which was consistent with the experimental results. Atomic EET supported the macrobond analysis, where the number of hydrogen bonds was primarily evaluated. At the same time, it was suggested that the parameters of the interaction energies of electrically neutral pairs would be smaller than those of charged pairs. The contribution from the bound water molecules to the crystal stabilization was discussed.

  19. Intermolecular interaction of voriconazole analogues with model membrane by DSC and NMR, and their antifungal activity using NMR based metabolic profiling.

    PubMed

    Kalamkar, Vaibhav; Joshi, Mamata; Borkar, Varsha; Srivastava, Sudha; Kanyalkar, Meena

    2013-11-01

    The development of novel antifungal agents with high susceptibility and increased potency can be achieved by increasing their overall lipophilicity. To enhance the lipophilicity of voriconazole, a second generation azole antifungal agent, we have synthesized its carboxylic acid ester analogues, namely p-methoxybenzoate (Vpmb), toluate (Vtol), benzoate (Vbz) and p-nitrobenzoate (Vpnb). The intermolecular interactions of these analogues with model membrane have been investigated using nuclear magnetic resonance (NMR) and differential scanning calorimetric (DSC) techniques. The results indicate varying degree of changes in the membrane bilayer's structural architecture and physico-chemical characteristics which possibly can be correlated with the antifungal effects via fungal membrane. Rapid metabolite profiling of chemical entities using cell preparations is one of the most important steps in drug discovery. We have evaluated the effect of synthesized analogues on Candida albicans. The method involves real time (1)H NMR measurement of intact cells monitoring NMR signals from fungal metabolites which gives Metabolic End Point (MEP). This is then compared with Minimum Inhibitory Concentration (MIC) determined using conventional methods. Results indicate that one of the synthesized analogues, Vpmb shows reasonably good activity. PMID:24012381

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  1. 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.

  2. Intermolecular interactions, charge-density distribution and the electrostatic properties of pyrazinamide anti-TB drug molecule: an experimental and theoretical charge-density study.

    PubMed

    Rajalakshmi, Gnanasekaran; Hathwar, Venkatesha R; Kumaradhas, Poomani

    2014-06-01

    An experimental charge-density analysis of pyrazinamide (a first line antitubercular drug) was performed using high-resolution X-ray diffraction data [(sin??/?)max = 1.1?Å(-1)] measured at 100?(2)?K. The structure was solved by direct methods using SHELXS97 and refined by SHELXL97. The total electron density of the pyrazinamide molecule was modeled using the Hansen-Coppens multipole formalism implemented in the XD software. The topological properties of electron density determined from the experiment were compared with the theoretical results obtained from CRYSTAL09 at the B3LYP/6-31G** level of theory. The crystal structure was stabilized by N-H...N and N-H...O hydrogen bonds, in which the N3-H3B...N1 and N3-H3A...O1 interactions form two types of dimers in the crystal. Hirshfeld surface analysis was carried out to analyze the intermolecular interactions. The fingerprint plot reveals that the N...H and O...H hydrogen-bonding interactions contribute 26.1 and 18.4%, respectively, of the total Hirshfeld surface. The lattice energy of the molecule was calculated using density functional theory (B3LYP) methods with the 6-31G** basis set. The molecular electrostatic potential of the pyrazinamide molecule exhibits extended electronegative regions around O1, N1 and N2. The existence of a negative electrostatic potential (ESP) region just above the upper and lower surfaces of the pyrazine ring confirm the ?-electron cloud. PMID:24892603

  3. Collecting high-order interactions in an effective pairwise intermolecular potential using the hydrated ion concept: The hydration of Cf3+

    NASA Astrophysics Data System (ADS)

    Galbis, Elsa; Hernández-Cobos, Jorge; Pappalardo, Rafael R.; Marcos, Enrique Sánchez

    2014-06-01

    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(H2O)n]m+(H2O)? 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 H2O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R_{{Cf-O}} in the range 2.43-2.48 Å, whereas the fourth one is closer to 9 with R_{{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.

  4. 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; Hernández-Cobos, Jorge

    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.

  5. In-Plane Intermolecular Interaction Assisted Assembly and Modified Electronic States of Metallofullerene Gd@C82.

    PubMed

    Chen, Jian; Qin, Zhihui; Pan, Jinbo; Huang, Min; Du, Shixuan; Cao, Gengyu

    2015-10-27

    Orientational configuration and electronic states of Gd@C82 bonding to Cu(111) have been thoroughly investigated by low-temperature scanning tunneling microscopy/spectroscopy (LT-STM/S) and differential conductance mapping complemented by first-principles calculations. We clarify that individual Gd@C82 energetically adopts tilting adsorption configuration with the scanning tunneling spectroscopy (STS) states readily assigned to the C82 cage/Cu(111) hybrid states and the Gd/cage hybrid states, respectively. Moreover, upon assembling and sufficient thermal activation, Gd@C82 fullerenes are inclined to restore the energetically favored tilting orientational configuration similar to an individual one. This suggests the feasibility of high-level integration of single-Gd@C82 based moletronic device with the performances almost unchanged by two-dimensional arrangement. Furthermore, by rationalizing the inter-Gd@C82 interaction induced slight energy offset of the electronic states, we qualitatively confirm the shown electronic hybrid states as Cu(111)-, C82 cage- and Gd-dominant hybrid states, respectively. PMID:26457573

  6. Specific intermolecular interactions of conserved water molecules with amino acids in the Galectin-1 carbohydrate recognition domain

    NASA Astrophysics Data System (ADS)

    Di Lella, Santiago; Petruk, Ariel A.; Armiño, Diego J. Alonso de; Álvarez, Rosa M. S.

    2010-08-01

    Water molecules, rigidly associated to protein surfaces, play a key role in stabilizing biomolecules and participating in their biological functions. Recent studies on the solvation properties of the carbohydrate recognition domain of Galectin-1 by means of molecular dynamic simulations have revealed the existence of several water sites which were well correlated to both the bound water molecules observed in the crystal structure of the protein in the free state and to some of the hydroxyl groups of the carbohydrate ligand observed in the crystal structure of the complexed protein. In this work, we present a study using quantum mechanical methods (B3LYP/6-311++G(3df,3dp)//B3LYP/6-31+G(d)) to determine the energy involved in the binding of these water molecules to specific amino acids in the carbohydrate recognition domain of the protein. By modeling the hydroxyl groups of the carbohydrate by methanol, the energies associated to the local interactions between the ligand and the protein have been evaluated by replacing specific water molecules with methanol. The values of the binding energies have been compared to those previously obtained by the molecular dynamic method.

  7. Eur. Phys. J. D 65, 177187 (2011) DOI: 10.1140/epjd/e2011-20093-4 On the role of the magnetic dipolar interaction in cold

    E-print Network

    2011-01-01

    dipolar interaction in cold and ultracold collisions: numerical and analytical results for NH(3 - ) + NH(3 of the magnetic dipolar interaction in cold and ultracold collisions: numerical and analytical results for NH(3 of the magnetic dipole-dipole interaction in cold and ultracold collisions. We focus on collisions between

  8. Theory of elastic interaction between arbitrary colloidal particles in confined nematic liquid crystals.

    PubMed

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

    2012-12-01

    We develop the method proposed by Chernyshuk and Lev [Phys. Rev. E 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not "feel" the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L??. PMID:23367965

  9. Crystal structures of 4-chloro-pyridine-2-carbo-nitrile and 6-chloro-pyridine-2-carbo-nitrile exhibit different inter-molecular ?-stacking, C-H?Nnitrile and C-H?Npyridine inter-actions.

    PubMed

    Montgomery, Matthew J; O'Connor, Thomas J; Tanski, Joseph M

    2015-07-01

    The two title compounds are isomers of C6H3ClN2 containing a pyridine ring, a nitrile group, and a chloro substituent. The mol-ecules of each compound pack together in the solid state with offset face-to-face ?-stacking, and inter-molecular C-H?Nnitrile and C-H?Npyridine inter-actions. 4-Chloro-pyridine-2-carbo-nitrile, (I), exhibits pairwise centrosymmetric head-to-head C-H?Nnitrile and C-H?Npyridine inter-actions, forming one-dimensional chains, which are ?-stacked in an offset face-to-face fashion. The inter-molecular packing of the isomeric 6-chloro-pyridine-2-carbo-nitrile, (II), which differs only in the position of the chloro substituent on the pyridine ring, exhibits head-to-tail C-H?Nnitrile and C-H?Npyridine inter-actions, forming two-dimensional sheets which are ?-stacked in an offset face-to-face fashion. In contrast to (I), the offset face-to-face ?-stacking in (II) is formed between mol-ecules with alternating orientations of the chloro and nitrile substituents. PMID:26279884

  10. Crystal structures of 4-chloro­pyridine-2-carbo­nitrile and 6-chloro­pyridine-2-carbo­nitrile exhibit different inter­molecular ?-stacking, C—H?Nnitrile and C—H?Npyridine inter­actions

    PubMed Central

    Montgomery, Matthew J.; O’Connor, Thomas J.; Tanski, Joseph M.

    2015-01-01

    The two title compounds are isomers of C6H3ClN2 containing a pyridine ring, a nitrile group, and a chloro substituent. The mol­ecules of each compound pack together in the solid state with offset face-to-face ?-stacking, and inter­molecular C—H?Nnitrile and C—H?Npyridine inter­actions. 4-Chloro­pyridine-2-carbo­nitrile, (I), exhibits pairwise centrosymmetric head-to-head C—H?Nnitrile and C—H?Npyridine inter­actions, forming one-dimensional chains, which are ?-stacked in an offset face-to-face fashion. The inter­molecular packing of the isomeric 6-chloro­pyridine-2-carbo­nitrile, (II), which differs only in the position of the chloro substituent on the pyridine ring, exhibits head-to-tail C—H?Nnitrile and C—H?Npyridine inter­actions, forming two-dimensional sheets which are ?-stacked in an offset face-to-face fashion. In contrast to (I), the offset face-to-face ?-stacking in (II) is formed between mol­ecules with alternating orientations of the chloro and nitrile substituents. PMID:26279884

  11. 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.

  12. Competing interactions in semiconductor quantum dots

    SciTech Connect

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

    2014-10-14

    In this study, 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.

  13. 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.

    2014-10-14

    In this study, 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 atmore »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.« less

  14. Jordan algebras arising from intermolecular recombination

    E-print Network

    Jordan algebras arising from intermolecular recombination Murray R. Bremner Department that a linearization of the opera- tion of intermolecular recombination from theoretical genetics satisfies that this new identity implies all the identities of degree 6 satisfied by intermolecular recombination

  15. 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; Williams, J.M.

    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.

  16. 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

  17. 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

  18. Intermolecular electrostatic energies using density fitting

    PubMed Central

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

    2009-01-01

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

  19. The long-range non-additive three-body dispersion interactions for the rare gases, alkali, and alkaline-earth atoms

    NASA Astrophysics Data System (ADS)

    Tang, Li-Yan; Yan, Zong-Chao; Shi, Ting-Yun; Babb, James F.; Mitroy, J.

    2012-03-01

    The long-range non-additive three-body dispersion interaction coefficients Z111, Z112, Z113, and Z122 are computed for many atomic combinations using standard expressions. The atoms considered include hydrogen, the rare gases, the alkali atoms (up to Rb), and the alkaline-earth atoms (up to Sr). The term Z111 arising from three mutual dipole interactions is known as the Axilrod-Teller-Muto coefficient or the DDD (dipole-dipole-dipole) coefficient. Similarly, the terms Z112, Z113, and Z122 arise from the mutual combinations of dipole (1), quadrupole (2), and octupole (3) interactions between atoms and they are sometimes known, respectively, as dipole-dipole-quadrupole, dipole-dipole-octupole, and dipole-quadrupole-quadrupole coefficients. Results for the four Z coefficients are given for the homonuclear trimers, for the trimers involving two like-rare-gas atoms, and for the trimers with all combinations of the H, He, and Li atoms. An exhaustive compilation of all coefficients between all possible atomic combinations is presented as supplementary data.

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

    PubMed

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

    1989-08-15

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

  1. Competing intermolecular interactions in the high-temperature solid phases of even saturated carboxylic acids (C10H19O2H to C20H39O2H).

    PubMed

    Moreno-Calvo, Evelyn; Gbabode, Gabin; Cordobilla, Raquel; Calvet, Teresa; Cuevas-Diarte, Miquel Angel; Negrier, Philippe; Mondieig, Denise

    2009-12-01

    Structural knowledge of the high-temperature phases of saturated carboxylic acids (C(n)H(2n-1)O(2)H) from C(6)H(11)O(2)H to C(23)H(45)O(2)H is now complete. Crystal structures of the high-temperature phases of even acids from decanoic (C(10)H(19)O(2)H) to eicosanoic (C(20)H(39)O(2)H) are reported. The crystal structures of the six compounds were determined from powder X-ray diffraction data following direct space methods and refined by the Rietveld method combined with force field geometry optimization. The combination proved to be a valuable approach to obtain structures that are chemically sensible and in close agreement with the powder pattern. At the end of the process solid-state DFT calculations were applied to improve the overall accuracy of the system but in this case DFT did not render better structures. The high-temperature solid phases of even carboxylic acids are all P2(1)/c with Z=4, the molecules are united into dimers via strong hydrogen bonds. Two major types of interactions govern the crystal packing of carboxylic acids, hydrogen bonds and van der Waals interactions. A survey of the intermolecular interactions has revealed that hydrogen bonds are the dominant interaction for acids with less than 23 carbon atoms in the alkyl chain while van der Waals interactions dominate the packing for acids with more than 23 carbon atoms. PMID:19862782

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

    NASA Astrophysics Data System (ADS)

    Han, Jianing; Gallagher, Tom

    2009-05-01

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

  3. Intermolecular Adhesion in Conjugated Polymers

    E-print Network

    Jeremy D. Schmit; Alex J. Levine

    2006-10-25

    Conjugated polymers are observed to aggregate in solution. To account for this observation we propose a inter-chain binding mechanism based on the intermolecular tunneling of the delocalized $\\pi$-electrons occurring at points where the polymers cross. This tunneling mechanism predicts specific bound structures of chain that depend on whether they are semiconducting or metallic. Semiconducting chains should form polyacene-like states exhibiting binding at every other site, while (doped) metallic chains can bind at each site. We also show that solitons co-localize with the intermolecular binding sites thereby strengthening the binding effect and investigate the conformational statistics of the resulting bimolecular aggregates.

  4. Two alternative derivations of the static contribution to the radiation-induced intermolecular energy shift

    SciTech Connect

    Salam, A. |

    2007-12-15

    Two contrasting physical viewpoints and calculational approaches are adopted within the framework of molecular quantum electrodynamics for the evaluation of the static contribution to the change in mutual interaction energy between a pair of electric dipole polarizable molecules in an intense radiation field. This term arises when a real photon is scattered by the same molecular center with coupling between the two bodies occurring via exchange of a single virtual photon. In one method it is found that utilization of an effective three-photon interaction operator enables the energy shift to be obtained using second order perturbation theory with summation over only four time-ordered diagrams, each of which contain collapsed interaction vertices. The result is then shown to be obtained even more easily in a second approach that involves calculating the expectation values for both molecules in the ground electronic state and the field containing N photons of mode (k-vector,{lambda}) of the electric dipole moments induced at each molecule by the incident field, which are coupled to the resonant dipole-dipole interaction tensor. The static contribution in question is shown to arise from the interaction of a permanent electric dipole moment in one species with the first hyperpolarizability of the other. Both methods are compared and contrasted with a previous computation in which contributions to the energy shift arising from 48 time-ordered diagrams were summed using fourth order perturbation theory.

  5. Interaction mechanism for energy transfer from Ce to Tb ions in silica

    NASA Astrophysics Data System (ADS)

    Seed Ahmed, H. A. A.; Chae, W. S.; Ntwaeaborwa, O. M.; Kroon, R. E.

    2016-01-01

    Energy transfer phenomena can play an important role in the development of luminescent materials. In this study, numerical simulations based on theoretical models of non-radiative energy transfer are compared to experimental results for Ce, Tb co-doped silica. Energy transfer from the donor (Ce) to the acceptor (Tb) resulted in a decrease in the Ce luminescence intensity and lifetime. The decrease in intensity corresponded best with the energy transfer models based on the exchange interaction and the dipole-dipole interaction. The critical transfer distance obtained from the fitting using both these models is around 2 nm. Since the exchange interaction requires a distance shorter than 1 nm to occur, the mechanism most likely to account for the energy transfer is concluded to be the dipole-dipole interaction. This is supported by an analysis of the lifetime data.

  6. Student Understanding of Intermolecular Forces: A Multimodal Study

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  7. Photoswitchable Adsorption in Metal-Organic Frameworks Based on Polar Guest-Host Interactions.

    PubMed

    Wang, Zhengbang; Grosjean, Sylvain; Bräse, Stefan; Heinke, Lars

    2015-12-01

    Reversible remote-controlled switching of the properties of nanoporous metal-organic frameworks (MOFs) is enabled by incorporating photoswitchable azobenzene. The interaction of the host material with different guest molecules, which is crucial for all applications, is precisely studied using thin MOF films of the type Cu2 (BDC)2 (AzoBipyB). A molecule-specific effect of the photoswitching, based on dipole-dipole interactions, is found. PMID:26455589

  8. Intensity and amplitude correlations in the fluorescence from atoms with interacting Rydberg states

    E-print Network

    Qing Xu; Klaus Mølmer

    2015-08-04

    We explore the fluorescence signals from a pair of atoms driven towards Rydberg states on a three-level ladder transition. The dipole--dipole interactions between Rydberg excited atoms significantly distort the dark state and electromagnetically induced transparency behavior observed with independent atoms and, thus, their steady state light emission. We calculate and analyze the temporal correlations between intensities and amplitudes of the signals emitted by the atoms and explain their origin in the atomic Rydberg state interactions.

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

    SciTech Connect

    An, Nguyen Ba; Kim, Jaewan; Kim, Kisik

    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.

  10. Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

    PubMed

    Chandrasekhar, Sosale; Naik, Tangali R Ravikumar; Nayak, Susanta K; Row, Tayur N Guru

    2010-06-15

    The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. PMID:20493694

  11. Nonradiative Interaction and Entanglement between Distant Atoms

    E-print Network

    Shahmoon, Ephraim

    2012-01-01

    We consider resonant dipole-dipole interactions between atomic dipoles placed in a waveguide. We find that when the resonant frequency of the dipoles is below the waveguide's cutoff, nonradiative interaction and entanglement at distances much larger than their resonant wavelength are possible. This interaction, mediated by virtual photons, is coherent and deterministic, in contrast to the probabilistic radiative interaction. The range of the interaction increases as the dipole-resonance approaches the cutoff frequency, a regime where the standard Markov approximation fails. We provide analytical theories for both the Markovian and non-Markovian regimes, supported by numerical simulations, and discuss possible experimental realizations.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  13. 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.

  14. Strongly Correlated 2D Quantum Phases with Cold Polar Molecules: Controlling the Shape of the Interaction Potential

    SciTech Connect

    Buechler, H. P.; Micheli, A.; Pupillo, G.; Zoller, P.; Demler, E.; Lukin, M.; Prokof'ev, N.

    2007-02-09

    We discuss techniques to tune and shape the long-range part of the interaction potentials in quantum gases of bosonic polar molecules by dressing rotational excitations with static and microwave fields. This provides a novel tool towards engineering strongly correlated quantum phases in combination with low-dimensional trapping geometries. As an illustration, we discuss the 2D superfluid-crystal quantum phase transition for polar molecules interacting via an electric-field-induced dipole-dipole potential.

  15. Effect of dipolar interactions on optical nonlinearity of two-dimensional nanocomposites

    E-print Network

    Panov, Andrey V

    2012-01-01

    In this work, we calculate the contribution of dipole-dipole interactions to the optical nonlinearity of the two-dimensional random ensemble of nanoparticles that possess a set of exciton levels. The analytical expressions for the contributions in the cases of TM and TE-polarized light waves are obtained. It is shown that the optical nonlinearity caused by the dipole-dipole interactions in the planar ensemble of the nanoparticles is several times smaller than the similar nonlinearity of the bulk nanocomposite. This type of optical nonlinearity is expected to be observed at timescales much larger than the quantum dot exciton rise time. The proposed method may be applied to various types of the nanocomposite shapes.

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

    NASA Technical Reports Server (NTRS)

    Matsuura, Yoshiki; Chernov, Alexander A.

    2002-01-01

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

  17. 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.

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

    PubMed

    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. PMID:22055980

  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. CLIP170 autoinhibition mimics intermolecular interactions with

    E-print Network

    Ikura, Mitsuhiko

    in the regulation of microtubule dynamics. To explore this at a structural level, we first determined the crystal and Supplementary Methods online). p150n adopts the b/b fold observed previously in the p150n­EB1 crystal structure hydrophobic residues (Phe52, Trp57 and Phe88; Supplementary Fig. 3 online). Red circled region is expa

  1. 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.

  2. Intermolecular Vibrations in Hydrophobic Amino Acid Crystals: Experiments and Calculations

    E-print Network

    Intermolecular Vibrations in Hydrophobic Amino Acid Crystals: Experiments and Calculations Michael-8107, United States *S Supporting Information ABSTRACT: Intermolecular vibrations of amino acid crystals occur not previously been compared. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids

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

    PubMed

    Nagy, Peter I

    2014-01-01

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

  4. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

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

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

    PubMed

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

    2008-08-01

    Intermolecular associations between a cationic lipid and two model polymers were evaluated from preparation and characterization of hybrid thin films cast on silicon wafers. The novel materials were prepared by spin-coating of a chloroformic solution of lipid and polymer on silicon wafer. Polymers tested for miscibility with the cationic lipid dioctadecyldimethylammonium bromide (DODAB) were polystyrene (PS) and poly(methyl methacrylate) (PMMA). The films thus obtained were characterized by ellipsometry, wettability, optical and atomic force microscopy, Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), and activity against Escherichia coli. Whereas intermolecular ion-dipole interactions were available for the PMMA-DODAB interacting pair producing smooth PMMA-DODAB films, the absence of such interactions for PS-DODAB films caused lipid segregation, poor film stability (detachment from the silicon wafer) and large rugosity. In addition, the well-established but still remarkable antimicrobial DODAB properties were transferred to the novel hybrid PMMA/DODAB coating, which is demonstrated to be highly effective against E. coli. PMID:18630858

  6. 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.

  7. Polynomial identities for ternary intermolecular recombination

    E-print Network

    Murray R. Bremner

    2010-08-11

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

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

    SciTech Connect

    Han Jianing

    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.

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

    NASA Astrophysics Data System (ADS)

    Han, Jianing

    2010-11-01

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

  10. Vibrational assignments, spectroscopic investigation (FT-IR and FT-Raman), NBO, MEP, HOMO?LUMO analysis and intermolecular hydrogen bonding interactions of 7-fluoroisatin, 7-bromoisatin and 1-methylisatin ? A comparative study

    NASA Astrophysics Data System (ADS)

    Polat, Turgay; Bulut, Fatih; Ar?can, Ilknur; Kandemirli, Fatma; Yildirim, Gürcan

    2015-12-01

    In this comprehensive study, theoretical and experimental studies were carried out on 7-fluoroisatin, 7-bromoisatin and 1-methylisatin using FT-Raman and FT-IR spectra. The optimized geometrical parameters and theoretical vibrational frequencies were calculated by means of density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set based on scaled quantum mechanical (SQM) method for the first time. The relative abundances of the possible tautomers or conformers found were calculated with respect to the Boltzmann distribution. Moreover, the harmonic vibrational frequencies including IR and Raman intensities, thermodynamic and electronic parameters were computed in detail. The effects of substituents -F, ?Br and -CH3 on the crucial characteristics pertaining to the title compound of isatin were investigated, and the obtained data were compared with each other. Natural bond orbital (NBO) analysis was applied to study the stability arising from charge delocalization along with the compound. The chemical reactivity parameters (chemical hardness and softness, electronegativity, chemical potential and electrophilicity index) were discussed clearly. The HOMO and LUMO energies determined showed that the serious charge transfer occurs in the title molecules studied. Furthermore, the size, shape, charge density distributions and chemical reactivity sites belonging to the molecules were obtained by mapping electron density isosurface with electrostatic potential surfaces (ESP). Additionally, the hydrogen-bonded complexes were simulated to describe the roles of intermolecular hydrogen bonding on the molecular structures and vibrational frequencies.

  11. The geometry of the nitroguanyl fragment in the simplest nitroguanidine derivatives in the absence of intermolecular interactions: The gas electron diffraction data on 1,1,3,3-tetramethyl-2-nitroguanidine

    NASA Astrophysics Data System (ADS)

    Khaikin, L. S.; Grikina, O. E.; Girichev, G. V.; Kovacs, A.; Dyugaev, K. P.; Astachov, A. M.

    2011-03-01

    The structures and force fields of the equilibrium forms of 2-nitroguanidine ( 1), 1,1,3,3-tetramethyl-2-nitroguanidine ( 2), and nitroguanyl azide ( 3) were determined in the MP2(full)/6-311G(3 df, 2 p) approximation; wagging-inversion motions of the N amine atoms were studied. The internal rotation potential function of the NO2 group was calculated for 1. Similar functions for 1 and 2 were also obtained in the MP2(full)/6-311G( d, p) approximation. Direct one-dimensional problems for a nonrigid model were solved by the variational method, and the distribution of torsional levels was obtained. In the region of potential minimum, rotation in both molecules had the character of large-amplitude motions. For the first time, electron diffractions data were obtained at 100°C for molecule 2 without noticeable traces of substance decomposition. A structural r e analysis was performed using the model of large-amplitude motions for characteristic NO2 group torsional vibrations. Vibrational corrections to internuclear distances and mean amplitudes were calculated taking into account nonlinear kinematic effects using the force fields obtained in this work. The geometry of molecule 2 calculated in the MP2(full)/6-311G(3 df, 2 p) approximation well corresponds to the gas electron diffraction data. The parameters of molecule 2 in the crystalline phase, however, differ substantially from the parameters of the free molecule. This corresponds with the suggestion of the influence of intermolecular H-bonds involving the imine nitrogen atom and nitro groups oxygen atoms.

  12. Cs Trilobite Molecules and Rydberg atom Interactions

    NASA Astrophysics Data System (ADS)

    Booth, Donald; Jin, Yang; Shaffer, James

    2014-05-01

    We present results on our Cs ultracold Rydberg atom experiments involving trilobite molecules and Rydberg atom interactions. Trilobite molecules are predicted to have giant, body-fixed permanent dipole moments (~ 1 kD). We present measurements of the Stark shifts of the trilobite states in Cs due to the application of a constant external electric field. We also will present progress on studies of anisotropic interactions between pairs of Rydberg atoms. We will focus on angular-dependent S-matrix calculations of collisions between 89D+89D Rydberg atom pairs in a 100 mV/cm electric field. In this field, the dipole-dipole interaction dominates over the van-der-Waals interaction, creating a large anisotropy in the potential surfaces. We acknowledge funding from the NSF and the AFOSR.

  13. 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.

  14. Stretched string with self-interaction at the Hagedorn point: Spatial sizes and black holes

    NASA Astrophysics Data System (ADS)

    Qian, Yachao; Zahed, Ismail

    2015-11-01

    We analyze the length, mass and spatial distribution of a discretized transverse string in D? dimensions with fixed end points near its Hagedorn temperature. We suggest that such a string may dominate the (holographic) Pomeron kinematics for dipole-dipole scattering at intermediate and small impact parameters. Attractive self-string interactions cause the transverse string size to contract away from its diffusive size, a mechanism reminiscent of the string-black hole transmutation. The string shows sizable asymmetries in the transverse plane that translate to primordial azimuthal asymmetries in the stringy particle production in the Pomeron kinematics for current pp and pA collisions at collider energies.

  15. Ultralong-range order in the Fermi-Hubbard model with long-range interactions

    NASA Astrophysics Data System (ADS)

    van Loon, Erik G. C. P.; Katsnelson, Mikhail I.; Lemeshko, Mikhail

    2015-08-01

    We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64 ×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase—the density correlation function—features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms.

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

    PubMed Central

    Jarvis, Samuel Paul

    2015-01-01

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

  17. Short-Range, Spin-Dependent Interactions of Electrons: A Probe for Exotic Pseudo-Goldstone Bosons

    NASA Astrophysics Data System (ADS)

    Terrano, W. A.; Adelberger, E. G.; Lee, J. G.; Heckel, B. R.

    2015-11-01

    We used a torsion pendulum and rotating attractor with 20-pole electron-spin distributions to probe dipole-dipole interactions mediated by exotic pseudo-Goldstone bosons with mbc2?500 ? eV and coupling strengths up to 14 orders of magnitude weaker than electromagnetism. This corresponds to symmetry-breaking scales F ?70 TeV , the highest reached in any laboratory experiment. We used an attractor with a 20-pole unpolarized mass distribution to improve laboratory bounds on C P -violating monopole-dipole forces with 1.5 ? eV

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  19. PIXEL analysis of interactions in organic and inorganic systems 

    E-print Network

    Maloney, Andrew Gerrard Patrick

    2015-06-30

    The PIXEL method has been used for several years to analyse intermolecular interactions in organic crystals. The simplicity and speed of the calculations, along with the breakdown of intermolecular energies into physical ...

  20. Quantitative tomographic imaging of intermolecular FRET in small animals

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

    Venkattraman, Ayyaswamy

    2014-12-09

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

  2. Hydrogen bonding effects on coordinated sulfoxides and relative role of intra- and inter-molecular interactions determining the dmso orientation in [RR'NHOH][ fac-RuCl 3(dmso) 3] compounds: a crystallographic and molecular mechanics study

    NASA Astrophysics Data System (ADS)

    Geremia, S.; Calligaris, M.; Kukushkin, Y. N.; Zinchenko, A. V.; Kukushkin, V. Yu.

    2000-01-01

    Compounds with hydroxyl ammonium cations, [RR'NHOH][ fac-RuCl 3(dmso-S) 3], with R=R'=H ( 1), R=Me, R'=H ( 2) and R=R'=Et ( 3), have been prepared and structurally characterized by X-ray analyses. The three compounds display chain-like structures, formed by hydrogen bonding between the hydroxyl ammonium cations and the chlorine and oxygen atoms of the ruthenium anion. H-bonding involving the dmso oxygen atoms causes a lengthening of the S-O bonds. The comparison of the solid state structures with results of Molecular Mechanics calculations show that the arrangement of the fac-dmso-S ligands is not determined by H-bonding or packing effects, but from intramolecular steric and electrostatic interactions. These give rise to hindered rotation about the Ru-S bonds.

  3. 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.

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

    PubMed

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

    2015-02-14

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

  5. Zinc(II) polymeric compounds with a chelating ligand bis(2-pyridylmethyl)amine (bispicam) directed by intermolecular C/N/O H?X (X = Cl, Br, I) interactions: Catalytic activities

    NASA Astrophysics Data System (ADS)

    Park, Byeong Kwon; Lee, Sun Hwa; Lee, Eun Yong; Kwak, Han; Lee, Young Min; Lee, Yu Jin; Jun, Je Yeol; Kim, Cheal; Kim, Sung-Jin; Kim, Youngmee

    2008-11-01

    [Zn(bispicam) 2] 2+ as a hydrogen-bond donor and three free halides (Cl -, Br - and I -) as hydrogen-bond acceptors were employed to investigate the role of non-classical C/N-H⋯X hydrogen bonding for construction of polymeric compounds. Three zinc salts (ZnCl 2, ZnBr 2 and ZnI 2) were reacted with bis(2-pyridylmethyl)amine (bispicam) to produce [Zn(bispicam) 2]Cl 21, [Zn(bispicam) 2]Br 22 and [Zn(bispicam) 2]I 23. Hydrogen bonding interactions between N amine-H and C-H of [Zn(bispicam) 2] 2+ cations and free halides, and between O water-H and free halides can play very important roles for construction of molecular packing and crystal structures. In addition, these hydrogen-bonded complexes 1, 2 and 3 were, interestingly, shown to carry out the catalytic transesterification of a range of esters with methanol at 50 °C under the mild conditions, though all these compounds are saturated with two bispicam ligands. To explain this unusual reactivity, it has been proposed that the hydrogen atom of amine N-H moiety in the complexes could do the acid-catalyzed transesterification.

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

    SciTech Connect

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

    2002-01-01

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

  7. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    NASA Astrophysics Data System (ADS)

    Gruodis, A.; Galikova, N.; Šarka, K.; Saul?, R.; Batiuškait?, D.; Saulis, G.

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

  8. Cooperativity between various types of polar solute-solvent interactions in aqueous media.

    PubMed

    Madeira, Pedro P; Bessa, Ana; Loureiro, Joana A; Álvares-Ribeiro, Luís; Rodrigues, Alírio E; Zaslavsky, Boris Y

    2015-08-21

    Partition coefficients of seven low molecular weight compounds were measured in multiple aqueous two-phase systems (ATPSs) formed by pairs of different polymers. The ionic composition of each ATPS was varied to include 0.01M sodium phosphate buffer (NaPB), pH 7.4 and 0.1M Na2SO4, 0.15M NaCl, and 0.15M NaClO4 all in 0.01M NaPB, pH 7.4. The differences between the solvent features of the coexisting phases in all the ATPSs were estimated from partitioning of a homologous series of dinitrophenylated-amino acids and by the solvatochromic method. The solute-specific coefficients for the compounds examined were determined by the multiple linear regression analysis using the modified linear solvation energy relationship equation. It is established that the solute specific coefficients characterizing different types of the solute-water interactions (dipole-dipole, dipole-ion, and H-bonding) for a given solute change in the presence of different salt additives in the solute specific manner. It is also found that these characteristics are linearly interrelated. It is suggested that there is a cooperativity between various types of solute-water interactions governed by the solute structure. PMID:26162665

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

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

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

  10. Molecular Alignment in Gaseous Expansions and Anisotropy of Intermolecular Forces

    NASA Astrophysics Data System (ADS)

    Aquilanti, Vincenzo

    2005-05-01

    Recently we experimentally demonstrated how a planar molecule tends to travel as a "frisbee" when a gaseous mixture with lighter carriers expands into a vacuum, the orientation being due to collisions. The molecule is benzene, the prototype of aromatic chemistry .The demonstration is via two complementary experiments: interrogating benzene by IR-laser light and controlling its orientation by selective scattering on a rare gas target. The results cast new light on the microscopic mechanism of collisional alignment (our earlier work regarded diatomic molecules, such as O2 and N2) and suggest a useful way to produce intense beams of aligned molecules, permitting studies of steric effects in gas-phase processes. This study has been extended to other simple hydrocarbons such as ethylene, acetylene and ethane, indicating that collisional alignment is effective also in these cases. Applications are in progress for molecule — surface scattering, opening expectations for nanocatalysis. Combining collisional studies of supersonic seeded beams of aligned molecules with results from scattering of rotationally hot molecular beams allows development of systematic characterization of intermolecular forces, particularly regarding molecular anisotropies and their roles is cluster formation: investigated systems include atmospheric gases, hydrocarbons, water. This extends our previous collisional studies on interactions of open-shell atoms, aligned by a magnetic field. The review presented here concludes with a sketch of accompanying theoretical developments, and by perspectives for collisional orientations and even chiral discrimination in linear flows or vortices.

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

    SciTech Connect

    Averbukh, V.; Cederbaum, L. S.

    2007-11-29

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

  12. Frontier orbital symmetry control of intermolecular electron transfer

    SciTech Connect

    Stevens, B.

    1990-11-01

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

  13. Real-space identification of intermolecular bonding with atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Qiu, Xiaohui

    2014-03-01

    A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms, whose formation and breaking result in chemical reactions and the production of new substances. Distinct from the covalent bond, the intermolecular interactions are often a vague concept elusive in experimental observations. Nevertheless, intermolecular interactions virtually affect all physical and chemical properties of substances in the condensed phases. The interactions between molecules, particularly the hydrogen bond, are responsible for the structural transformations and functions of biological molecules. Because most of the molecular characterization techniques are more sensitive to the covalent structures of the molecules, it remains a challenge to quantitatively study the weak interactions between molecules despite the tremendous efforts toward this goal. Here we report a real-space identification of the formation of hydrogen bonding between molecules adsorbed on metal substrate using a non-contact atomic force microscope (nc-AFM). The atomically resolved molecular structures with unprecedented details enable a precise determination of the characteristics of the hydrogen bond network, including bonding sites, orientations and lengths. The observed bond contrast was interpreted by ab initio density functional calculations that indicate the electron density contribution from the hybridized electronic state of hydrogen bond. Given the extensively discussion on the nature of hydrogen bonding and the recent redefinition by IUPAC, the observation of hydrogen bonding in real-space may be a stimulating evidence for theoretical chemistry. Meanwhile, the direct identification of local bonding configurations by nc-AFM would advance the understanding of intermolecular interactions in complex molecules with multiple active sites, offering complementary structural information essential for various applications in materials and biological sciences.

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    PubMed

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

    2010-09-01

    The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents. PMID:20698713

  16. Vibronic spectra of perylene bisimide oligomers: effects of intermolecular charge-transfer excitation and conformational flexibility.

    PubMed

    Gao, Fang; Zhao, Yi; Liang, WanZhen

    2011-03-31

    We have recently presented a theoretical study on the temperature-dependent absorption and photoluminescence spectroscopy of rubrene multichromophores by combining the time-dependent long-range-corrected density functional theory with the Frenkel exciton model (Gao; et al. J. Phys. Chem. A2009, 113, 12847). The spectra of rubrene multichromophores up to heptamers have been calculated and the effects of exciton-phonon coupling and temperature on the photophysical properties of both H- and J-aggregated oligomers were addressed. However, in that work the contribution of intermolecular charge-transfer excitons (CTEs) to vibronic spectra was not addressed. Here we take into account the effect of CTEs for the absorption and emission spectra of the aggregated perylene bisimide (PBI) oligomers in order to have a quantitative explanation to the experimental absorption and emission spectra of the PBI dyes. The role of intermolecular CTEs is discussed for different intermolecular orientations and distances. The simulations demonstrate that the contribution of CTEs becomes significant when the intermolecular distance is less than 4.5 Å for the ?-? stacked PBI aggregates, and the mixed exciton model is prerequisite to explain the experimentally observed red-shift of the absorption spectra in this case. The large Stokes shift of the emission spectra can be reproduced by our model, and it is induced by the asymmetric nature of the lowest excitonic state of the H-aggregated oligomers. The experimentally observed broad emission bands come from two species with different conformations. As for J-aggregated PBI oligomers, the interactions of FEs induce the red-shift and the increase of the relative intensity of 0-0 peak of the absorption spectra with more aggregated units. PMID:21384839

  17. Photon-Mediated Interaction between Two Distant Atoms

    E-print Network

    Stefan Rist; Jürgen Eschner; Markus Hennrich; Giovanna Morigi

    2008-05-06

    We study the photonic interactions between two distant atoms which are coupled by an optical element (a lens or an optical fiber) focussing part of their emitted radiation onto each other. Two regimes are distinguished depending on the ratio between the radiative lifetime of the atomic excited state and the propagation time of a photon between the two atoms. In the two regimes, well below saturation the dynamics exhibit either typical features of a bad resonator, where the atoms act as the mirrors, or typical characteristics of dipole-dipole interaction. We study the coherence properties of the emitted light and show that it carries signatures of the multiple scattering processes between the atoms. The model predictions are compared with the experimental results in J. Eschner {\\it et al.}, Nature {\\bf 413}, 495 (2001).

  18. Hyper-chaotic Magnetisation Dynamics of Two Interacting Dipoles

    NASA Astrophysics Data System (ADS)

    Urzagasti, D.; Becerra-Alonso, D.; Pérez, L. M.; Mancini, H. L.; Laroze, D.

    2015-12-01

    The present work is a numerical study of the deterministic spin dynamics of two interacting anisotropic magnetic particles in the presence of a time-dependent external magnetic field using the Landau-Lifshitz equation. Particles are coupled through the dipole-dipole interaction. The applied magnetic field is made of a constant longitudinal amplitude component and a time-dependent transversal amplitude component. Dynamical states obtained are represented by their Lyapunov exponents and bifurcation diagrams. The dependence on the largest and the second largest Lyapunov exponents, as a function of the magnitude and frequency of the applied magnetic field, and the relative distance between particles, is studied. The system presents multiple transitions between regular and chaotic behaviour depending on the control parameters. In particular, the system presents consistent hyper-chaotic states.

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

    SciTech Connect

    Salam, A.

    2013-12-28

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

  20. Magnetic interactions in native horse spleen ferritin below the superparamagnetic blocking temperature

    NASA Astrophysics Data System (ADS)

    Allen, P. D.; St. Pierre, T. G.; Street, R.

    1998-01-01

    The magnetic interactions in a freeze-dried native horse spleen ferritin were quantified by measuring 5 K IRM and DCD remanence curves using a SQUID magnetometer. Irreversible and reversible components of magnetic moment were determined for a range of fields to ± 30 kOe and attributed to blocked and unblocked SPM particles, respectively. This separation allowed the proportion and mean magnetic properties of each population to be determined. By fitting to a modified Langevin, the mean magnetic moment per particle of the unblocked population was calculated to be 15 ? B, whilst constituting 67% of the magnetic moment at 5 K. Inter-particle interactions in ferritin were quantified using Henkel and ? I plots, showing that ferritin particles weakly interact, with ? I < 3%. This finding is consistent with a weak dipole-dipole interaction between otherwise magnetically independent particles.

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

    SciTech Connect

    Wunner, G.; Cartarius, H.; Fabcic, T.; Koeberle, P.; Main, J.; Schwidder, T.

    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.

  2. Coexistence of alternating ferromagnetic and antiferromagnetic intermolecular interactions in organic compounds. Synthesis, structure, thermal stability, and magnetic properties of 2,4-hexadiynylenedioxybis[2-(p,phenylene)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl] diradical

    SciTech Connect

    Hernandez-Gasio, E.; Mas, M.; Molins, E.; Rovira, C.; Veciana, J.; Borras-Almenar, J.J.; Coronada, E.

    1994-12-01

    A crystalline phase of the title diradical has been prepared and characterized by X-ray diffraction, IR, UV-vis, and EPR spectroscopies, and magnetic susceptibility measurements. This phase belongs to the C2/c space group [a = 16.57(2) {angstrom}, b = 16.116(2) {angstrom}, c = 13.10(1) {angstrom}, {beta} = 123.05(4){degrees}, V = 2931(4) {angstrom}{sup 3}, Z = 4, d{sub calc} = 1.30 g cm{sup {minus}3}, T = 21{degrees}C, R{sub u} = 0.092, R{sub w} = 0.116]. The molecular structure of the diradical is characterized by an asymmetrical Z-shaped conformation. The most relevant features observed in the molecular packing are the large interdiacetylene separations - the shortest one is 8.285 {angstrom}-and the alternation in the characteristics of the intermolecular contacts between the radical side groups of the DA; which are jointed by hydrogen bonds between the oxygen atoms of NO groups and aromatic hydrogen atoms. On the basis of accepted structural criteria, this solid-state structure should not support a single-crystal topochemical polymerization and, accordingly, the UV-induced polymerization is not achieved. Thermal treatment, however, turns the crystals from blue to dark brown. Thermal analyses under nitrogen, performed with DSC and TGA techniques, reveal an explosive and complex decomposition, at temperatures higher than 90{degrees}C, with an evolution of gaseous NO (GC-MS) and a destruction of most of the radical centers of diradical molecules, as demonstrated by EPR and magnetic measurements. The study of the temperature dependence of the EPR signals of very diluted solutions of diradical 1 shows that it has a thermally modulated intramolecular exchange interaction due to the flexibility of the spacers joining the two radical centers and, furthermore, that when this diradical adopts a rigid conformation the two radical moieties are magnetically isolated (J{sup intra}/k {approximately} 0 K). 44 refs., 12 figs., 3 tabs.

  3. Statistical Model for Intermolecular Adhesion in ?-Conjugated Polymers

    NASA Astrophysics Data System (ADS)

    Schmit, Jeremy D.; Levine, Alex J.

    2008-05-01

    We propose an interchain binding mechanism in ?-conjugated polymers based on the intermolecular tunneling of the delocalized electrons occurring at points where the polymers cross. This mechanism predicts specific bound structures of chains that depend on whether they are semiconducting or metallic. Semiconducting chains should form polyacenelike states exhibiting binding at every other site, while (doped) metallic chains can bind at each site. We also show that solitons colocalize with the intermolecular binding sites thereby strengthening the binding effect and investigate the conformational statistics of the resulting bimolecular aggregates.

  4. Strong impact of protonation and deprotonation on intermolecular Coulombic decay

    NASA Astrophysics Data System (ADS)

    Kryzhevoi, Nikolai V.; Cederbaum, Lorenz S.

    2012-11-01

    Intermolecular Coulombic decay (ICD) is an ultrafast relaxation mechanism of a highly excited system embedded in a chemical environment. Our theoretical investigation of ammonia clusters shows that the ICD efficiency can be regulated by protonation or deprotonation. It is suggested that by varying ICD rate through changing the environmental pH value a control over the relaxation dynamics can be achieved.

  5. Experimental Proof of Resonant Auger Decay Driven Intermolecular Coulombic Decay

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    Resonant Auger decay driven Intermolecular Coulombic Decay through synchrotron radiation in gas phase carbon monoxided dimers and nitrogen dimers has been studied. We report the first experiment where the low-energy ICD-electron has been measured in coincidence with the ionic fragments and Resonant Auger ICD has been proved experimentally.

  6. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

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

  7. Effects of salt on intermolecular polyelectrolyte complexes formation between cationic microgel and polyanion.

    PubMed

    Ogawa, Kazuyoshi

    2015-12-01

    The study of interpolyelectrolyte complex (IPEC) formation between cationic microgel and polyanion was presented. The size and molecular weight of cationic microgel are much larger than those of linear anionic polyelectrolyte. The resulting IPEC was divided by dynamic light scattering (DLS), static light scattering (SLS), and turbidity or spectrometry; (i) water-soluble intra-particle complexes consisting of one microgel to which linear polyelectrolytes bind; (ii) complex coacervates (inter-particle complexes composed of aggregated intra-particle complexes); and (iii) insoluble amorphous precipitates. These types depended on not only the mixing ratio of polyanion to cationic microgel but also salt concentration. This trend was discussed from IPEC's composition, thermodynamics of IPEC formation and the salt effect on intermolecular interactions which were expected in IPEC formation. The results obtained from the use of microgel in IPEC's study suggested that not only electrostatic interaction but also hydrophobic interaction play an important role in the aggregation or association of IPEC. PMID:26472211

  8. Magnetic interactions in silica coated nanoporous assemblies of CoFe2O4 nanoparticles with cubic magnetic anisotropy

    NASA Astrophysics Data System (ADS)

    Laureti, S.; Varvaro, G.; Testa, A. M.; Fiorani, D.; Agostinelli, E.; Piccaluga, G.; Musinu, A.; Ardu, A.; Peddis, D.

    2010-08-01

    Magnetic interactions in silica coated spherical nanoporous assemblies of CoFe2O4 nanoparticles have been investigated by low temperature field dependent remanent magnetization (MDCD and MIRM) and magnetization relaxation measurements. The synthesis procedure leads to the formation of spherical aggregates of about 50-60 nm in diameter composed of hexagonal shaped nanocrystals with shared edges. The negative deviation from the non-interacting case in the Henkel plot indicates the predominance of dipole-dipole interactions favouring the demagnetized state, although the presence of exchange interactions in the porous system cannot be excluded. The activation volume, derived from time dependent magnetization measurements, turns out to be comparable with the particle physical volume, thus indicating, in agreement with static and dynamic irreversible magnetization measurements, that the magnetization reversal actually involves individual crystals.

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

    PubMed Central

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

    2014-01-01

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

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

    E-print Network

    Baik, Mu-Hyun

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

  11. Statistical thermodynamics of fluids with both dipole and quadrupole moments.

    PubMed

    Benavides, Ana L; Delgado, Francisco J García; Gámez, Francisco; Lago, Santiago; Garzón, Benito

    2011-06-21

    New Gibbs ensemble simulation data for a polar fluid modeled by a square-well potential plus dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions are presented. This simulation data is used in order to assess the applicability of the multipolar square-well perturbation theory [A. L. Benavides, Y. Guevara, and F. del Ri?o, Physica A 202, 420 (1994)] to systems where more than one term in the multipole expansion is relevant. It is found that this theory is able to reproduce qualitatively well the vapor-liquid phase diagram for different multipolar moment strengths, corresponding to typical values of real molecules, except in the critical region. Hence, this theory is used to model the behavior of substances with multiple chemical bonds such as carbon monoxide and nitrous oxide and we found that with a suitable choice of the values of the intermolecular parameters, the vapor-liquid equilibrium of these species is adequately estimated. PMID:21702567

  12. Entanglement between two qubits one of which interacts with a thermal field

    E-print Network

    Eugene Bashkirov; Michail Mastyugin

    2015-05-16

    In this paper, we have investigated the entanglement between two dipole coupled two-level atoms. The model, in which only one atom is trapped in an lossless cavity and interacts with single-mode thermal field, and the other one can be spatially moved freely outside the cavity has been carried out. We have considered the effect of the atomic coherence on the entanglement behavior. We have shown that a thermal field might cause high entanglement between the atoms both for coherent and incoherent initial atomic states only for small values of the cavity mean photon number. In the considered model the atoms would get entangled even when both atoms are initially in the excited state. We have also derived that the degree of entanglement is weakly dependent on the strength of dipole-dipole interaction for coherent initial states.

  13. Intermolecular Hydrogen Bonding in Peptide and Modified Jeffamine Organogels

    NASA Astrophysics Data System (ADS)

    Savin, Daniel; Richardson, Adam

    2011-03-01

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

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed

    Glock, Carsten; Görls, Helmar; Westerhausen, Matthias

    2012-07-18

    Calciate-mediated intermolecular hydroamination of diphenylbutadiyne with N-phenyl and N-isopropyl-substituted anilines yields E- and Z-isomers of the corresponding 1-anilino-1,4-diphenylbut-1-ene-3-yne. In the case of HNPh(2) solely heterobimetallic K(2)Ca(NPh(2))(4) is able to effectively catalyze this hydroamination reaction in tetrahydrofuran at elevated temperatures. PMID:22684250

  17. 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.

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

    PubMed

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

    2013-03-14

    Low frequency Raman spectra of ionic liquids have been obtained as a function of pressure up to ca. 4.0 GPa at room temperature and as a function of temperature along the supercooled liquid and glassy state at atmospheric pressure. Intermolecular vibrations are observed at ~20, ~70, and ~100 cm(-1) at room temperature in ionic liquids based on 1-alkyl-3-methylimidazolium cations. The component at ~100 cm(-1) is assigned to librational motion of the imidazolium ring because it is absent in non-aromatic ionic liquids. There is a correspondence between the position of intermolecular vibrational modes in the normal liquid state and the spectral features that the Raman spectra exhibit after partial crystallization of samples at low temperatures or high pressures. The pressure-induced frequency shift of the librational mode is larger than the other two components that exhibit similar frequency shifts. The lowest frequency vibration observed in a glassy state corresponds to the boson peak observed in light and neutron scattering spectra of glass-formers. The frequency of the boson peak is not dependent on the length scale of polar?non-polar heterogeneity of ionic liquids, it depends instead on the strength of anion-cation interaction. As long as the boson peak is assigned to a mixing between localized modes and transverse acoustic excitations of high wavevectors, it is proposed that the other component observed in Raman spectra of ionic liquids has a partial character of longitudinal acoustic excitations. PMID:23514505

  19. 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

  20. Contributions of different parts of spin-spin interactions to quantum correlations in a spin ring model in an external magnetic field

    E-print Network

    S. I. Doronin; E. B. Fel'dman; E. I. Kuznetsova

    2015-05-14

    We study quantum correlations in a bipartite heteronuclear $(N-1)\\times1$ system in an external magnetic field. The system consists of a spin ring with an arbitrary number $N-1$ of spins on the ring and one spin in its center. The spins on the ring are connected by secular dipole-dipole interactions and interact with the central spin through the Heisenberg $zz$-interaction. We show that the quantum discord, describing quantum correlations between the ring and the central spin, can be obtained analytically for this model in the high temperature approximation. The model allows us to find contributions of different parts of the spin-spin interactions to quantum correlations. We also investigate the evolution of quantum and classical correlations at different numbers of spins.

  1. Theoretical calculations: can Gibbs free energy for intermolecular complexes be predicted efficiently and accurately?

    PubMed

    Isayev, Olexandr; Gorb, Leonid; Leszczynski, Jerzy

    2007-07-15

    The theoretical study has been performed to refine the procedure for calculations of Gibbs free energy with a relative accuracy of less than 1 kcal/mol. Three benchmark intermolecular complexes are examined via several quantum-chemical methods, including the second-order Moller-Plesset perturbation (MP2), coupled cluster (CCSD(T)), and density functional (BLYP, B3LYP) theories augmented by Dunnings correlation-consistent basis sets. The effects of electron correlation, basis set size, and anharmonicity are systematically analyzed, and the results are compared with available experimental data. The results of the calculations suggest that experimental accuracy can be reached only by extrapolation of MP2 and CCSD(T) total energies to the complete basis set. The contribution of anharmonicity to the zero point energy and TDeltaSint values is fairly small. The new, economic way to reach chemical accuracy in the calculations of the thermodynamic parameters of intermolecular interactions is proposed. In addition, interaction energy (De) and free energy change (DeltaA) for considered species have been evaluated by Carr-Parrinello molecular dynamics (CPMD) simulations and static BLYP-plane wave calculations. The free energy change along the reaction paths were determined by the thermodynamic integration/"Blue Moon Ensemble" technique. Comparison between obtained values, and available experimental and conventional ab initio results has been made. We found that the accuracy of CPMD simulations is affected by several factors, including statistical uncertainty and convergence of constrained forces (TD integration), and the nature of DFT (density functional theory) functional. The results show that CPMD technique is capable of reproducing interaction and free energy with an accuracy of 1 kcal/mol and 2-3 kcal/mol respectively. PMID:17340602

  2. 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

  3. Long-range potentials, including retardation, for the interaction of two alkali-metal atoms

    NASA Astrophysics Data System (ADS)

    Marinescu, M.; Babb, J. F.; Dalgarno, A.

    1994-10-01

    The retarded long-range potentials for the dispersion interaction arising from induced multipole moments of two ground-state alkali-metal atoms are evalulated as functions of the separation R for Li, Na, K, Rb, and Cs. Accurate atomic properties, determined using published model potentials, are utilized. Values for the potentials are given over a wide range of R. Results for H are also given. For small R the results reproduce the accepted values for the unretarded dispersion dipole-dipole (van der Waals), dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole coefficients, while for R-->? the Casimir-Polder potentials, due to retardation or effects due to the finite speed of light, are obtained. The overlap between the retardation potentials and terms arising from the Breit-Pauli Hamiltonian is explored.

  4. 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.

  5. Long-range interactions between a He(2 {sup 3}S) atom and a He(2 {sup 3}P) atom for like isotopes

    SciTech Connect

    Zhang, J.-Y.; Yan, Z.-C.; Vrinceanu, D.; Babb, J. F.; Sadeghpour, H. R.

    2006-02-15

    For the interactions between a He(2 {sup 3}S) atom and a He(2 {sup 3}P) atom for like isotopes, we report perturbation theoretic calculations using accurate variational wave functions in Hylleraas coordinates of the coefficients determining the potential energies at large internuclear separations. We evaluate the coefficient C{sub 3} of the first order resonant dipole-dipole energy and the van der Waals coefficients C{sub 6}, C{sub 8}, and C{sub 10} for the second order energies arising from the mutual perturbations of instantaneous electric dipole, quadrupole, and octupole interactions. We also evaluate the leading contribution to the third-order energy. We establish definitive values including treatment of the finite nuclear mass for the {sup 3}He(2 {sup 3}S)-{sup 3}He(2 {sup 3}P) and {sup 4}He(2 {sup 3}S)-{sup 4}He(2 {sup 3}P) interactions.

  6. 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.

  7. Asymmetric intermolecular Pauson-Khand reaction of symmetrically substituted alkynes.

    PubMed

    Ji, Yining; Riera, Antoni; Verdaguer, Xavier

    2009-10-01

    The asymmetric intermolecular Pauson-Khand reaction of symmetric alkynes has been accomplished for the first time. N-Phosphino-p-tolylsulfinamide (PNSO) ligands have been identified as efficient ligands in this process. The chirality of the cobalt S-bonded sulfinyl moiety was found to direct olefin insertion into one of the two possible cobalt-carbon bonds in the alkyne complex. Reaction of symmetric alkynes allows for a simplified experimental protocol since there is no need for separation of diastereomeric complexes. PMID:19739661

  8. A New Approach to Empirical Intermolecular and Conformational Potential Energy Functions. I. Description of Model and Derivation of Parameters

    PubMed Central

    Shipman, Lester L.; Burgess, Antony W.; Scheraga, Harold A.

    1975-01-01

    An empirical potential energy function based on the interactions of the electrons and nuclei in molecules has been developed and tested. The potential energy of interaction is approximated by the sum of the coulombic interactions between all point charge centers (electrons and nuclei), an exponential repulsion to represent electron-electron overlap repulsion, and an R-6 (R = distance) attraction to simulate dispersion and other attractive energies between the heavy atom fragments of the molecules. The parameters of the potential energy function have been determined from experimental gas-phase and crystal data. The results indicate that both intramolecular and intermolecular interaction energies can be treated with the same set of parameters. In comparison to other empirical interaction potentials now in use, there are fewer independent parameters, there is no need for intrinsic torsional potentials to obtain the correct rotational barriers, and there is no need for special hydrogen bonding functions to account for the directionality and energetics of hydrogen bonding. PMID:16592221

  9. Intra- and intermolecular energy transfer in highly excited ozone complexes.

    PubMed

    Ivanov, Mikhail V; Grebenshchikov, Sergy Yu; Schinke, Reinhard

    2004-06-01

    The energy transfer of highly excited ozone molecules is investigated by means of classical trajectories. Both intramolecular energy redistribution and the intermolecular energy transfer in collisions with argon atoms are considered. The sign and magnitude of the intramolecular energy flow between the vibrational and the rotational degrees of freedom crucially depend on the projection K(a) of the total angular momentum of ozone on the body-fixed a axis. The intermolecular energy transfer in single collisions between O(3) and Ar is dominated by transfer of the rotational energy. In accordance with previous theoretical predictions, the direct vibrational de-excitation is exceedingly small. Vibration-rotation relaxation in multiple Ar+O(3) collisions is also studied. It is found that the relaxation proceeds in two clearly distinguishable steps: (1) During the time between collisions, the vibrational degrees of freedom are "cooled" by transfer of energy to rotation; even at low pressure equilibration of the internal energy is slow compared to the time between collisions. (2) In collisions, mainly the rotational modes are "cool" by energy transfer to argon. PMID:15268022

  10. Pom1 gradient buffering through intermolecular auto-phosphorylation

    PubMed Central

    Hersch, Micha; Hachet, Olivier; Dalessi, Sascha; Ullal, Pranav; Bhatia, Payal; Bergmann, Sven; Martin, Sophie G

    2015-01-01

    Concentration gradients provide spatial information for tissue patterning and cell organization, and their robustness under natural fluctuations is an evolutionary advantage. In rod-shaped Schizosaccharomyces pombe cells, the DYRK-family kinase Pom1 gradients control cell division timing and placement. Upon dephosphorylation by a Tea4-phosphatase complex, Pom1 associates with the plasma membrane at cell poles, where it diffuses and detaches upon auto-phosphorylation. Here, we demonstrate that Pom1 auto-phosphorylates intermolecularly, both in vitro and in vivo, which confers robustness to the gradient. Quantitative imaging reveals this robustness through two system’s properties: The Pom1 gradient amplitude is inversely correlated with its decay length and is buffered against fluctuations in Tea4 levels. A theoretical model of Pom1 gradient formation through intermolecular auto-phosphorylation predicts both properties qualitatively and quantitatively. This provides a telling example where gradient robustness through super-linear decay, a principle hypothesized a decade ago, is achieved through autocatalysis. Concentration-dependent autocatalysis may be a widely used simple feedback to buffer biological activities. PMID:26150232

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

    SciTech Connect

    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.

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

    PubMed

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

    2014-09-01

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

  13. Supramolecular interactions in the solid state

    PubMed Central

    Resnati, Giuseppe; Boldyreva, Elena; Bombicz, Petra; Kawano, Masaki

    2015-01-01

    In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials. PMID:26594375

  14. Supramolecular interactions in the solid state.

    PubMed

    Resnati, Giuseppe; Boldyreva, Elena; Bombicz, Petra; Kawano, Masaki

    2015-11-01

    In the last few decades, supramolecular chemistry has been at the forefront of chemical research, with the aim of understanding chemistry beyond the covalent bond. Since the long-range periodicity in crystals is a product of the directionally specific short-range intermolecular interactions that are responsible for molecular assembly, analysis of crystalline solids provides a primary means to investigate intermolecular interactions and recognition phenomena. This article discusses some areas of contemporary research involving supramolecular interactions in the solid state. The topics covered are: (1) an overview and historical review of halogen bonding; (2) exploring non-ambient conditions to investigate intermolecular interactions in crystals; (3) the role of intermolecular interactions in morphotropy, being the link between isostructurality and polymorphism; (4) strategic realisation of kinetic coordination polymers by exploiting multi-interactive linker molecules. The discussion touches upon many of the prerequisites for controlled preparation and characterization of crystalline materials. PMID:26594375

  15. Short-Range, Spin-Dependent Interactions of Electrons: A Probe for Exotic Pseudo-Goldstone Bosons.

    PubMed

    Terrano, W A; Adelberger, E G; Lee, J G; Heckel, B R

    2015-11-13

    We used a torsion pendulum and rotating attractor with 20-pole electron-spin distributions to probe dipole-dipole interactions mediated by exotic pseudo-Goldstone bosons with m_{b}c^{2}?500???eV and coupling strengths up to 14 orders of magnitude weaker than electromagnetism. This corresponds to symmetry-breaking scales F?70??TeV, the highest reached in any laboratory experiment. We used an attractor with a 20-pole unpolarized mass distribution to improve laboratory bounds on CP-violating monopole-dipole forces with 1.5???eV

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

    SciTech Connect

    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.

  17. Intermolecular Coulomb Decay at Weakly Coupled Heterogeneous Interfaces

    NASA Astrophysics Data System (ADS)

    Grieves, Gregory A.; Orlando, Thomas M.

    2011-07-01

    Surface ejection of H+(H2O)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 (2a1-1), 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+(H2O)n=1-8 desorption with kinetic energies that vary with initiating state, final state, and interatomic or molecular distances.

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

    SciTech Connect

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

    2015-04-14

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

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

    PubMed Central

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

    2014-01-01

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

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

    E-print Network

    McGehee, Michael

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

  1. Localization of atomic ensembles via superfluorescence RID B-9093-2009 RID A-5077-2009 

    E-print Network

    Macovei, Mihai; Evers, Joerg; Keitel, Christoph H.; Zubairy, M. Suhail

    2007-01-01

    to the static dipole-dipole interaction potential?i.e., ? jl = 3? 4?krjl?3 ?1 ? 3 cos 2? jl? . ?8? For lower atomic densities the collective parameters jl and ? jl vanish because the atoms react independently from each other in this particular case... the dipole-dipole interaction potential over all directions. Inter- estingly, the static dipole-dipole interaction given by Eq. ?8? vanishes in this case. Then, according to the second term in Eq. ?7?, the averaged dipole-dipole interactions among the two...

  2. On the theory of double quantum NMR in polymer systems: The second cumulant approximation for many spin I = 1/2 systems

    SciTech Connect

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

    2013-11-21

    General analytical expressions for Double Quantum Nuclear Magnetic Resonance (DQ NMR) kinetic curves of many-spin I = 1/2 systems are derived with an accuracy of the second cumulant approximation. The expressions obtained exactly describe the initial part of the kinetic curves and provide a reasonable approximation up to times of about the effective spin-relaxation time. For the case when the system contains two isolated spins, this result exactly reproduces known expressions. In the case of polymer melts, the intermolecular magnetic dipole-dipole interactions significantly influence the time dependence of the DQ NMR kinetic curves.

  3. Theoretical study on electromagnetically induced transparency in molecular aggregate models using quantum Liouville equation method

    SciTech Connect

    Minami, Takuya; Nakano, Masayoshi

    2015-01-22

    Electromagnetically induced transparency (EIT), which is known as an efficient control method of optical absorption property, is investigated using the polarizability spectra and population dynamics obtained by solving the quantum Liouville equation. In order to clarify the intermolecular interaction effect on EIT, we examine several molecular aggregate models composed of three-state monomers with the dipole-dipole coupling. On the basis of the present results, we discuss the applicability of EIT in molecular aggregate systems to a new type of optical switch.

  4. On the theory of Double Quantum NMR in polymer systems: the second cumulant approximation for many spin I=1/2 systems

    E-print Network

    N. Fatkullin; C. Mattea; S. Stapf

    2013-09-20

    General analytical expressions for Double Quantum Nuclear Magnetic Resonance (NMR) kinetic curves of many-spin I=1/2 systems are derived with an accuracy of the second cumulant approximation. The expressions obtained exactly describe the initial part of the kinetic curves and provide a reasonable approximation up to times of about twice the effective spin-relaxation time. For the case when the system contains two isolated spins, this result exactly reproduces known expressions. In the case of polymer melts, the intermolecular magnetic dipole-dipole interactions significantly influence the time dependence of the DQ NMR kinetic curves.

  5. Computational approaches for identifying inhibitors of protein interactions 

    E-print Network

    Mehio, Wissam

    2011-06-27

    Inter-molecular interaction is at the heart of biological function. Proteins can interact with ligands, peptides, small molecules, and other proteins to serve their structural or functional purpose. With advances in ...

  6. Influence of intermolecular amide hydrogen bonding on the geometry, atomic charges, and spectral modes of acetanilide: An ab initio study

    NASA Astrophysics Data System (ADS)

    Binoy, J.; Prathima, N. B.; Murali Krishna, C.; Santhosh, C.; Hubert Joe, I.; Jayakumar, V. S.

    2006-08-01

    Acetanilide, a compound of pharmaceutical importance possessing pain-relieving properties due to its blocking the pulse dissipating along the nerve fiber, is subjected to vibrational spectral investigation using NIR FT Raman, FT-IR, and SERS. The geometry, Mulliken charges, and vibrational spectrum of acetanilide have been computed using the Hartree-Fock theory and density functional theory employing the 6-31G (d) basis set. To investigate the influence of intermolecular amide hydrogen bonding, the geometry, charge distribution, and vibrational spectrum of the acetanilide dimer have been computed at the HF/6-31G (d) level. The computed geometries reveal that the acetanilide molecule is planar, while twisting of the secondary amide group with respect to the phenyl ring is found upon hydrogen bonding. The trans isomerism and “amido” form of the secondary amide, hyperconjugation of the C=O group with the adjacent C-C bond, and donor-acceptor interaction have been investigated using computed geometry. The carbonyl stretching band position is found to be influenced by the tendency of the phenyl ring to withdraw nitrogen lone pair, intermolecular hydrogen bonding, conjugation, and hyperconjugation. A decrease in the NH and C=O bond orders and increase in the C-N bond orders due to donor-acceptor interaction can be observed in the vibrational spectra. The SERS spectral analysis reveals that the flat orientation of the molecule on the adsorption plane is preferred.

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

    PubMed

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

    2015-03-01

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

  8. The Smc5/6 Complex Is an ATP-Dependent Intermolecular DNA Linker.

    PubMed

    Kanno, Takaharu; Berta, Davide G; Sjögren, Camilla

    2015-09-01

    The structural maintenance of chromosome (SMC) protein complexes cohesin and condensin and the Smc5/6 complex (Smc5/6) are crucial for chromosome dynamics and stability. All contain essential ATPase domains, and cohesin and condensin interact with chromosomes through topological entrapment of DNA. However, how Smc5/6 binds DNA and chromosomes has remained largely unknown. Here, we show that purified Smc5/6 binds DNA through a mechanism that requires ATP hydrolysis by the complex and circular DNA to be established. This also promotes topoisomerase 2-dependent catenation of plasmids, suggesting that Smc5/6 interconnects two DNA molecules using ATP-regulated topological entrapment of DNA, similar to cohesin. We also show that a complex containing an Smc6 mutant that is defective in ATP binding fails to interact with DNA and chromosomes and leads to cell death with concomitant accumulation of DNA damage when overexpressed. Taken together, these results indicate that Smc5/6 executes its cellular functions through ATP-regulated intermolecular DNA linking. PMID:26299966

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

    SciTech Connect

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

    2015-03-01

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

  10. Glycosaminoglycan and DNA Binding Induced Intra- and Intermolecular Exciton Coupling of the bis-4-Aminoquinoline Surfen.

    PubMed

    Zsila, Ferenc

    2015-09-01

    Despite the diverse biological activities of the glycosaminoglycan (GAG) antagonist surfen, the molecular details of its interaction with biomacromolecules remain poorly understood. Therefore, heparin and DNA binding properties of surfen were studied by circular dichroism (CD) and UV absorption spectroscopy methods. High-affinity (Ka ?~?10(7) ?M(-1)) association of surfen to the chiral heparin chain gives rise to a characteristic biphasic CD pattern due to the conformational twist of the aminoquinoline moieties around the central urea bridge. At higher drug loading, intermolecular stacking of surfen molecules alters the induced CD profile and also provokes strong UV hypochromism. In contrast to the right-handed heparin template, binding of surfen to the left-helicity chondroitin sulfate chains produces inverted CD pattern. Large UV hypochromism as well as polyphasic induced ellipticity bands indicate that surfen intercalates between the base pairs of calf-thymus DNA. Extensive CD spectroscopic changes observed at higher drug binding ratios refer to cooperative binding interactions between the intercalated drug molecules. The inherent conformational flexibility of surfen demonstrated here for the first time is important in its binding to distinct macromolecular targets and should be considered for rational drug design of novel GAG antagonists. PMID:26096963

  11. Development of a flexible intra- and intermolecular empirical potential function for large molecular systems

    SciTech Connect

    Oie, T.; Maggiora, M.; Christoffersen, R.E.; Duchamp, D.J.

    1981-01-01

    The development of a flexible intra- and intermolecular empirical potential function is described, which is designed for investigating the geometric structure of large molecular systems. The intramolecular components in the potential consist of harmonic bond stretching and angle bending terms, out-of-plane deformation terms, and torsional terms; intermolecular components include nonbonding, hydrogen bonding, and electrostatic germs. Bond lengths, angles, and torsional angles are predicted to within 2% of experiment, with most cases being within 1%. The suitability of the intermolecular potential was tested by crystal packing calculations; in all cases the results obtained were in excellent agreement with experiment.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Lackinger, M.; Heckl, W. M.

    2011-11-01

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

  14. 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.

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

    NASA Technical Reports Server (NTRS)

    Gruszka, Marcin; Borysow, Aleksandra

    1994-01-01

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

  16. 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)

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

    SciTech Connect

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

    1995-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  20. Dynamics of intermolecular Auger decay at a surface-chemisorbate interface

    NASA Astrophysics Data System (ADS)

    Matyba, Piotr; Carr, Adra; Chen, Cong; Murnane, Margaret M.; Kapteyn, Henry C.; Miller, David L.; Keller, Mark W.; Peng, Guowen; Mavrikakis, Manos; Eich, Steffen

    2014-03-01

    We use ultrafast high harmonic x-ray pulses to follow the relaxation dynamics of the 2p core-hole in Na chemisorbed on graphene/Ni(111). A core-excited Na atom cannot fill the 2p core-hole through Auger decay since the 3s shell has only one electron. In Na dimers or metal however, Auger decay is possible via interatomic or LVV Auger decay since the 3s electrons are shared or form a valence band (VB). The lifetimes of the 2p core-hole in dimers (15 +/-8 fs) and metal (51 +/-7 fs) are relatively long due to coupling and many body interactions. In a submonolayer of Na on graphene/Ni(111), the 3s electrons do not form a VB but populate the empty ?* state of graphene. Our measurements show that the LVV-like decay is still possible in such a system. Moreover, the lifetime of the 2p core-hole is exceptionally short (<2 fs to 7 fs depending on the coverage) when compared to Na dimers or metal. We conclude that this fast decay is mediated by the graphene and its delocalized ? and ? * electrons, and due to the strong Na-graphene bonding, is akin to Auger rather than to intermolecular Coulomb decay.

  1. Shaping interactions between polar molecules with far-off-resonant light

    SciTech Connect

    Lemeshko, Mikhail

    2011-05-15

    We show that dressing polar molecules with a far-off-resonant optical field leads to new types of intermolecular potentials, which undergo a crossover from the inverse power to oscillating behavior depending on the intermolecular distance, and whose parameters can be tuned by varying the laser intensity and wavelength. We present analytic expressions for the potential energy surfaces, thereby providing direct access to the parameters of an optical field required to design intermolecular interactions experimentally.

  2. Intermolecular dynamics of substitued benzene and cyclohexane liquids, studied by femtosecond nonlinear-optical polarization spectroscopy

    SciTech Connect

    Chang, Y.J.; Castner, E.W. Jr.

    1996-02-29

    Femtosecond time-resolved optical-heterodyne detected Raman-induced Kerr effect spectroscopy (OHD-RIKES) is shown to be a powerful and comprehensive tool for studying the intermolecular dynamics occurring in liquids. The observed dynamics include both the underdamped or coherent inertial motions, and the longer time scale diffusive relaxation. The inertial dynamics include phonon-like intermolecular vibrations, intermolecular collisions, and librational caging motions. Data are presented and analyzed for a series of five liquids: cyclohexane, methylcyclohexane, toluene, benzyl alcohol, and benzonitrile, listed in order of increasing polarity. We explore the effects of aromaticity (e.g., methylcyclohexane vs toluene), symmetry reduction (cyclohexane vs methylcyclohexane), and substitution effects (e.g., substituted benzene series) on the ultrafast intermolecular dynamics, for a group of molecular liquids of similar size and volume. We analyze the intermolecular dynamics in both the time and frequency domains by means of Fourier transformations. When Fourier-transformed into the frequency domain, the OHD-RIKES ultrafast transients of the intermolecular dynamics can be directly compared with the frequency domain spectra obtained from the far-infrared absorption and depolarized Raman techniques. This is done using the Gaussian librational caging model of Lynden-Bell and Steele, which results in a power-law scaling relation between dipole and polarizability time correlation functions. 122 refs., 7 figs., 7 tabs.

  3. 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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Jahnke, T.

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  7. Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force.

    PubMed

    Ghoufi, Aziz; Malfreyt, Patrice

    2006-12-14

    The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum. PMID:17176145

  8. 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...

  9. Role of the Strength of Drug-Polymer Interactions on the Molecular Mobility and Crystallization Inhibition in Ketoconazole Solid Dispersions.

    PubMed

    Mistry, Pinal; Mohapatra, Sarat; Gopinath, Tata; Vogt, Frederick G; Suryanarayanan, Raj

    2015-09-01

    The effects of specific drug-polymer interactions (ionic or hydrogen-bonding) on the molecular mobility of model amorphous solid dispersions (ASDs) were investigated. ASDs of ketoconazole (KTZ), a weakly basic drug, with each of poly(acrylic acid) (PAA), poly(2-hydroxyethyl methacrylate) (PHEMA), and polyvinylpyrrolidone (PVP) were prepared. Drug-polymer interactions in the ASDs were evaluated by infrared and solid-state NMR, the molecular mobility quantified by dielectric spectroscopy, and crystallization onset monitored by differential scanning calorimetry (DSC) and variable temperature X-ray diffractometry (VTXRD). KTZ likely exhibited ionic interactions with PAA, hydrogen-bonding with PHEMA, and weaker dipole-dipole interactions with PVP. On the basis of dielectric spectroscopy, the ?-relaxation times of the ASDs followed the order: PAA > PHEMA > PVP. In addition, the presence of ionic interactions also translated to a dramatic and disproportionate decrease in mobility as a function of polymer concentration. On the basis of both DSC and VTXRD, an increase in strength of interaction translated to higher crystallization onset temperature and a decrease in extent of crystallization. Stronger drug-polymer interactions, by reducing the molecular mobility, can potentially delay the crystallization onset temperature as well as crystallization extent. PMID:26070543

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

    PubMed Central

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

    2008-01-01

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

  11. Photoinduced intra- and intermolecular electron transfer in solutions and in solid organized molecular assemblies.

    PubMed

    Lemmetyinen, Helge; Tkachenko, Nikolai V; Efimov, Alexander; Niemi, Marja

    2011-01-14

    The present paper highlights results of a systematic study of photoinduced electron transfer, where the fundamental aspects of the photochemistry occurring in solutions and in artificially or self-assembled molecular systems are combined and compared. In photochemical electron transfer (ET) reactions in solutions the electron donor, D, and acceptor, A, have to be or to diffuse to a short distance, which requires a high concentration of quencher molecules and/or long lifetimes of the excited donor or acceptor, which cannot always be arranged. The problem can partly be avoided by linking the donor and acceptor moieties covalently by a single bond, molecular chain or chains, or rigid bridge, forming D-A dyads. The covalent combination of porphyrin or phthalocyanine donors with an efficient electron acceptor, e.g. fullerene, has a two-fold effect on the electron transfer properties. Firstly, the electronic systems of the D-A pair result in a formation of an exciplex intermediate upon excitation both in solutions and in solid phases. The formation of the exciplex accelerates the ET rate, which was found to be as fast as >10(12) s(-1). Secondly, the total reorganization energy can be as small as 0.3 eV, even in polar solvents, which allows nanosecond lifetimes for the charge separated (CS) state. Molecular assemblies can form solid heterogeneous, but organized systems, e.g. molecular layers. This results in more complex charge separation and recombination dynamics. A distinct feature of the ET in organized assemblies is intermolecular interactions, which open a possibility for a charge migration both in the acceptor and in the donor layers, after the primary intramolecular exciplex formation and charge separation in the D-A dyad. The intramolecular ET is fast (35 ps) and efficient, but the formed interlayer CS states have lifetimes in microsecond or even second time domain. This is an important result considering possible applications. PMID:21031207

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

    PubMed

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

    2012-05-10

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

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

    PubMed

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

    2015-12-15

    A mesoporous silica SBA-15 is modified with an array of amine-containing organosilanes including (i) propylamine, SiCH2CH2CH2NH2 (MONO), (ii) propylethylenediamine, SiCH2CH2CH2NHCH2CH2NH2 (DI), (iii) propyldiethylenetriamine, SiCH2CH2CH2NHCH2CH2NHCH2CH2NH2 (TRI), and (iv) propyltriethylenetetramine, SiCH2CH2CH2NHCH2CH2N(CH2CH2NH2)2 (TREN) and the low loading silane adsorbents (?0.45 mmol silane/g) are evaluated for their CO2 adsorption properties, with a focus on gaining insight into the propensity for intramolecular vs intermolecular CO2 adsorption. Adsorption isotherms at low CO2 coverages are measured while simultaneously recording the heat evolved via a Tian-Calvet calorimeter. The results are compared on a silane molecule efficiency basis (mol CO2 adsorbed/mol silane) to assess the potential for intramolecular CO2 adsorption, employing two amine groups in a single silane molecule. As the number of amines in the silane molecule increases (MONO < DI < TREN ? TRI), the silane molecule efficiency is enhanced owing to the ability to intramolecularly capture CO2. Analysis of the CO2 uptake for samples with the surface silanols removed by capping demonstrates that cooperative uptake due to amine-CO2-silanol interactions is also possible over these adsorbents and is the primary mode of sorption for the MONO material at the studied low silane loading. As the propensity for intramolecular CO2 capture increases due to the presence of multiple amines in a single silane molecule (MONO < DI < TREN ? TRI), the measured heat of adsorption also increases. This study of various amine-containing silanes at low coverage is the first to provide significant, direct evidence for intramolecular CO2 capture in a single silane molecule. Furthermore, it provides evidence for the relative heats of adsorption for physisorption on a silanol laden surface (ca. 37 kJ/mol), a silanol-capped surface (ca. 25 kJ/mol), via amine-CO2-silanol interactions (ca. 46 kJ/mol), and via amine-CO2-amine interactions at low surface coverages (ca. 65 kJ/mol). PMID:26602305

  14. 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.

  15. 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.

  16. 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.

  17. A simple and reliable approach to docking proteinprotein complexes from very sparse NOE-derived intermolecular distance restraints

    E-print Network

    Clore, G. Marius

    -derived intermolecular distance restraints Chun Tang & G. Marius Clore* Laboratory of Chemical Physics, National-derived intermolecular distance restraints (as few as three from a single point) in combination with a novel rep distance restraints, a van der Waals repulsion potential and the `reduced' radius of gyration potential

  18. On the theory of proton solid echo in polymer melts

    E-print Network

    Fatkullin, N; Mattea, C; Stapf, S

    2015-01-01

    Based on a modified Anderson-Weiss approximation (N. Fatkullin, A. Gubaidullin, C. Mattea, S.Stapf, J. Chem. Phys. 137 (2012), 224907) an improved theory of proton spin solid echo in polymer melts is formulated, taking into account contribution from intermolecular magnetic dipole-dipole interactions. The solid echo build-up function defined by the relation , where , and are the respective signals arising from ( ),( ) and ( ) spin echo experiments, where is an operator rotating the spin system on the angle relatively axis , is investigated. It is shown that the intermolecular part of this function at short times , where is a characteristic time for flip-flop transitions between proton spins, contains information about the relative mean squared displacements of polymer segments at different macromolecules, opening up a new opportunity for obtaining information about polymer dynamics in the millisecond regime.

  19. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    SciTech Connect

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

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  20. Salting Effects as an Illustration of the Relative Strength of Intermolecular Forces

    ERIC Educational Resources Information Center

    Person, Eric C.; Golden, Donnie R.; Royce, Brenda R.

    2010-01-01

    This quick and inexpensive demonstration of the salting of an alcohol out of an aqueous solution illustrates the impact of intermolecular forces on solubility using materials familiar to many students. Ammonium sulfate (fertilizer) is added to an aqueous 35% solution of isopropyl alcohol (rubbing alcohol and water) containing food coloring as a…

  1. Cell Adhesion Strength Is Controlled by Intermolecular Spacing of Adhesion Receptors

    E-print Network

    Schwarz, Ulrich

    Cell Adhesion Strength Is Controlled by Intermolecular Spacing of Adhesion Receptors C. Selhuber numerous cellular processes such as spreading, adhesion, migration, and proliferation. Using force the strength of cell adhesion. For spacings R90 nm, focal contact formation was inhibited and the detachment

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

    PubMed

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

    2016-01-01

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

  3. Mean field theory for the intermolecular and intramolecular conformational transitions of a single flexible polyelectrolyte chain

    NASA Astrophysics Data System (ADS)

    Shew, Chwen-Yang; Yoshikawa, Kenichi

    2007-04-01

    The diMarzio theory has been extended to elucidate the intermolecular and intramolecular phase segregations of a single flexible chain polyelectrolyte in dilute salt-free solutions. At the long chain limit, this theory yields the formalism obtained from the more sophisticated Edward Hamiltonian for polyelectrolyte problems. The calculated phase diagram exhibits the features of a first-order phase transition, with continuous and discontinuous transitions separated by a critical point. Under the discontinuous transition, the polyelectrolyte chain exhibits coexistent expanded and collapsed conformational states, same as intermolecular phase segregation. For a limiting long chain, the mean chain size at critical point is roughly 90% of the size of an ideal chain. Such a result implies that partial contraction within a chain molecule is required to collapse a flexible polyelectrolyte chain. Moreover, the theory predicts that for a longer chain, intramolecular segregated conformations differ significantly from intermolecular segregated conformations, but the difference becomes small for shorter chains. Besides, the charge needed to induce intramolecular segregation is smaller than that of intermolecular segregation for a given chain length. These findings are consistent with previous literature results.

  4. Mean field theory for the intermolecular and intramolecular conformational transitions of a single flexible polyelectrolyte chain.

    PubMed

    Shew, Chwen-Yang; Yoshikawa, Kenichi

    2007-04-14

    The diMarzio theory has been extended to elucidate the intermolecular and intramolecular phase segregations of a single flexible chain polyelectrolyte in dilute salt-free solutions. At the long chain limit, this theory yields the formalism obtained from the more sophisticated Edward Hamiltonian for polyelectrolyte problems. The calculated phase diagram exhibits the features of a first-order phase transition, with continuous and discontinuous transitions separated by a critical point. Under the discontinuous transition, the polyelectrolyte chain exhibits coexistent expanded and collapsed conformational states, same as intermolecular phase segregation. For a limiting long chain, the mean chain size at critical point is roughly 90% of the size of an ideal chain. Such a result implies that partial contraction within a chain molecule is required to collapse a flexible polyelectrolyte chain. Moreover, the theory predicts that for a longer chain, intramolecular segregated conformations differ significantly from intermolecular segregated conformations, but the difference becomes small for shorter chains. Besides, the charge needed to induce intramolecular segregation is smaller than that of intermolecular segregation for a given chain length. These findings are consistent with previous literature results. PMID:17444749

  5. 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.

  6. 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…

  7. Simulation of the intermolecular vibrational spectra of liquid water and water clusters

    E-print Network

    Mukamel, Shaul

    are believed to be as follows:3 The 60 cm-' peak results from the bending of the hydrogen bonds between waterSimulation of the intermolecular vibrational spectra of liquid water and water clusters Wayne B and infrared spectra of liquid water and water clusters in the frequency range O-1000 cm-`. The librational

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

    SciTech Connect

    Chen, Yu-Chun; Tang, Ping-Han; Wu, Ten-Ming; National Center for Theoretical Sciences, Hsinchu 300, Taiwan

    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.

  9. 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

  10. Separation of the attractive and repulsive contributions to the adsorbate-adsorbate interactions of polar adsorbates on Si(100)

    NASA Astrophysics Data System (ADS)

    Lin, Ying-Hsiu; Jeng, Horng-Tay; Lin, Deng-Sung

    2015-11-01

    Dissociative adsorption of H2O, NH3, CH3OH and CH3NH2 polar molecules on the Si(100) surface results in a 1:1 mixture of two adsorbates (H and multi-atomic fragment A = OH, NH2, CH3O, CH3NH, respectively) on the surface. By using density functional theory (DFT) calculations, the adsorption geometry, the total energies and the charge densities for various possible ordered structures of the mixed adsorbate layer have been found. Analyzing the systematic trends in the total energies unveils concurrently the nearest-neighbor interactions ENN and the next nearest-neighbor interactions ENNN between two polar adsorbates A. In going from small to large polar adsorbates, ENN's exhibit an attractive-to-repulsive crossover behavior, indicating that they include competing attractive and repulsive contributions. Exploration of the charge density distributions allows the estimation of the degree of charge overlapping between immediately neighboring A's, the resulting contribution of the steric repulsions, and that of the attractive interactions to the corresponding ENN's. The attractive contributions to nearest neighboring adsorbate-adsorbate interactions between the polar adsorbates under study are shown to result from hydrogen bonds or dipole-dipole interactions.

  11. A comparison of numerical simulations and analytical theory of the dynamics of interacting magnetic vortices

    SciTech Connect

    Asmat-Uceda, Martin; Buchanan, Kristen S.; Cheng, Xuemei; Wang, Xiao; Clarke, David J.; Tchernyshyov, Oleg

    2015-03-28

    Magnetostatic interactions between vortices in closely spaced planar structures are important for applications including vortex-based magnonic crystals and spin torque oscillator networks. Analytical theories that include magnetostatic interaction effects have been proposed but have not yet been rigorously tested. Here, we compare micromagnetic simulations of the dynamics of magnetic vortices confined in three disks in an equilateral triangle configuration to analytical theories that include coupling. Micromagnetic simulations show that the magnetostatic coupling between the disks leads to splitting of the gyrotropic resonance into three modes and that the frequency splitting increases with decreasing separation. The temporal profiles of the magnetization depend on the vortex polarities and chiralities; however, the frequencies depend only on the polarity combinations and will fall into one of two categories: all polarities equal or one polarity opposite to the others, where the latter leads to a larger frequency splitting. Although the magnitude of the splitting observed in the simulations is larger than what is expected based on purely dipolar interactions, a simple analytical model that assumes dipole-dipole coupling captures the functional form of the frequency splitting and the motion patterns just as well as more complex models.

  12. Anisotropy of the magnetoviscous effect in a cobalt ferrofluid with strong interparticle interaction

    NASA Astrophysics Data System (ADS)

    Linke, J. M.; Odenbach, S.

    2015-12-01

    The anisotropy of the magnetoviscous effect (MVE) of a cobalt ferrofluid has been studied in a slit die viscometer for three orientations of the applied magnetic field: in the direction of the fluid flow (??1), the velocity gradient (??2), and the vorticity (??3). The majority of the cobalt particles in the ferrofluid exhibit a strong dipole-dipole interaction, which corresponds to a weighted interaction parameter of ?w?10.6. Thus the particles form extended microstructures inside the fluid which lead to enhanced MVE ratios ??2/??1>3 and ??3/??1>0.3 even for strong shearing and weak magnetic fields compared to fluids which contain non-interacting spherical particles with ??2/??1?1 and ??3/??1=0. Furthermore, a non-monotonic increase has been observed in the shear thinning behavior of ??2 for weak magnetic fields <10 kA/m, which cannot be explained solely by the magnetization of individual particles and the formation and disintegration of linear particle chains but indicates the presence of heterophase structures.

  13. Interaction between colloidal particles on an oil-water interface in dilute and dense phases

    NASA Astrophysics Data System (ADS)

    Parolini, Lucia; Law, Adam D.; Maestro, Armando; Buzza, D. Martin A.; Cicuta, Pietro

    2015-05-01

    The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system.

  14. Interaction between colloidal particles on an oil-water interface in dilute and dense phases.

    PubMed

    Parolini, Lucia; Law, Adam D; Maestro, Armando; Buzza, D Martin A; Cicuta, Pietro

    2015-05-20

    The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system. PMID:25924056

  15. An empirical multi-parameter anisotropic intermolecular potential, collision-induced absorption and predicted collision-induced light scattering spectra for CF 4-He

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Maroulis, G.

    2011-09-01

    An approximate anisotropic intermolecular potential for the interaction of CF 4 with He is developed by simultaneously fitting the Exponential Morse-Morse-Morse-Spline-van der Waals (EM3SV) potential form to high energy beam results, interaction pressure virial coefficients, diffusion coefficients, mixture viscosity and thermal conductivity. The collision-induced absorption spectrum of this system at 213 K has been calculated using the empirical models of the induced dipole moment and the interaction potential. Theoretical zeroth, first and second moments of this spectrum using various models for the induced dipole moment and interatomic potential are compared to the experimental values. Also, with this potential and with a suitable model for the anisotropy, the lineshape calculations have been used to predict a reasonable experimental spectrum of the induced light scattering. The results show that these models of the potential, the induced dipole moment and the induced anisotropy are the most accurate models reported to date for this mixture.

  16. Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory

    NASA Astrophysics Data System (ADS)

    Li, Arvin Huang-Te; Chao, Sheng D.

    2006-09-01

    We have calculated the intermolecular interaction potentials of the methane dimer at the minimum-energy D3d conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order Møller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with the Perdew-Wang (PW91) functional as the exchange or the correlation part. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions (STO-nG) (n=3-6) [Quantum Theory of Molecular and Solids: The Self-Consistent Field for Molecular and Solids (McGraw-Hill, New York, 1974), Vol. 4], Pople's medium size basis sets of Krishnan et al. [J. Chem. Phys. 72, 650 (1980)] [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets [J. Chem. Phys. 90, 1007 (1989)] (cc-pVXZ and aug-cc-pVXZ) (X =D, T, and Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d,2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (˜0.01kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the destined C6 value from molecular polarizability calculations. The slow convergence could indicate the inefficacy of using the MP2 calculations with Gaussian-type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energy calculated using the PW91PW91 functional and the equilibrium bond length calculated using the PW91VP86 functional are close to the MP2 results at the basis set limit.

  17. Intermolecular potentials of the methane dimer calculated with Møller-Plesset perturbation theory and density functional theory.

    PubMed

    Li, Arvin Huang-Te; Chao, Sheng D

    2006-09-01

    We have calculated the intermolecular interaction potentials of the methane dimer at the minimum-energy D(3d) conformation using the Hartree-Fock (HF) self-consistent theory, the correlation-corrected second-order Møller-Plesset (MP2) perturbation theory, and the density functional theory (DFT) with the Perdew-Wang (PW91) functional as the exchange or the correlation part. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In the MP2 calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions (STO-nG) (n=3-6) [Quantum Theory of Molecular and Solids: The Self-Consistent Field for Molecular and Solids (McGraw-Hill, New York, 1974), Vol. 4], Pople's medium size basis sets of Krishnan et al. [J. Chem. Phys. 72, 650 (1980)] [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets [J. Chem. Phys. 90, 1007 (1989)] (cc-pVXZ and aug-cc-pVXZ) (X=D, T, and Q). With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d,2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (approximately 0.01 kcal/mol). Up to the largest basis set used, the asymptotic dispersion coefficient has not converged to the destined C6 value from molecular polarizability calculations. The slow convergence could indicate the inefficacy of using the MP2 calculations with Gaussian-type functions to model the asymptotic behavior. Both the basis set superposition error (BSSE) corrected and uncorrected results are presented to emphasize the importance of including such corrections. Only the BSSE corrected results systematically converge to the destined potential curve with increasing basis size. The DFT calculations generate a wide range of interaction patterns, from purely unbound to strongly bound, underestimating or overestimating the binding energy. The binding energy calculated using the PW91PW91 functional and the equilibrium bond length calculated using the PW91VP86 functional are close to the MP2 results at the basis set limit. PMID:16965085

  18. Transfer of dipolar gas through the discrete localized mode.

    PubMed

    Bai, Xiao-Dong; Zhang, Ai-Xia; Xue, Ju-Kui

    2013-12-01

    By considering the discrete nonlinear Schrödinger model with dipole-dipole interactions for dipolar condensate, the existence, the types, the stability, and the dynamics of the localized modes in a nonlinear lattice are discussed. It is found that the contact interaction and the dipole-dipole interactions play important roles in determining the existence, the type, and the stability of the localized modes. Because of the coupled effects of the contact interaction and the dipole-dipole interactions, rich localized modes and their stability nature can exist: when the contact interaction is larger and the dipole-dipole interactions is smaller, a discrete bright breather occurs. In this case, while the on-site interaction can stabilize the discrete breather, the dipole-dipole interactions will destabilize the discrete breather; when both the contact interaction and the dipole-dipole interactions are larger, a discrete kink appears. In this case, both the on-site interaction and the dipole-dipole interactions can stabilize the discrete kink, but the discrete kink is more unstable than the ordinary discrete breather. The predicted results provide a deep insight into the dynamics of blocking, filtering, and transfer of the norm in nonlinear lattices for dipolar condensates. PMID:24483540

  19. HIGH SENSITIVITY FOURIER TRANSFORM NMR. INTERMOLECULAR INTERACTIONS BETWEEN ENVIRONMENTAL TOXIC SUBSTANCES AND BIOLOGICAL MACROMOLECULES

    EPA Science Inventory

    This project explored the feasibility of developing new techniques for evaluation of the effects of environmental toxic materials on complex biopolymer systems using high sensitivity Fourier transform nuclear magnetic resonance (nmr) spectroscopy. Commercial instrumentation avail...

  20. Intermolecular interactions and charge transfer transitions in aromatic hydrocarbon-tetracyanoethylene complexes.

    PubMed

    Aquino, Adélia A J; Borges, Itamar; Nieman, Reed; Köhn, Andreas; Lischka, Hans

    2014-10-14

    A comprehensive theoretical study of the electronically excited states in complexes between tetracyanoethylene (TCNE) and three aromatic electron donors, benzene, naphthalene and anthracene, was performed with a focus on charge transfer (CT) transitions. The results show that the algebraic diagrammatic construction method to second order (ADC(2)) provides excellent possibilities for reliable calculations of CT states. Significant improvements in the accuracy of the computed transition energies are obtained by using the scaled opposite-spin (SOS) variant of ADC(2). Solvent effects were examined on the basis of the conductor-like screening model (COSMO) which has been implemented recently in the ADC(2) method. The dielectric constant and the refractive index of dichloromethane have been chosen in the COSMO calculations to compare with experimental solvatochromic effects. The computation of optimized ground state geometries and enthalpies of formation has been performed at the second-order Møller-Plesset perturbation theory (MP2) level. By comparison with experimental data and with high-level coupled-cluster methods including explicitly correlated (F12) wave functions, the importance of the SOS approach is demonstrated for the ground state as well. In the benzene-TCNE complex, the two lowest electronic excitations are of CT character whereas in the naphthalene and anthracene TCNE complexes three low-lying CT states are observed. As expected, they are strongly stabilized by the solvent. Geometry optimization in the lowest excited state allowed the calculation of fluorescence transitions. Solvent effects lead to a zero gap between S1 and S0 for the anthracene-TCNE complex. Therefore, in the series of benzene-TCNE to anthracene a change from a radiative to a nonradiative decay mechanism to the ground state is to be expected. PMID:25156236

  1. 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 ...

  2. Measuring LCSTs by Novel Temperature Gradient Methods: Evidence for Intermolecular Interactions in Mixed Polymer Solutions

    E-print Network

    * Department of Chemistry, Texas A&M UniVersity, College Station, Texas 77845-3012 Received December 11, 2002 the precipitation mechanisms are often complex, it is generally accepted that the desorption of water molecules from, prolonged temperature ramping is required to minimize hysteresis.11 Furthermore, the speed of data

  3. 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.

  4. 92 Genome Informatics 15(2): 92101 (2004) IRIS: Intermolecular RNA Interaction Search

    E-print Network

    Pervouchine, Dmitri D.

    2004-01-01

    of Bioengineering and Bioinformatics, Moscow State University, Vorobiovy gory, 119899 Moscow, Russia Abstract Here and for the design of artificial riboregulators such as antisense drugs. Keywords: rioboregulator, riboswitch, micro

  5. Room temperature ionic liquids: A simple model. Effect of chain length and size of intermolecular potential on critical temperature

    NASA Astrophysics Data System (ADS)

    Chapela, Gustavo A.; Guzmán, Orlando; Díaz-Herrera, Enrique; del Río, Fernando

    2015-04-01

    A model of a room temperature ionic liquid can be represented as an ion attached to an aliphatic chain mixed with a counter ion. The simple model used in this work is based on a short rigid tangent square well chain with an ion, represented by a hard sphere interacting with a Yukawa potential at the head of the chain, mixed with a counter ion represented as well by a hard sphere interacting with a Yukawa potential of the opposite sign. The length of the chain and the depth of the intermolecular forces are investigated in order to understand which of these factors are responsible for the lowering of the critical temperature. It is the large difference between the ionic and the dispersion potentials which explains this lowering of the critical temperature. Calculation of liquid-vapor equilibrium orthobaric curves is used to estimate the critical points of the model. Vapor pressures are used to obtain an estimate of the triple point of the different models in order to calculate the span of temperatures where they remain a liquid. Surface tensions and interfacial thicknesses are also reported.

  6. Ground state of ?-conjugated polymer chains forming an intermolecular charge-transfer complex as probed by Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Bruevich, V. V.; Makhmutov, T. Sh.; Elizarov, S. G.; Nechvolodova, E. M.; Paraschuk, D. Yu.

    2007-10-01

    The intermolecular charge-transfer complex (CTC) between the conjugated polymer MEH-PPV and the low-molecular organic acceptor trinitrofluorenone (TNF) has been studied by Raman and optical absorption spectroscopy. On mixing MEH-PPV with TNF, an absorption band due to the CTC appeared in the optical gap of the polymer, whereas, in the Raman spectra, characteristic bands of the polymer are shifted and their widths and intensities change. The low-frequency shift of the strongest band at 1580 cm-1 in the Raman spectrum of the polymer, assigned to the symmetric stretching vibration of the phenyl group, is shown to be due to electron density transfer from the ?-conjugated system of the polymer to the acceptor and is as large as 5 cm-1, which corresponds to a charge transfer on the order of 0.1 e -1. Even at a low acceptor concentration (one TNF molecule per 10 monomer units of the polymer), most Raman-active conjugated chains are involved in the CTC. It is suggested that conjugated segments of the polymer can form a CTC of variable composition MEH-PPV: TNF = 1: X, where 0.1 ? X ? 0.5 (for each monomer unit of the polymer), and one TNF molecule can thereby interact with two conjugated segments of MEH-PPV. The conjugated polymer chains involved in the CTC can become more planar, and their interaction with the local environment can noticeably change; however, their conjugation length, most likely, remains unaltered.

  7. 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.

  8. Supramolecular Magnetic Brushes: The Impact of Dipolar Interactions on the Equilibrium Structure

    PubMed Central

    2015-01-01

    The equilibrium structure of supramolecular magnetic filament brushes is analyzed at two different scales. First, we study the density and height distributions for brushes with various grafting densities and chain lengths. We use Langevin dynamics simulations with a bead–spring model that takes into account the cross-links between the surface of the ferromagnetic particles, whose magnetization is characterized by a point dipole. Magnetic filament brushes are shown to be more compact near the substrate than nonmagnetic ones, with a bimodal height distribution for large grafting densities. This latter feature makes them also different from brushes with electric dipoles. Next, in order to explain the observed behavior at the filament scale, we introduce a graph theory analysis to elucidate for the first time the structure of the brush at the scale of individual beads. It turns out that, in contrast to nonmagnetic brushes, in which the internal structure is determined by random density fluctuations, magnetic forces introduce a certain order in the system. Because of their highly directional nature, magnetic dipolar interactions prevent some of the random connections to be formed. On the other hand, they favor a higher connectivity of the chains’ free and grafted ends. We show that this complex dipolar brush microstructure has a strong impact on the magnetic response of the brush, as any weak applied field has to compete with the dipole–dipole interactions within the crowded environment. PMID:26538768

  9. Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

    PubMed Central

    2015-01-01

    We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic ?/? content is achieved de novo without any biases in the force field toward a particular secondary structure. The dipoles created by the dummy particles interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. We have also characterized the role of dipole–dipole and dipole–charge interactions in shaping the secondary and supersecondary structure of proteins. Formation of helix bundles and ?-strands are also discussed. PMID:24932137

  10. Intermolecular binding of blueberry pectin-rich fractions and anthocyanin.

    PubMed

    Lin, Z; Fischer, J; Wicker, L

    2016-03-01

    Pectin was extracted from blueberry powder into three fractions of water soluble (WSF), chelator soluble (CSF) and sodium carbonate soluble (NSF). The fractions were incubated with cyanidin-3-glucoside (C3G), a mixture of five anthocyanidins (cyanidin, pelargonidin, malvidin, petunidin and delphinidin) or blueberry juice at pH 2.0-4.5. Free anthocyanins and bound anthocyanin-pectin mixtures were separated by ultrafiltration. WSF bound the least amount of anthocyanin at all pH values. CSF had stronger anthocyanin binding ability at pH 2.0-3.6, while NSF had stronger anthocyanin binding ability at pH 3.6-4.5. The pectin and anthocyanin binding was lowest at pH 4.5 and higher at pH 2.0-3.6. Nearly doubling C3G pigment content increased bound anthocyanin percentage by 16-23% at pH 3.6, which favored anthocyanin aromatic stacking, compared to 3-9% increase at pH 2.0. Ionic interaction between anthocyanin flavylium cations and free pectic carboxyl groups, and anthocyanin stacking may be two major mechanisms for pectin and anthocyanin binding. PMID:26471644

  11. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    A modified correlation spectroscopy revamped by asymmetric z-gradients echo detection (CRAZED) sequence was applied to investigate the behavior of intermolecular double-quantum longitudinal relaxation processes in the tilted rotating frame. Theoretical formalism based on dipolar field theory was presented in detail. Spectroscopic measurements and quantitative analysis demonstrated that the signal intensities and intermolecular double-quantum off-resonance longitudinal relaxation time in the rotating frame (T1?, DQC eff) are inversely correlated with the tilt angle (?), while positively correlated with the effective frequency of spin-locking field (?e). Magnetic resonance imaging experiments of an agarose phantom also prove the validity of the theoretical analysis and demonstrated the feasibility of imaging based on T1?, DQC eff . The rotating-frame double-quantum relaxation measurements are useful for probing slow-motion molecules and this study provides the guidance for optimization of the spin-lock experiments.

  14. Estimation of Some Parameters from Morse-Morse-Spline-Van Der Waals Intermolecular Potential

    SciTech Connect

    Coroiu, I.

    2007-04-23

    Some parameters such as transport cross-sections and isotopic thermal diffusion factor have been calculated from an improved intermolecular potential, Morse-Morse-Spline-van der Waals (MMSV) potential proposed by R.A. Aziz et al. The treatment was completely classical and no corrections for quantum effects were made. The results would be employed for isotope separations of different spherical and quasi-spherical molecules.

  15. Intermolecular Dynamical Charge Fluctuations in Water: A Signature of the H-Bond Network

    NASA Astrophysics Data System (ADS)

    Sharma, Manu; Resta, Raffaele; Car, Roberto

    2005-10-01

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

  16. Intermolecular [3+2] Annulation of Cyclopropylanilines with Alkynes, Enynes, and Diynes via Visible Light Photocatalysis

    PubMed Central

    Nguyen, Theresa H.; Morris, Scott A.; Zheng, Nan

    2015-01-01

    One-step synthesis of carbocycles substituted with amines from simple starting materials remains rare. We recently developed intermolecular [3+2] annulation of cyclopropylanilines with alkenes and alkynes that enable this one-step synthesis. Herein, we report our findings for a fullscale study of the annulation. Significant expansion of the substrate scope for both cyclopropylanilines and alkynes is achieved. A range of structurally diverse carbocycles substituted with amines is prepared. PMID:26120292

  17. C60 chain phases on ZnPc/Ag(111) surfaces: Supramolecular organization driven by competing interactions.

    PubMed

    Jin, W; Liu, Q; Dougherty, D B; Cullen, W G; Reutt-Robey, J E; Weeks, J; Robey, S W

    2015-03-14

    Serpentine chain C60 phases were observed in scanning tunneling microscopy (STM) images of C60 layers on zinc phthalocyanine (ZnPc) or pentacene covered Ag(111) and Au(111) surfaces. This low-density, quasi-one-dimensional organization contrasts starkly with the close-packed hexagonal phases observed for C60 layers on bare metal substrates. STM was employed to perform a detailed investigation of these chain structures for C60/ZnPc/Ag(111) heterolayers. Motivated by the similarity of these chain phases, and the chain and stripe organization occurring in dipole-fluid systems, we investigated a model based on competing van der Waals attractions and electrostatic repulsions between C60 molecules as an explanation for the driving force behind these monolayer phases. Density functional theory (DFT) calculations revealed significant charge transfer to C60 from the Ag(111) substrate, through the intervening ZnPc layer, inducing electrostatic interactions between C60 molecules. Molecular dynamics simulations performed with attractive van der Waals interactions plus repulsive dipole-dipole interactions reproduced the C60 chain phases with dipole magnitudes consistent with DFT calculations. PMID:25770499

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

    PubMed Central

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

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  19. Weak intramolecular and intermolecular hydrogen bonding of benzyl alcohol, 2-phenylethanol and 2-phenylethylamine in the adsorption on graphitized thermal carbon black.

    PubMed

    Varfolomeeva, V V; Terentev, A V

    2015-10-01

    The paper discusses the role of weak intra- and intermolecular hydrogen bonds in the adsorption of benzyl alcohol, 2-phenylethanol and 2-phenylethylamine on graphitized thermal carbon black (GTCB). Using the B3LYP/aug-cc-pVDZ, B3LYP/aug-cc-pVTZ methods and the molecular-statistical theory of adsorption we found the structural and energetic parameters of the conformers to be stable in the gas phase and in the adsorbed state. The contribution of weak OH?, NH?, CHO hydrogen bonds to the stabilization of the conformers was defined by the method of non-covalent interactions (NCI). Based on the difference in the experimental and calculated values of the Henry constant ??ln?K1 < 0.25 (K1, cm(3) m(-2)) a high predictive power of molecular-statistical calculation of the thermodynamic characteristics of adsorption (TCA) has been shown. To obtain a high predictive power of molecular-statistical calculation it was necessary to take due account of the structural features of flexible molecules in the adsorbed state. A significant impact of the weak OH?GTCB intermolecular hydrogen bond of benzyl alcohol on the TCA values has been established. PMID:26327209

  20. Simulations of dipolar fluids using effective many-body isotropic interactions

    NASA Astrophysics Data System (ADS)

    Sindt, Julien O.; Camp, Philip J.

    2015-07-01

    The partition function of a system with pairwise-additive anisotropic dipole-dipole interactions is equal to that of a hypothetical system with many-body isotropic interactions [G. Stell, Phys. Rev. Lett. 32, 286 (1974)]. The effective many-body interactions contain n-body contributions of all orders. Each contribution is known as an expansion in terms of the particle-particle distances r, and the coefficients are temperature dependent. The leading-order two-body term is the familiar -r-6 attraction, and the leading-order three-body term is equivalent to the Axilrod-Teller interaction. In this work, a fluid of particles with the leading-order two-body and three-body interactions is compared to an equivalent dipolar soft-sphere fluid. Molecular simulations are used to determine the conditions under which the effective many-body interactions reproduce the fluid-phase structures of the dipolar system. The effective many-body interaction works well at moderately high temperatures but fails at low temperatures where particle chaining is expected to occur. It is shown that an adjustment of the coefficients of the two-body and three-body terms leads to a good description of the structure of the dipolar fluid even in the chaining regime, due primarily to the ground-state linear configuration of the three-body Axilrod-Teller interaction. The vapor-liquid phase diagrams of systems with different Axilrod-Teller contributions are determined. As the strength of the three-body interaction is increased, the critical temperature and density both decrease and disappear completely above a threshold strength, where chaining eventually suppresses the condensation transition.

  1. A convergent intermolecular Diels-Alder approach to the spirocycles found in the marine neurotoxic agents, the gymnodimines 

    E-print Network

    Cohn, Stephen Todd

    1999-01-01

    Several approaches to the spirochetes found in the marine neurotoxic agents, the gymnodimines, were studied. The strategy involved intermolecular Dials-Alder reactions of ?-exomethylene lactones and lactams. A convergent racemic synthesis...

  2. 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

  3. 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.

  4. Folding of oligoviologens induced by radical-radical interactions.

    PubMed

    Wang, Yuping; Frasconi, Marco; Liu, Wei-Guang; Liu, Zhichang; Sarjeant, Amy A; Nassar, Majed S; Botros, Youssry Y; Goddard, William A; Stoddart, J Fraser

    2015-01-21

    We report the synthesis of a series of homologous oligoviologens in which different numbers of 4,4'-bipyridinium (BIPY(2+)) subunits are linked by p-xylylene bridges, as a prelude to investigating how their radical cationic forms self-assemble both in solution and in the solid state. The strong radical-radical interactions between the radical cationic forms of the BIPY(2+) units-namely, BIPY(•+)-in these oligoviologens induce intra- or intermolecular folding of these homologues. UV/Vis/NIR spectroscopic studies and DFT quantum mechanics indicate that the folding of the shorter oligoviologens is dominated by intermolecular radical-radical interactions. In addition to intermolecular interactions, strong intramolecular radical-radical interactions, which give rise to an NIR absorption band at 900 nm, tend to play a crucial role in governing the folding of the longer oligoviologens. The solid-state superstructure of the oligoviologen with three BIPY(2+) units reveals that two intertwining chains fold together to form a dimer, stabilized by intermolecular radical-radical interactions. These dimers continue to stack in an infinite column through intermolecular radical-radical interactions between them. This research features an artificial biomimetic system which sustains delicate secondary and tertiary structures, reminiscent of those present in nucleic acids and proteins. PMID:25493585

  5. Computer Simulations of Critical Phenomena in Systems with Long-Range Interactions: a Study of Ising Dipoles and Self-Organized Criticality in Earthquakes.

    NASA Astrophysics Data System (ADS)

    Xu, Huang-Jian

    This thesis discusses scaling and critical behavior of two different models. One model describes Ising dipoles, originates in condensed matter physics, and depicts equilibrium critical phenomena. The other model, taken from the earth sciences, describes faulting instabilities and the resulting earthquakes, and involves self-organized criticality--a non-equilibrium phenomenon. Both models are characterized by long range interactions, with a resulting sensitivity to boundary conditions. The ordering properties of Ising dipoles on lattices are studied in a mean field theory and by Monte Carlo simulations. The mean field theory is manifestly shape independent in zero external field. In the case of dipoles on a diluted lattice the mean field theory predicts a critical concentration above which the low temperature phase is ferroelectric (or anti-ferroelectric depending on the lattice structure). Extensive Monte Carlo simulation results are in agreement with those of mean field theory. We propose a finite size scaling form that includes logarithmic corrections for systems at the critical dimensionality. In the case of dipoles on a body centered tetragonal lattice we found that the finite scaling form significantly improved the data collapse over the scaling form with mean field exponents. With lattice parameters appropriate to the Ising ferromagnetic compound LiHoF_4, we obtain a ferromagnetic transition temperature T -1.51 K in excellent agreement with experiment. This indicates that the material LiHoF_4 is dominated by the dipole-dipole interaction: since in the simulations we only include dipole dipole interactions. For dipoles on the simple cubic lattice, the ordered state is made up of anti-ferromagnetic rows. The critical exponents obtained by finite size scaling are beta~ 1/7, gamma ~ 8/7 and o~ 1/7. These results are in good agreement with those of high temperature series expansions. A model of self-organized ruptures in an elastic medium is developed; and applied to earthquakes. In the model the local ruptures are represented by double couples to be consistent with elastic theory. The explicit form of this double couple source is derived. The system is driven by slowly increasing the shear stress. The model evolves towards a self-organized critical state in which the earthquake distribution follows the Gutenberg-Richter law with an exponent in agreement with observational data. By modeling the local static fatigue for the rocks, we also obtained Omori's law for the rate of aftershocks. The effects of annealing are investigated.

  6. A fast-Fourier transform method to solve continuum-electrostatics problems with truncated electrostatic interactions: Algorithm and application to ionic solvation and ion-ion interaction

    NASA Astrophysics Data System (ADS)

    Peter, Christine; van Gunsteren, Wilfred F.; Hünenberger, Philippe H.

    2003-12-01

    An iterative algorithm based on fast-Fourier transforms is presented that solves the equations of continuum electrostatics for systems of heterogeneous dielectric permittivity (e.g., solute cavity in a solvent) under periodic boundary conditions. The method makes explicit use of the charge-dipole and dipole-dipole interaction tensors, and is thus applicable both to Coulombic interactions (Ewald scheme) and cutoff-based electrostatic interactions described by any polynomial function (including a Coulombic r-1 term), as commonly used in molecular dynamics simulations. The latter case includes, in particular, straight truncation of Coulombic interactions and truncation including a reaction-field correction. After testing and validation by comparison with existing methods, the algorithm is used to investigate the effect of cutoff truncation and artificial periodicity in explicit-solvent simulations of ionic solvation and ion-ion interactions. Both cutoff truncation and artificial periodicity are found to significantly affect the polarization around a spherical ion and its solvation free energy. The nature and magnitude of the two perturbations are analyzed in detail, and approximate analytical correction terms are derived to be applied to the results of explicit-solvent simulations. Cutoff truncation induces strong alterations in the potential of mean force for the interaction between two spherical ions. The present observations based on continuum electrostatics help to rationalize artifacts previously reported from explicit-solvent simulations involving cutoff truncation and, in particular, the unphysical attraction of like charges and repulsion of opposite charges, and the corresponding alterations in the relative stabilities of contact, solvent-separated, and free ion pairs.

  7. Spectral lineshapes of collision-induced absorption (CIA) and collision-induced light scattering (CILS) for molecular nitrogen using isotropic intermolecular potential. New insights and perspectives

    NASA Astrophysics Data System (ADS)

    El-Kader, M. S. A.; Mostafa, S. I.; Bancewicz, T.; Maroulis, G.

    2014-08-01

    The rototranslational collision-induced absorption (CIA) at different temperatures and collision-induced light scattering (CILS) at room temperature of nitrogen gas are analyzed in terms of new isotropic intermolecular potential, multipole-induced dipole functions and interaction-induced pair polarizability models, using quantum spectral lineshape computations. The irreducible spherical form for the induced operator of light scattering mechanisms was determined. The high frequency wings are discussed in terms of the collision-induced rotational Rayleigh effect and estimates for the dipole-octopole polarizability E4, is obtained and checked with the ab initio theoretical value. The quality of the present potential has been checked by comparing between calculated and experimental thermo-physical and transport properties over a wide temperature range, which are found to be in good agreement.

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

    NASA Astrophysics Data System (ADS)

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

    2004-03-01

    Femtosecond pump probe spectroscopy was employed to measure intramolecular vibrational energy redistribution (IVR) and intermolecular vibrational energy transfer (VET) of benzene in the gas phase and in supercritical (sc) CO 2. We observe two IVR time scales the faster of which proceeds within ? 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.

  9. Intermolecular hydrogen bonding of steroid compounds: PFG NMR diffusion study, cold-spray ionization (CSI)-MS and X-ray analysis.

    PubMed

    Shikii, Kazuaki; Seki, Hiroko; Sakamoto, Shigeru; Sei, Yoshihisa; Utsumi, Hiroaki; Yamaguchi, Kentaro

    2005-07-01

    An extensive analysis of hydrogen bonding of steroid compounds in diluted solution is preformed by pulsed field gradient (PFG) NMR and cold-spray ionization (CSI)-MS, in the solid state by X-ray crystallographic analysis. The formation of hydrogen bond interaction are quantified and discussed. Although X-ray analysis in the crystalline state and CSI-MS measurement in solution suggested that the observed diffusion coefficient D(obs) of the steroid compounds may vary in accordance with the number of hydrogen bonds, the actual observed D(obs) value determined from the diffusion studies diminished constantly without correlation on the decreasing numbers of hydrogen bonds. Comparison of two different calibration profiles of calculated molecular volume (V(cal)) vs. D(obs), which are obtained from compounds possessing no hydrogen bonding and the steroid compounds, formation of a chain structure (cluster) based on intermolecular hydrogen bonding of the steroid compounds is unambiguously confirmed. PMID:15997137

  10. Using corresponding state theory to obtain intermolecular potentials to calculate pure liquid shock Hugoniots

    SciTech Connect

    Hobbs, M.L.

    1997-12-01

    Determination of product species, equations-of-state (EOS) and thermochemical properties of high explosives and pyrotechnics remains a major unsolved problem. Although, empirical EOS models may be calibrated to replicate detonation conditions within experimental variability (5--10%), different states, e.g. expansion, may produce significant discrepancy with data if the basic form of the EOS model is incorrect. A more physically realistic EOS model based on intermolecular potentials, such as the Jacobs Cowperthwaite Zwisler (JCZ3) EOS, is needed to predict detonation states as well as expanded states. Predictive capability for any EOS requires a large species data base composed of a wide variety of elements. Unfortunately, only 20 species have known JCZ3 molecular force constants. Of these 20 species, only 10 have been adequately compared to experimental data such as molecular scattering or shock Hugoniot data. Since data in the strongly repulsive region of the molecular potential is limited, alternative methods must be found to deduce force constants for a larger number of species. The objective of the present study is to determine JCZ3 product species force constants by using a corresponding states theory. Intermolecular potential parameters were obtained for a variety of gas species using a simple corresponding states technique with critical volume and critical temperature. A more complex, four parameter corresponding state method with shape and polarity corrections was also used to obtain intermolecular potential parameters. Both corresponding state methods were used to predict shock Hugoniot data obtained from pure liquids. The simple corresponding state method is shown to give adequate agreement with shock Hugoniot data.

  11. Effect of interaction of electromagnetic fields with a resonant medium in epr when the saturating field is small compared with the local field

    NASA Astrophysics Data System (ADS)

    Glazkov, Yu. V.; Dubovets, V. G.; Ugolev, I. I.

    2006-07-01

    We propose a system of Bloch equations, modified to take into account the presence of a dipole-dipole reservoir (DDR), for the case when the saturating magnetic field is small compared with the local field. We take into account the transverse and longitudinal magnetizations in the equation for the DDR, in contrast to our previous papers in which we took into account only the longitudinal magnetization. Using the system obtained, we solve the problem of the interaction of three fields, where one is the saturating field, the second is the probe field, and the third is a combination field that is the result of the interaction of the first two fields in a resonant medium. We have studied the imaginary and real parts of the susceptibility of the system at the probe field frequency, both when the interacting waves have different frequencies and when they have matching frequencies (the degenerate case). We have compared the results with those we obtained previously. For the degenerate case, we consider the frequency dependence of the parametric coupling coefficient of the waves. We show that weak waves can be enhanced as they pass through a layer of a resonant absorbing medium.

  12. Copper-catalyzed intermolecular trifluoromethylarylation of alkenes: mutual activation of arylboronic acid and CF3+ reagent.

    PubMed

    Wang, Fei; Wang, Dinghai; Mu, Xin; Chen, Pinhong; Liu, Guosheng

    2014-07-23

    A novel copper-catalyzed intermolecular trifluoromethylarylation of alkenes is developed using less active ether-type Togni's reagent under mild reaction conditions. Various alkenes and diverse arylboronic acids are compatible with these conditions. Preliminary mechanistic studies reveal that a mutual activation process between arylboronic acid and CF3(+) reagent is essential. In addition, the reaction might involve a rate-determining transmetalation, and the final aryl C-C bond is derived from reductive elimination of the aryl(alkyl)Cu(III) intermediate. PMID:24983408

  13. 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.

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

    PubMed Central

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

    2014-01-01

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

  15. 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.

  16. Modification of PEGylated enzyme with glutaraldehyde can enhance stability while avoiding intermolecular crosslinking†

    PubMed Central

    McShane, M. J.

    2015-01-01

    We demonstrate an enzyme stabilization approach whereby a model enzyme is PEGylated, followed by controlled chemical modification with glutaraldehyde. Using this stabilization strategy, size increases and aggregation due to intermolecular crosslinking are avoided. Immediately following synthesis, the PEGylated enzyme with and without glutaraldehyde modification possessed specific activities of 372.9 ± 20.68 U/mg and 373.9 ± 15.14 U/mg, respectively (vs. 317.7 ± 19.31 U/mg for the native enzyme). The glutaraldehyde-modified PEGylated enzyme retains 73% original activity after 4 weeks at 37 °C (vs. 2% retention for control). PMID:26052433

  17. Interactions between polyacrylonitrile and solvents: density functional theory study and two-dimensional infrared correlation analysis.

    PubMed

    Wu, Qing-Yun; Chen, Xiao-Na; Wan, Ling-Shu; Xu, Zhi-Kang

    2012-07-19

    Polyacrylonitrile (PAN) is a semicrystalline polymer with high polarity and is usually processed from solutions. Selected solvents for processing influence both the structure and properties of PAN products. We describe the interactions between PAN and various solvents by theoretical calculation based on density functional theories (DFT), and by experimental methods of Fourier transform infrared (FTIR) spectra and two-dimensional infrared (2D-IR) correlation analysis. The selected solvents include dimethyl sulfone (DMSO2), dimethyl sulfoxide (DMSO), ethylene carbonate (EC), propylene carbonate (PC), N,N-dimethyl formamide (DMF), and N,N-dimethyl acetamide (DMAc). Calculation results show that the PAN model monomer (PAN') interacts with each solvent through dipole-dipole interaction and formed PAN'-solvent complexes. Each complex displays an antiparallel alignment of interacting pair between the C?N group of PAN' and the polar group of solvent molecule (S?O or C?O group). The calculated binding energies (?E) reveal that PAN' preferentially interacts with solvent in the order of DMSO2 > DMSO > EC > PC > DMF > DMAc. Red shifts of vibration frequencies are observed for C?N, S?O, and C?O stretching bands. The C?N stretching band shifts from 2245 cm(-1) in PAN to 2240, 2242, and 2241 cm(-1) in PAN-DMSO, PAN-EC, and PAN-DMF mixtures, respectively, indicating the existence of PAN-solvent interactions. Moreover, 2D-IR correlation analysis shows that as the PAN content increases, DMSO molecules vary prior to PAN-DMSO complexes, and change earlier than PAN bulk. However, PAN-EC and PAN-DMF mixtures follow the order of PAN bulk > PAN-solvent complexes > solvent molecules. This combination of theoretical simulation and experimental characterization is useful in selection of solvents for PAN or even other polar polymers and can provide an insight into the physical behavior of PAN-solvent complexes. PMID:22702536

  18. Off-resonance rotating frame spin-lattice NMR relaxation studies of phosphorus metabolite rotational diffusion in bovine lens homogenates

    SciTech Connect

    Caines, G.H.; Schleich, T.; Morgan, C.F. ); Farnsworth, P.N. )

    1990-08-21

    The rotational diffusion behavior of phosphorus metabolites present in calf lens cortical and nuclear homogenates was investigated by the NMR technique of {sup 31}P off-resonance rotating frame spin-lattice relaxation as a means of assessing the occurrence and extent of phosphorus metabolite-lens protein interactions. {sup 31}P NMR spectra of calf lens homogenates were obtained at 10 and 18{degree}C at 7.05 T. Effective rotational correlation times ({tau}{sub 0,eff}) for the major phosphorus metabolites present in cortical and nuclear bovine calf lens homogenates were derived from nonlinear least-squares analysis of R vs {omega}{sub e} data with the assumption of isotropic reorientational motion. Intramolecular dipole-dipole ({sup 1}H-{sup 31}P, {sup 31}P-{sup 31}P), chemical shift anisotropy (CSA), and solvent (water) translational intermolecular dipole-dipole ({sup 1}H-{sup 31}P) relaxation contributions were assumed in the analyses. A fast-exchange model between free and bound forms, was employed in the analysis of the metabolite R vs {omega}{sub e} curves to yield the fraction of free (unbound) metabolite ({Theta}{sub free}). The results of this study establish the occurrence of significant temperature-dependent (above and below the cold cataract phase transition temperature) binding of ATP (cortex) and PME (nucleus) and p{sub i} (nucleus) in calf lens.

  19. Polymer Interaction in a Model Bioblend

    Technology Transfer Automated Retrieval System (TEKTRAN)

    EBU/PS blends of varying compositions were investigated using TGA, MDSC, and FTIR-PAS methods. The goal of the investigation was that of probing for the presence or lack of intermolecular interactions between the two polymers. The TGA investigation showed at least one blend composition with better...

  20. Joint experimental and computational investigation of the structural and spectroscopic properties of poly(vinylidene fluoride) polymorphs.

    PubMed

    Milani, Alberto; Castiglioni, Chiara; Radice, Stefano

    2015-04-01

    State-of-the-art density functional theory calculations are here adopted for the investigation of the crystal structure and of the vibrational properties of ?, ?, ?, and ? phases of poly(vinylidene fluoride) (PVDF), in comparison with IR and Raman measurements. DFT calculations allowed a detailed interpretation of the IR and Raman spectra of ? and ? phases, giving vibrational assignments useful for qualitative and quantitative characterization of these systems. From a molecular perspective, the computational investigation of the crystal structure and the spectra of PVDF polymorphs helped in clarifying the role of supramolecular dipole-dipole interactions, which indeed modulate the vibrational properties of these systems, indicating also that intermolecular interaction could play a significant role in the modulation of ferroelectric properties. Furthermore, the combined experimental and computational approach allowed us to identify and characterize the thermally and mechanically induced ? phase, shedding light on the far-IR marker bands of this elusive phase of PVDF. PMID:25775384

  1. Preparation and magnetic properties of Mn12 clusters with 4-cyanobenzenecarboxylate ligand, [Mn12O12(O2CC6H4-p-CN)16(H2O)4] and its tetraphenylphosphonium salts

    NASA Astrophysics Data System (ADS)

    Sasnovskaya, V. D.; Kushch, L. A.; Yagubskii, E. B.; Sulimenkov, I. V.; Kozlovskiy, V. I.; Zagaynova, V. S.; Makarova, T. L.

    2012-09-01

    The new Mn12 magnetic clusters with 4-cyanobenzenecarboxylate ligand, [Mn12O12(O2CC6H4-p-CN)16(H2O)4] (1) and its singly (2) and doubly (3) reduced analogs as their tetraphenylphosphonium salts, have been synthesized and characterized by elemental analyses, Raman, ESI-MS spectra and magnetic measurements with a SQUID magnetometer. Unlike the known Mn12 oxocarboxylate clusters, which are very soluble in CH3CN or CH2Cl2, the complex 1 is not dissolved in organic solvents providing an indication for strong intermolecular interactions which lead to strong dipole-dipole interactions between clusters and affect the magnetic behavior. The one-electron and two-electron reduced clusters (2, 3) contain the bulk counterion and dissolve in CH3CN. They show magnetic properties characteristic for anion Mn12 single-molecule magnets.

  2. Optimization of the anisotropic united atoms intermolecular potential for n-alkanes: improvement of transport properties.

    PubMed

    Nieto-Draghi, Carlos; Ungerer, Philippe; Rousseau, Bernard

    2006-07-28

    The parameters of the anisotropic united atom (AUA) intermolecular potential for n-alkanes originally proposed by Toxvaerd [J. Chem. Phys. 93, 4290 (1990)] [AUA(3)] was optimized by Ungerer et al. [J. Chem. Phys. 112, 5499 (2000)] [AUA(4)] on the basis of equilibrium properties (vapor pressures, vaporization enthalpies, and liquid densities). In this work we analyze the influence of the torsion potential in the internal and collective dynamics of the AUA model. The modified potential [AUA(4m)] preserves all the intermolecular parameters and only explores an increment in the trans-gauche and gauche(+)-gauche(-) transition barrier of the torsion potential. This modification better reproduce different transport properties (shear viscosity, self-diffusion coefficient, and internal relaxation times), keeping the accuracy achieved in our previous work for equilibrium properties. An extensive investigation of the shear viscosity of ethane, n-pentane, n-dodecane, and n-eicosane in a wide range of pressures and temperatures shows that the AUA(4m) improves the accuracy of the original AUA(4), reducing the absolute average deviation from 30% to 14.5%. Finally, the self-diffusion coefficient of n-hexane computed with the new model in the range of 223-333 K and from 0.1 to 295 MPa is in better agreement with respect to the experimental data than the original model. PMID:16942166

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

    NASA Astrophysics Data System (ADS)

    Ç?rak, Ça?r?; Sert, Yusuf; Ucun, Fatih

    2014-06-01

    In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

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

    NASA Astrophysics Data System (ADS)

    Ç?rak, Ça?r?; Sert, Yusuf; Ucun, Fatih

    2013-09-01

    In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and ?-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

  5. Intermolecular Forces as a Key to Understanding the Environmental Fate of Organic Xenobiotics

    NASA Astrophysics Data System (ADS)

    Casey, Ryan E.; Pittman, Faith A.

    2005-02-01

    Environmental education for undergraduate nonscience majors and high school students is key in fostering an increased understanding of environmental issues among the general public. We have developed an environmental chemistry module that can be used in high schools or undergraduate nonscience courses to relate chemical structures and properties to the macroscopic behavior of environmentally relevant organic chemicals like pesticides, PCBs, and solvents. The module introduces the concepts of intermolecular forces, polarity, and partitioning to explain complex phenomena such as environmental transport and biomagnification of xenobiotics (human-made chemicals). The level 1 version 2.11 model, developed by Trent University, is used in a laboratory segment that allows students to explore the relationship between chemical properties and environmental distribution. The initial material on polarity and intermolecular forces can lead to additional applications, including: bioaccumulation and biomagnification of organic chemicals; toxicology or pharmacology (ability of molecules to cross membranes); and groundwater contamination. This module can enhance chemistry courses by presenting detailed applications and allowing students to make powerful, verifiable predictions. See Featured Molecules .

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

    PubMed

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

    2014-11-01

    Translation of foot-and-mouth disease virus RNA initiates at one of two start codons leading to the synthesis of two forms of leader proteinase L(pro) (Lab(pro) and Lb(pro)). These forms free themselves from the viral polyprotein by intra- and intermolecular self-processing and subsequently cleave the cellular eukaryotic initiation factor (eIF) 4 G. During infection, Lb(pro) removes six residues from its own C-terminus, generating sLb(pro). We present the structure of sLb(pro) bound to the inhibitor E64-R-P-NH2, illustrating how sLb(pro) can cleave between Lys/Gly and Gly/Arg pairs. In intermolecular cleavage on polyprotein substrates, Lb(pro) was unaffected by P1 or P1' substitutions and processed a substrate containing nine eIF4GI cleavage site residues whereas sLb(pro) failed to cleave the eIF4GI containing substrate and cleaved appreciably more slowly on mutated substrates. Introduction of 70 eIF4GI residues bearing the Lb(pro) binding site restored cleavage. These data imply that Lb(pro) and sLb(pro) may have different functions in infected cells. PMID:25240326

  7. Theoretical studies of molecular interactions

    SciTech Connect

    Lester, W.A. Jr.

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  8. Effects of next-nearest-neighbor interactions on discrete multibreathers corresponding to Davydov model with saturable nonlinearities

    NASA Astrophysics Data System (ADS)

    Tchinang Tchameu, J. D.; Tchawoua, C.; Togueu Motcheyo, A. B.

    2015-12-01

    The influence of next-nearest-neighbor interactions (next-NNI) of dipole-dipole type is analyzed in Davydov model with saturable nonlinearities. We analytically study the regions of discrete modulational instability (MI) of plane carrier waves and it appears that this region decreases as the number of nearest neighbors, m, increases. We also show via the instability growth rate (gain) that when m increases, bandwidth of instability decreases. Otherwise, it is noted that the saturation also has an antagonistic effect on the gain. Numerical simulations indicate that the presence of next-NNI induced downward corrections of the time of onset of MI. After having sought Discrete Soliton (DS) and Discrete Multihump soliton (DMHS) numerically with m = 1; 2; 3, the next-nearest neighbor dependence of the width and height of these solutions is discussed. A study of mobility is achieved and it results that next-NNI increase the speed of DMHS. Furthermore, the collisions of two DMHS are performed and it emerges mainly that next-NNI lead to the formation of large stationary solitons.

  9. The interplay of thiophilic and hydrogen bonding interactions in the supramolecular architecture of phenylmercury 4-hydroxypiperidine dithiocarbamate

    NASA Astrophysics Data System (ADS)

    Prasad, Rajendra; Yadav, Reena; Trivedi, Manoj; Kociok-Köhn, Gabriele; Kumar, Abhinav

    2016-01-01

    A new phenylmercury(II) dithiocarbamate complex [PhHg(S2CN(CH2)4CH(OH)], (1) has been synthesized and characterized by elemental analyses, IR, 1H and 13C NMR spectroscopy and X-ray crystallography. The crystal structure of 1 shows a linear arrangement at the Hg(II) centre of the molecule through bonding of the sulphur atom of the dithiocarbamate ligand and the carbon atom of the aromatic ring. Weak intermolecular thiophilic Hg···S interactions lead to a "head-to-tail" dimer and the presence of a hydroxyl group at the periphery of piperidine moiety generates a 1D-chain network through intermolecular O···H interactions. The nature of weak intra- and intermolecular Hg···S, H···S and intermolecular O···H interactions have been assessed with the help of ab initio calculations and atoms-in-molecules (AIM) approach.

  10. Strong anisotropy of momentum-relaxation time induced by intermolecular vibrations of single-crystal organic semiconductors

    NASA Astrophysics Data System (ADS)

    Ishii, Hiroyuki; Kobayashi, Nobuhiko; Hirose, Kenji

    2013-11-01

    We present a theoretical study of the relationships between intermolecular vibrations and anisotropic transport properties of pentacene and rubrene single-crystal organic semiconductors. Using our wave-packet approach based on the Kubo formula beyond the effective-mass approximation with the assumption of an isotropic momentum-relaxation time, we find that the intermolecular vibrations induce a strong anisotropic momentum-relaxation time but moderate the anisotropy of carrier mobility much more than that of the effective mass. This clarifies the mechanism behind the deviation of the anisotropic ratio of mobility from that of effective mass observed in angle-resolved photoelectron spectroscopy experiments.

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

    SciTech Connect

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

    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 bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger–Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants ( C{sub 11} , C{sub 12} , C{sub 13} , C{sub 33} , C{sub 44} , and C{sub 66} ), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.

  12. Intermolecular Coulombic Decay in Biology: The Initial Electron Detachment from FADH(-) in DNA Photolyases.

    PubMed

    Harbach, Philipp H P; Schneider, Matthias; Faraji, Shirin; Dreuw, Andreas

    2013-03-21

    Intermolecular coulombic decay (ICD) is an efficient mechanism of low-energy electron generation in condensed phases and is discussed as their potential source in living cells, tissues, and materials. The first example of ICD as an operating mechanism in real biological systems, that is, in the DNA repair enzymes photolyases, is presented. Photolyase function involves light-induced electron detachment from a reduced flavin adenine dinucleotide (FADH(-)), followed by its transfer to the DNA-lesion triggering repair of covalently bound nucleobase dimers. Modern quantum chemical methods are employed to demonstrate that the transferred electron is efficiently generated via a resonant ICD process between the antenna pigment and the FADH(-) cofactors. PMID:26291360

  13. Cobalt-catalysed site-selective intra- and intermolecular dehydrogenative amination of unactivated sp3 carbons

    PubMed Central

    Wu, Xuesong; Yang, Ke; Zhao, Yan; Sun, Hao; Li, Guigen; Ge, Haibo

    2015-01-01

    Cobalt-catalysed sp2 C–H bond functionalization has attracted considerable attention in recent years because of the low cost of cobalt complexes and interesting modes of action in the process. In comparison, much less efforts have been devoted to the sp3 carbons. Here we report the cobalt-catalysed site-selective dehydrogenative cyclization of aliphatic amides via a C–H bond functionalization process on unactivated sp3 carbons with the assistance of a bidentate directing group. This method provides a straightforward synthesis of monocyclic and spiro ?- or ?-lactams with good to excellent stereoselectivity and functional group tolerance. In addition, a new procedure has been developed to selectively remove the directing group, which enables the synthesis of free ?- or ?-lactam compounds. Furthermore, the first cobalt-catalysed intermolecular dehydrogenative amination of unactivated sp3 carbons is also realized. PMID:25753366

  14. Influence of intermolecular hydrogen bonds on the luminescence properties of {alpha}-substituted cinnamonitriles

    SciTech Connect

    Mikhlina, Ya. A.; Bolotin, B. M.; Uzhinov, B. M. Volchkov, V. V.; Kuz'mina, L. G.

    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.

  15. 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.

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

    PubMed

    Ito, Soichi; Nagami, Takanori; Nakano, Masayoshi

    2015-12-17

    Vibronic coupling plays a crucial role in singlet fission whereby a singlet exciton splits into two triplet excitons. In order to reveal the physicochemical origin of the vibronic coupling associated with singlet fission as well as to clarify its relationship with chemical structure, we evaluate relevant vibronic couplings from the viewpoint of their spatial contributions described by vibronic coupling density. From the analysis using a model tetracene dimer, a typical singlet fission system, the frequency dependence of vibronic couplings in each electronic state is found to be significantly different from that of another depending on the nature of the electronic structure (intra/intermolecular excitation) and the related vibrational motion. These findings contribute not only to the fundamental understanding of the singlet fission mechanism from the viewpoint of vibronic couplings but also to opening a new path to designing highly efficient singlet fission materials through phonon-bath engineering. PMID:26673196

  17. Brief history of intermolecular and intersurface forces in complex fluid systems.

    PubMed

    Israelachvili, Jacob; Ruths, Marina

    2013-08-01

    We review the developments of ideas, concepts, and theories of intermolecular and intersurface forces and how these were influenced (or ignored) by observations of nature and, later, systematic experimentation. The emphasis of this review is on the way things gradually changed: experimentation replaced rhetoric, measurement and quantification replaced hand waving, energy replaced force in calculations, discrete atoms replaced the (continuum) aether, thermodynamics replaced mechanistic models, randomness and probability replaced certainty, and delicate experiments on the subnanoscale revealed fascinating self-assembling structures and complex behavior of even the simplest systems. We conclude by discussing today's unresolved challenges: how complex "dynamic" multicomponent--especially living biological--systems that receive a continuous supply of energy can be far from equilibrium and not even in any steady state. Such systems, never static but evolving in both space and time, are still far from being understood both experimentally and theoretically. PMID:23659277

  18. Intermolecular C-H Bond Activation Promoted by a Titanium Alkylidyne Brad C. Bailey, Hongjun Fan, Erich W. Baum, John C. Huffman, Mu-Hyun Baik,* and

    E-print Network

    Baik, Mu-Hyun

    Intermolecular C-H Bond Activation Promoted by a Titanium Alkylidyne Brad C. Bailey, Hongjun Fan to perform intermolecular activation of inert C-H bonds.3-7 We now report that transient titanium alkylidynes of a titanium alkyli- dene complex (PNP)TidCHtBu(OTf) supported by a pincer ligand (PNP ) N-[2-P(CHMe2

  19. Applications and Analogies: Phototherapy and the Treatment of Hyperbilirubinemia: A Demonstration of Intra- versus Intermolecular Hydrogen Bonding.

    ERIC Educational Resources Information Center

    Wilbraham, Antony C.

    1984-01-01

    Background information and procedures are provided for a demonstration of intramolecular versus intermolecular hydrogen bonding. The demonstration is based on structural changes in bilirubin molecules which lead to changes in physical properties. A list of further investigations to try is included. (JN)

  20. Stability of van der Waals compounds and investigation of the intermolecular potential in helium-xenon mixtures

    E-print Network

    Vos, Willem L.

    Stability of van der Waals compounds and investigation of the intermolecular potential in helium-xenon mixtures Jean-Louis Barrat and Willem L. Vos Ecole Normale Superieure de Lyon, Laboratoire de Physique, 46 the occurrenceof a Ne(He)2 compound, that was recently found by Jean-Louis, Loubeyre, and Charon-Gerard. I

  1. 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

  2. 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

  3. Volume 41, number 2 CHEMICAL PHYSICS LETTERS 15 July 1976 EXPERIMENTAL DETERMINATION OF THE TRIPLET EXCITON INTERMOLECULAR ENTERACTION

    E-print Network

    Fayer, Michael D.

    to the rate of exciton inelastic scattering, the exciton transport coherence length is calculated. I EXCITON INTERMOLECULAR ENTERACTION MATRIX ELEMENT AND THE EXCITON-PHONON SCATTERING RATE IN MOLECULAR-phonon scattering must be determined [2-S] _ An exciton wave packet composed of a linear combina- tion of wave

  4. Docking of Protein-Protein Complexes on the Basis of Highly Ambiguous Intermolecular Distance Restraints Derived from

    E-print Network

    Clore, G. Marius

    Restraints Derived from 1HN/15N Chemical Shift Mapping and Backbone 15N-1H Residual Dipolar Couplings Using ambiguous, intermolecular distance restraints (comprising between 400 and 3000 individual distances-HPr and IIAGlc-HPr complexes, all structures satisfying the experimental restraints (i.e., both the ambiguous

  5. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Entanglement Properties Between Two Spatially Separated Atoms with Cascade Configuration in Free Space

    NASA Astrophysics Data System (ADS)

    Yang, Guo-Hui; Zhang, Jun-Feng; Miao, Xiang-Yang; Zhou, Ling

    2010-03-01

    We investigate the entanglement properties between two identical atoms with cascade configuration through the retarded dipole-dipole interaction in free space when their spatial separation is on the order of radiation wavelength or less. We analyze the function of Hamiltonian induced by dipole-dipole interaction. By solving master equation, we show that the spontaneous emission induce entanglement and destroy entanglement too. We also show the long life time of entanglement within cascade configuration.

  6. Investigation of chromophore-chromophore interaction by electro-optic measurements, linear dichroism, x-ray scattering, and density-functional calculations

    SciTech Connect

    Apitz, D.; Bertram, R.P.; Benter, N.; Buse, K.; Hieringer, W.; Andreasen, J.W.; Nielsen, M.M.; Johansen, P.M.

    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.

  7. Non-linear QCD dynamics in two-photon interactions at high energies

    SciTech Connect

    Carvalho, F.; Navarra, F. S.; Cazaroto, E.; Goncalves, V. P.

    2013-03-25

    Assuming that the dipole - dipole cross section can be related with the dipole - proton cross section, we calculate the total {gamma}{gamma}, {gamma}*{gamma}* cross-sections and the real photon structure function F{sup {gamma}}{sub 2}(x,Q{sup 2}) using the recent solution of the BK equation with running coupling constant.

  8. Report on dipole-dipole resistivity and technology transfer at the Ahuachapan Geothermal field Ahuachapan, El Salvador

    SciTech Connect

    Fink, J.B. )

    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.

  9. Four-body long-range interactions between ultracold weakly-bound diatomic molecules

    E-print Network

    Lepers, Maxence; Luc-Koenig, Eliane; Dulieu, Olivier

    2015-01-01

    Using the multipolar expansion of electrostatic and magnetostatic potential energies, we characterize the long-range interactions between two weakly-bound diatomic molecules, taking as an example the paramagnetic Er$_2$ Feshbach molecules which were produced recently. Since inside each molecule, individual atoms conserve their identity, the intermolecular potential energy can be expanded as the sum of pairwise atomic potential energies. In the case of Er$_2$ Feshbach molecules, we show that the interaction between atomic magnetic dipoles gives rise to the usual $R^{-3}$ term of the multipolar expansion, with $R$ the intermolecular distance, but also to additional terms scaling as $R^{-5}$, $R^{-7}$, and so on. Those terms are due to the interaction between effective molecular multipole moments, and are strongly anisotropic with respect to the orientation of the molecules. Similarly the atomic pairwise van der Waals interaction results in $R^{-6}$, $R^{-8}$, ... terms in the intermolecular potential energy. By...

  10. 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)=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=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

  11. Rh(I)-bisphosphine-catalyzed asymmetric, intermolecular hydroheteroarylation of ?-substituted acrylate derivatives.

    PubMed

    Filloux, Claire M; Rovis, Tomislav

    2015-01-14

    Asymmetric hydroheteroarylation of alkenes represents a convenient entry to elaborated heterocyclic motifs. While chiral acids are known to mediate asymmetric addition of electron-rich heteroarenes to Michael acceptors, very few methods exploit transition metals to catalyze alkylation of heterocycles with olefins via a C-H activation, migratory insertion sequence. Herein, we describe the development of an asymmetric, intermolecular hydroheteroarylation reaction of ?-substituted acrylates with benzoxazoles. The reaction provides 2-substitued benzoxazoles in moderate to excellent yields and good to excellent enantioselectivities. Notably, a series of mechanistic studies appears to contradict a pathway involving enantioselective protonation of a Rh(I)-enolate, despite the fact that such a mechanism is invoked almost unanimously in the related addition of aryl boronic acids to methacrylate derivatives. Evidence suggests instead that migratory insertion or beta-hydride elimination is enantiodetermining and that isomerization of a Rh(I)-enolate to a Rh(I)-heterobenzyl species insulates the resultant ?-stereocenter from epimerization. A bulky ligand, CTH-(R)-Xylyl-P-Phos, is crucial for reactivity and enantioselectivity, as it likely discourages undesired ligation of benzoxazole substrates or intermediates to on- or off-cycle rhodium complexes and attenuates coordination-promoted product epimerization. PMID:25545834

  12. Site- and energy-selective slow-electron production through intermolecular Coulombic decay

    NASA Astrophysics Data System (ADS)

    Gokhberg, Kirill; Koloren?, P?emysl; Kuleff, Alexander I.; Cederbaum, Lorenz S.

    2014-01-01

    Irradiation of matter with light tends to electronically excite atoms and molecules, with subsequent relaxation processes determining where the photon energy is ultimately deposited and electrons and ions produced. In weakly bound systems, intermolecular Coulombic decay (ICD) enables very efficient relaxation of electronic excitation through transfer of the excess energy to neighbouring atoms or molecules that then lose an electron and become ionized. Here we propose that the emission site and energy of the electrons released during this process can be controlled by coupling the ICD to a resonant core excitation. We illustrate this concept with ab initio many-body calculations on the argon-krypton model system, where resonant photoabsorption produces an initial or `parent' excitation of the argon atom, which then triggers a resonant-Auger-ICD cascade that ends with the emission of a slow electron from the krypton atom. Our calculations show that the energy of the emitted electrons depends sensitively on the initial excited state of the argon atom. The incident energy can thus be adjusted both to produce the initial excitation in a chosen atom and to realize an excitation that will result in the emission of ICD electrons with desired energies. These properties of the decay cascade might have consequences for fundamental and applied radiation biology and could be of interest in the development of new spectroscopic techniques.

  13. Radical Reactivity in the Condensed Phase: Intermolecular versus Intramolecular Reactions of Alkoxy Radicals.

    PubMed

    Carrasquillo, Anthony J; Daumit, Kelly E; Kroll, Jesse H

    2015-06-18

    Condensed-phase alkoxy (RO) radicals can undergo unimolecular (e.g., intramolecular H atom abstraction) reactions as well as bimolecular (intermolecular H atom abstraction) reactions, though the competition between these two channels is not well constrained. Here, we examine this branching by generating RO radicals from the photolysis of a large alkyl nitrite (C20H41ONO) in hexanes and nebulizing the mixture into an aerosol mass spectrometer for analysis. Product ions associated with unimolecular (isomerization) reactions were observed to increase upon photolysis. However, no formation of the C20 alcohol (C20H41OH, the expected product from RO + RH reactions) was observed, suggesting that bimolecular reactions are at most a minor channel for this condensed-phase system (involving saturated hydrocarbons). This result, combined with previous studies of liquid-phase RO radicals carried out at higher concentrations, suggests that when 1,5-H atom abstraction reactions are facile (i.e., in which a 1,5-H atom shift from a secondary or tertiary carbon can occur), this channel will dominate over bimolecular reactions. PMID:26266621

  14. Intermolecular potentials and the accurate prediction of the thermodynamic properties of water

    SciTech Connect

    Shvab, I.; Sadus, Richard J.

    2013-11-21

    The ability of intermolecular potentials to correctly predict the thermodynamic properties of liquid water at a density of 0.998 g/cm{sup 3} for a wide range of temperatures (298–650 K) and pressures (0.1–700 MPa) is investigated. Molecular dynamics simulations are reported for the pressure, thermal pressure coefficient, thermal expansion coefficient, isothermal and adiabatic compressibilities, isobaric and isochoric heat capacities, and Joule-Thomson coefficient of liquid water using the non-polarizable SPC/E and TIP4P/2005 potentials. The results are compared with both experiment data and results obtained from the ab initio-based Matsuoka-Clementi-Yoshimine non-additive (MCYna) [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007)] potential, which includes polarization contributions. The data clearly indicate that both the SPC/E and TIP4P/2005 potentials are only in qualitative agreement with experiment, whereas the polarizable MCYna potential predicts some properties within experimental uncertainty. This highlights the importance of polarizability for the accurate prediction of the thermodynamic properties of water, particularly at temperatures beyond 298 K.

  15. In Vivo Noninvasive Detection of Brown Adipose Tissue through Intermolecular Zero-Quantum MRI

    PubMed Central

    Branca, Rosa T.; Zhang, Le; Warren, Warren S.; Auerbach, Edward; Khanna, Arjun; Degan, Simone; Ugurbil, Kamil; Maronpot, Robert

    2013-01-01

    The recent discovery of active Brown Adipose Tissue (BAT) in adult humans has opened new avenues for obesity research and treatment, as reduced BAT activity seem to be implicated in human energy imbalance, diabetes, and hypertension. However, clinical applications are currently limited by the lack of non-invasive tools for measuring mass and function of this tissue in humans. Here we present a new magnetic resonance imaging method based on the normally invisible intermolecular multiple-quantum coherence 1H MR signal. This method, which doesn’t require special hardware modifications, can be used to overcome partial volume effect, the major limitation of MR-based approaches that are currently being investigated for the detection of BAT in humans. With this method we can exploit the characteristic cellular structure of BAT to selectively image it, even when (as in humans) it is intimately mixed with other tissues. We demonstrate and validate this method in mice using PET scans and histology. We compare this methodology with conventional 1H MR fat fraction methods. Finally, we investigate its feasibility for the detection of BAT in humans. PMID:24040203

  16. 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. Work supported by DRDC Suffield (Dr. Julian J. Lee).

  17. Site- and energy-selective slow-electron production through intermolecular Coulombic decay.

    PubMed

    Gokhberg, Kirill; Koloren?, P?emysl; Kuleff, Alexander I; Cederbaum, Lorenz S

    2014-01-30

    Irradiation of matter with light tends to electronically excite atoms and molecules, with subsequent relaxation processes determining where the photon energy is ultimately deposited and electrons and ions produced. In weakly bound systems, intermolecular Coulombic decay (ICD) enables very efficient relaxation of electronic excitation through transfer of the excess energy to neighbouring atoms or molecules that then lose an electron and become ionized. Here we propose that the emission site and energy of the electrons released during this process can be controlled by coupling the ICD to a resonant core excitation. We illustrate this concept with ab initio many-body calculations on the argon-krypton model system, where resonant photoabsorption produces an initial or 'parent' excitation of the argon atom, which then triggers a resonant-Auger-ICD cascade that ends with the emission of a slow electron from the krypton atom. Our calculations show that the energy of the emitted electrons depends sensitively on the initial excited state of the argon atom. The incident energy can thus be adjusted both to produce the initial excitation in a chosen atom and to realize an excitation that will result in the emission of ICD electrons with desired energies. These properties of the decay cascade might have consequences for fundamental and applied radiation biology and could be of interest in the development of new spectroscopic techniques. PMID:24362566

  18. Hadamard-encoded high-resolution NMR spectroscopy via intermolecular single-quantum coherences

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    NMR spectroscopy plays an important role in metabolite studies because it can provide atomic level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues are hampered by the magnetic field inhomogeneities originating from variations in macroscopic magnetic susceptibility, which lead to broad spectral lines and subsequently obscure metabolite signals. A new pulse sequence based on intermolecular single-quantum coherences was proposed to obtain one-dimensional high-resolution NMR spectra in inhomogeneous magnetic fields via Hadamard encoding. The new method can provide resolution-improved spectra directly through one-dimensional acquisition within a relatively short acquisition time. Theoretical derivation was performed and the conclusion was tested by solution samples in purposely de-shimmed magnetic fields and pig brain tissue sample. The experimental results show that this sequence can yield useful structural information, even when the field inhomogeneity is sufficiently severe to erase almost all spectral information with conventional one-dimensional single-quantum coherence techniques. Moreover, good solvent suppression efficiency can be achieved by this sequence. This sequence may provide a promising way for high-resolution NMR spectroscopy of biological tissue.

  19. Pressure waves generated by metastable intermolecular composites in an aqueous environment

    NASA Astrophysics Data System (ADS)

    Maines, G.; Radulescu, M.; Bacciochini, A.; Jodoin, B.; Lee, J. J.

    2014-05-01

    In the present study, pressure waves generated by a metastable intermolecular composite (MIC) have been measured experimentally in an aqueous environment and correlated with flame speed measurements. Underwater experiments were performed in a 1.0 L high-pressure chamber mounted with high-resolution pressure transducers and designed with optical access. Samples consisting of a stoichiometric mixture of aluminium and copper(II)-oxide particles were evaluated. Two types of samples were synthesized; a mixture of micron-sized raw powders, and ball-milled powders with a fine-scale nano-structure. A planetary mill was used to refine reactant powders from micron- to nano-scale dimensions. The dynamics of the pressure wave and high-pressure gas bubble were monitored via pressure histories and high-speed Schlieren visualization. The effect of reactant particle size has been evaluated quantitatively. The dynamics of the pressure wave were correlated with the rate of expansion of the high-pressure gas bubble.

  20. Resolution enhancement in MR spectroscopy of red bone marrow fat via intermolecular double-quantum coherences

    NASA Astrophysics Data System (ADS)

    Bao, Jianfeng; Cui, Xiaohong; Huang, Yuqing; Zhong, Jianhui; Chen, Zhong

    2015-08-01

    High-resolution 1H magnetic resonance spectroscopy (MRS) is generally inaccessible in red bone marrow (RBM) tissues using conventional MRS techniques. This is because signal from these tissues suffers from severe inhomogeneity in the main static B0 field originated from the intrinsic honeycomb structures in trabecular bone. One way to reduce effects of B0 field inhomogeneity is by using the intermolecular double quantum coherence (iDQC) technique, which has been shown in other systems to obtain signals insensitive to B0 field inhomogeneity. In the present study, we employed an iDQC approach to enhance the spectral resolution of RBM. The feasibility and performance of this method for achieving high resolution MRS was verified by experiments on phantoms and pig vertebral bone samples. Unsaturated fatty acid peaks which overlap in the conventional MRS were well resolved and identified in the iDQC spectrum. Quantitative comparison of fractions of three types of fatty acids was performed between iDQC spectra on the in situ RMB and conventional MRS on the extracted fat from the same RBM. Observations of unsaturated fatty acids with iDQC MRS may provide valuable information and may hold potential in diagnosis of diseases such as obesity, diabetes, and leukemia.

  1. On atom-atom 'short contact' bonding interactions in crystals.

    PubMed

    Lecomte, Claude; Espinosa, Enrique; Matta, Cherif F

    2015-03-01

    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

  2. Ab initio intermolecular potential of Ar-C2H2 refined using high-resolution spectroscopic data.

    PubMed

    Lauzin, Clément; Coudert, Laurent H; Herman, Michel; Liévin, Jacques

    2013-12-19

    The high-resolution infrared spectra of the ?1 + ?3 (2CH) band of the Ar-C2H2 complex has been recorded from 6544 to 6566 cm(-1). The previously reported K(a) = 1 ? 0, 2 ? 1, and 0 ? 1 subbands were observed and the K(a) = 1 ? 2, 2 ? 3, and 3 ? 2 subbands were assigned for the first time. The intermolecular potential energy surface of this complex has been calculated ab initio and optimized by fitting the new high-resolution data. Refined intermolecular potential energy surfaces have been obtained for the ground vibrational state and for the excited v1 = v3 = 1 stretching state. For the former state, the results of the analysis are satisfactory and the microwave transitions of the complex are reproduced with a root-mean-square deviation of 5 MHz. For the latter state, systematic discrepancies arise in the analysis. PMID:24111882

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

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

  4. Detection of Iron-labeled Single Cells by MR Imaging Based on Intermolecular Double Quantum Coherences at 14 T

    PubMed Central

    Cho, Jee-Hyun; Hong, Kwan Soo; Cho, Janggeun; Chang, Suk-Kyu; Cheong, Chaejoon; Lee, Na Hee; Kim, Hyeonjin; Warren, Warren S.; Ahn, Sangdoo; Lee, Chulhyun

    2013-01-01

    To evaluate the efficiency and feasibility of intermolecular multiple quantum coherence (iMQC) magnetic resonance (MR) imaging for single cell detection, we obtained intermolecular double quantum coherence (iDQC) and conventional gradient echo (GE) images of macrophage cells labeled by contrast agents in gel. The iDQC images obtained with echo-planar readout visualized the labeled cells effectively and with a higher contrast than seen in conventional GE images, especially at low planar resolutions and with thick slices. This implies that iDQC imaging with contrast agents could be a good alternative to conventional MR imaging for detecting labeled single cells or cell tracking under favorable conditions. PMID:22436467

  5. Diffusion-controlled intermolecular electron transfer studied by transient absorption and degenerate four-wave mixing measurements

    NASA Astrophysics Data System (ADS)

    Assel, M.; Höfer, T.; Laubereau, A.; Kaiser, W.

    1995-03-01

    The time dependence of intermolecular electron transfer kinetics is studied by two experimental techniques: transient absorption measurements and degenerate four-wave mixing after excitation of the donor molecules by picosecond UV pulses. In the system perylene/phthalic anhydride the electron transfer rate depends strongly on the concentration of the acceptor molecule phthalic anhydride. The value agrees with theoretical calculations based on a diffusion-controlled process.

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

    PubMed

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

    2015-10-28

    X-ray absorption/emission spectroscopy (XAS/XES) at the N K-edge of iron protoporphyrin IX chloride (FePPIX-Cl, or hemin) has been carried out for dissolved monomers in DMSO, dimers in water and for the solid state. This sequence of samples permits identification of characteristic spectral features associated with the hemin intermolecular bonding. These characteristic features are further analyzed and understood at the molecular orbital (MO) level based on the DFT calculations. PMID:26455378

  7. Concise NMR approach for molecular dynamics characterizations in organic solids.

    PubMed

    Aliev, Abil E; Courtier-Murias, Denis

    2013-08-22

    Molecular dynamics characterisations in solids can be carried out selectively using dipolar-dephasing experiments. Here we show that the introduction of a sum of Lorentzian and Gaussian functions greatly improve fittings of the "intensity versus time" data for protonated carbons in dipolar-dephasing experiments. The Lorentzian term accounts for remote intra- and intermolecular (1)H-(13)C dipole-dipole interactions, which vary from one molecule to another or for different carbons within the same molecule. Thus, by separating contributions from weak remote interactions, more accurate Gaussian decay constants, T(dd), can be extracted for directly bonded (1)H-(13)C dipole-dipole interactions. Reorientations of the (1)H-(13)C bonds lead to the increase of T(dd), and by measuring dipolar-dephasing constants, insight can be gained into dynamics in solids. We have demonstrated advantages of the method using comparative dynamics studies in the ? and ? polymorphs of glycine, cyclic amino acids L-proline, DL-proline and trans-4-hydroxy-L-proline, the Ala residue in different dipeptides, as well as adamantane and hexamethylenetetramine. It was possible to distinguish subtle differences in dynamics of different carbon sites within a molecule in polymorphs and in L- and DL-forms. The presence of overall molecular motions is shown to lead to particularly large differences in dipolar-dephasing experiments. The differences in dynamics can be attributed to differences in noncovalent interactions. In the case of hexamethylenetetramine, for example, the presence of C-H···N interactions leads to nearly rigid molecules. Overall, the method allows one to gain insight into the role of noncovalent interactions in solids and their influence on the molecular dynamics. PMID:23879450

  8. Engineered two-dimensional Ising interactions in a trapped-ion quantum simulator with hundreds of spins.

    PubMed

    Britton, Joseph W; Sawyer, Brian C; Keith, Adam C; Wang, C-C Joseph; Freericks, James K; Uys, Hermann; Biercuk, Michael J; Bollinger, John J

    2012-04-26

    The presence of long-range quantum spin correlations underlies a variety of physical phenomena in condensed-matter systems, potentially including high-temperature superconductivity. However, many properties of exotic, strongly correlated spin systems, such as spin liquids, have proved difficult to study, in part because calculations involving N-body entanglement become intractable for as few as N???30 particles. Feynman predicted that a quantum simulator--a special-purpose 'analogue' processor built using quantum bits (qubits)--would be inherently suited to solving such problems. In the context of quantum magnetism, a number of experiments have demonstrated the feasibility of this approach, but simulations allowing controlled, tunable interactions between spins localized on two- or three-dimensional lattices of more than a few tens of qubits have yet to be demonstrated, in part because of the technical challenge of realizing large-scale qubit arrays. Here we demonstrate a variable-range Ising-type spin-spin interaction, J(i,j), on a naturally occurring, two-dimensional triangular crystal lattice of hundreds of spin-half particles (beryllium ions stored in a Penning trap). This is a computationally relevant scale more than an order of magnitude larger than previous experiments. We show that a spin-dependent optical dipole force can produce an antiferromagnetic interaction J(i,j) proportional variant d(-a)(i,j), where 0???a???3 and d(i,j) is the distance between spin pairs. These power laws correspond physically to infinite-range (a = 0), Coulomb-like (a = 1), monopole-dipole (a = 2) and dipole-dipole (a = 3) couplings. Experimentally, we demonstrate excellent agreement with a theory for 0.05???a???1.4. This demonstration, coupled with the high spin count, excellent quantum control and low technical complexity of the Penning trap, brings within reach the simulation of otherwise computationally intractable problems in quantum magnetism. PMID:22538611

  9. The oscillatory behavior, static and dynamic analyses of a micro/nano gyroscope considering geometric nonlinearities and intermolecular forces

    NASA Astrophysics Data System (ADS)

    Mojahedi, M.; Ahmadian, M. T.; Firoozbakhsh, K.

    2013-12-01

    The nonlinear dynamic and static deflection of a micro/nano gyroscope under DC voltages and base rotation are investigated. The gyroscope undertakes two coupled bending motions along the drive and sense directions and subjected to electrostatic actuations and intermolecular forces. The nonlinear governing equations of motion for the system with the effect of electrostatic force, intermolecular tractions and base rotation are derived using extended Hamilton principle. Under constant voltage, the gyroscope finds the preformed shape. First, the deflection of the micro/nano gyroscope under electrostatic forces is obtained by static and dynamic analyses. Furthermore, the static and dynamic instability of the system are investigated. Afterward the oscillatory behavior of the pre-deformed micro/nano gyroscope around equilibrium is studied. The effects of intermolecular and nonlinear parameters on the static and dynamic deflection, natural frequencies and instability of the micro/nano gyroscope are studied. The presented model can be used to exactly determine static and the dynamic behavior of vibratory micro/nano gyroscopes.

  10. Comparative Study of the Intermolecular Dynamics and Physical Properties of Branched and Linear Alkyl Chain Imidazolium Ionic Liquids

    NASA Astrophysics Data System (ADS)

    Xue, Lianjie; Bardak, Fehmi; Tamas, George; Gurung, Eshan; Quitevis, Edward; Koh, Yung; Simon, Sindee

    2014-03-01

    The optical Kerr effect (OKE) spectra, densities, viscosities, and transition temperatures of 1-alkyl-3-methylimidazolium bis{(trifluoromethane)sulfonyl}amide ionic liquids (ILs) with branched alkyl chains, -Cn-3CH(CH3)2 (branched ILs), were measured and compared to those with linear alkyl chains, -Cn-1CH3 (linear ILs), for n = 3, 4, 5, 6 and 7. The results show that a branched IL has a higher viscosity and transition temperature Tg than the corresponding linear IL with the same n, whereas the densities of each branched/linear IL pair are the same within experimental error. For short alkyl chains (n =3 and 4) the intermolecular part of the OKE spectrum of the branched ILs tends to be narrower and lower in frequency than that of the linear ILs. This suggests that branching softens the intermolecular modes. For long alkyl chains (n =5-7), the difference between the intermolecular spectrum of the branched IL and that of the linear IL with the same n decreases, which indicates that the branching effect becomes smaller when the alkyl chains get longer. This work was supported by NSF grant CHE-1153077.

  11. Site-specific intermolecular valence-band dispersion in ?-phase crystalline films of cobalt phthalocyanine studied by angle-resolved photoemission spectroscopy

    SciTech Connect

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2014-12-14

    The valence band structure of ?-phase crystalline films of cobalt phthalocyanine (CoPc) grown on Au(111) is investigated by using angle-resolved photoemission spectroscopy (ARPES) with synchrotron radiation. The photo-induced change in the ARPES peaks is noticed in shape and energy of the highest occupied molecular orbital (HOMO, C 2p) and HOMO-1 (Co 3d) of CoPc, and is misleading the interpretation of the electronic properties of CoPc films. From the damage-free normal-emission ARPES measurement, the clear valence-band dispersion has been first observed, showing that orbital-specific behaviors are attributable to the interplay of the intermolecular ?-? and ?-d interactions. The HOMO band dispersion of 0.1 eV gives the lower limit of the hole mobility for ?-CoPc of 28.9 cm{sup 2} V{sup ?1} s{sup ?1} at 15 K. The non-dispersive character of the split HOMO-1 bands indicates that the localization of the spin state is a possible origin of the antiferromagnetism.

  12. Intermolecular polarizabilities in H{sub 2}-rare-gas mixtures (H{sub 2}–He, Ne, Ar, Kr, Xe): Insight from collisional isotropic spectral properties

    SciTech Connect

    G?az, Waldemar Bancewicz, Tadeusz; Godet, Jean-Luc; Gustafsson, Magnus; Maroulis, George; Haskopoulos, Anastasios

    2014-08-21

    The report presents results of theoretical and numerical analysis of the electrical properties related to the isotropic part of the polarizability induced by interactions within compounds built up of a hydrogen H{sub 2} molecule and a set of noble gas atoms, Rg, ranging from the least massive helium up to the heaviest xenon perturber. The Cartesian components of the collisional polarizabilities of the H{sub 2}–Rg systems are found by means of the quantum chemistry methods and their dependence on the intermolecular distance is determined. On the basis of these data, the spherical, symmetry adapted components of the trace polarizability are derived in order to provide data sets that are convenient for evaluating collisional spectral profiles of the isotropic polarized part of light scattered by the H{sub 2}–Rg mixtures. Three independent methods of numerical computing of the spectral intensities are applied at room temperature (295 K). The properties of the roto-translational profiles obtained are discussed in order to determine the role played by contributions corresponding to each of the symmetry adapted parts of the trace polarizability. By spreading the analysis over the collection of the H{sub 2}–Rg systems, evolution of the spectral properties with the growing masses of the supermolecular compounds can be observed.

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

    SciTech Connect

    Cie?lik, Marcin; Derewenda, Zygmunt S.

    2009-05-01

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

  14. Human recombinant resistin protein displays a tendency to aggregate by forming intermolecular disulfide linkages.

    PubMed

    Aruna, Battu; Ghosh, Sudip; Singh, Anil K; Mande, Shekhar C; Srinivas, V; Chauhan, Radha; Ehtesham, Nasreen Z

    2003-09-16

    Resistin, a small cysteine rich protein secreted by adipocytes, has been proposed to be a link between obesity and type II diabetes by modulating the insulin signaling pathway and thus inducing insulin resistance. Resistin protein, with 11 cysteine residues, was not significantly homologous at the amino acid level to any other known cysteine rich proteins. Resistin cDNA derived from human subcutaneous adipose tissue was expressed in Escherichia coli as an N-terminal six-His-tag fusion protein. The overexpressed recombinant resistin was purified to homogeneity from inclusion bodies, after solubilization in 8 M urea, using a metal affinity column. While MALDI-TOF mass spectrometric analysis of the purified protein generated a single peak corresponding to the estimated size of 11.3 kDa, the protein exhibited a concentration-dependent oligomerization which is evident from size exclusion chromatography. The oligomeric structure was SDS-insensitive but beta-mercaptoethanol-sensitive, pointing to the importance of disulfide linkages in resistin oligomerization. Estimation of free cysteine residues using the NBD-Cl assay revealed a concentration- and time-dependent increase in the extent of formation of disulfide linkages. The presence of intermolecular disulfide bond(s), crucial in maintaining the global conformation of resistin, was further evident from fluorescence emission spectra. Circular dichroism spectra revealed that recombinant resistin has a tendency to reversibly convert from alpha-helical to beta-sheet structure as a direct function of protein concentration. Our novel observations on the biophysical and biochemical features of human resistin, particularly those shared with prion proteins, may have a bearing on its likely physiological function. PMID:12962478

  15. 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

  16. Structural features of intra- and intermolecular G-quadruplexes derived from telomeric repeats.

    PubMed

    Víglaský, Viktor; Bauer, Lubos; Tlucková, Katarína

    2010-03-16

    The 3' strand of telomeres is composed of tandem repeats of short G-rich sequences which protrude as single-stranded DNA overhangs. These repeats are G(3)T(2)A in humans and G(4)T(2) and G(4)T(4) in the ciliates Tetrahymena and Oxytricha, respectively. We analyzed different quadruplex-forming sequences derived from telomeric sequences, G(3+k)(T(n+k)G(3+k))(3) and G(3+k)(T(2)AG(3+k))(3), in the presence of Li(+), Na(+), and K(+) through the use of circular dichroism, UV spectroscopy, and electrophoresis, where k = 0 or 1 and n = 1-3. Results obtained under the given conditions can provide more detailed information about the quadruplex structure. The major findings are as follows. (i) G-Repeats in solution form a mix of topologically different structures; only G(3)(T(2)G(3))(3) and G(3)(TG(3))(3) repeats preferentially form the parallel interstrand structure. (ii) The Tetrahymena repeat can form at least two intramolecular conformers with different strand orientations and levels of stability. (iii) G-Quadruplex conformation and molecularity strongly depend on the type and concentration of ions used in the solution. The formation of intramolecular quadruplexes is governed by the length of the loops connecting G-runs. Intermolecular G-quadruplex forms are more likely to form in a higher concentration of ions for sequences where G-runs are separated by only one or two nucleotides. PMID:20143878

  17. Fluorescence studies of the excited-state intermolecular proton-transfer reaction of 1-azacarbazole

    NASA Astrophysics Data System (ADS)

    Reynolds, Lewis E. Lambert

    The excited-state intermolecular proton-transfer reaction of 1-azacarbazole (1AC) has been studied in isolated hydrogen-bonded complexes and bulk protic solvents using steady-state and time-resolved fluorescence spectroscopy. Linear free-energy relationships for 1AC and the related molecule 7-azaindole (7AI) suggest the reaction rate may be separated into contributions from an intrinsic proton-transfer rate and a solvent factor. Progress toward determining the magnitude of each of these contributions is documented. The catalytic tautomerization of 1AC in binary complexes with acetic acid is very rapid, and using an irreversible proton-transfer kinetic scheme the rate constant is estimated to be kPT = (1.5 +/- 0.5) x 1012 s-1. Noncatalytic reactions of 1AC in complexes with lactams and amides are measurably slower, and the observed kinetics are compared to model calculations estimating the driving force of the reaction. The solvent-catalyzed reaction rates of 1AC and 7AI appear extraordinarily slow in diols and water when compared to reactions in neat alcohols. However, the excited-state reaction in ethylene glycol may be compared on an equal footing to that in methanol if the effects of hydrogen-bond dynamics as measured by the solvent dielectric relaxation time (tau1) are considered. In addition to a discussion of the anomalous reactions observed in hydroxylic solvents, the noncatalytic excited-state reaction of 1AC in bulk amides is examined. The reaction mechanism is further elucidated in a study of the excited-state tautomerization of 1AC in methanol/methanol-OD mixtures. Although the experimental results do not allow the double-proton-transfer reaction to be classified either as stepwise or concerted, recent published studies suggest that a stepwise mechanism may be preferred. The significance of the observed kinetic isotope effects is discussed.

  18. Intermolecular Electron-Transfer Reactions in Soluble Methane Monooxygenase: A Role for Hysteresis in Protein Function

    PubMed Central

    Blazyk, Jessica L.; Gassner, George T.

    2005-01-01

    Electron transfer from reduced nicotinamide adenine dinucleotide (NADH) to the hydroxylase component (MMOH) of soluble methane monooxygenase (sMMO) primes its non-heme diiron centers for reaction with dioxygen to generate high-valent iron intermediates that convert methane to methanol. This intermolecular electron-transfer step is facilitated by a reductase (MMOR), which contains [2Fe-2S] and flavin adenine dinucleotide (FAD) prosthetic groups. To investigate interprotein electron transfer, chemically reduced MMOR was mixed rapidly with oxidized MMOH in a stopped-flow apparatus, and optical changes associated with reductase oxidation were recorded. The reaction proceeds via four discrete kinetic phases corresponding to the transfer of four electrons into the two dinuclear iron sites of MMOH. Pre-equilibrating the hydroxylase with sMMO auxiliary proteins MMOB or MMOD severely diminishes electron-transfer throughput from MMOR, primarily by shifting the bulk of electron transfer to the slowest pathway. The biphasic reactions for electron transfer to MMOH from several MMOR ferredoxin analogues are also inhibited by MMOB and MMOD. These results, in conjunction with the previous finding that MMOB enhances electron-transfer rates from MMOR to MMOH when preformed MMOR-MMOH-MMOB complexes are allowed to react with NADH [Gassner, G. T.; Lippard, S. J. Biochemistry 1999, 38, 12768-12785], suggest that isomerization of the initial ternary complex is required for maximal electron-transfer rates. To account for the slow electron transfer observed for the ternary precomplex in this work, a model is proposed in which conformational changes imparted to the hydroxylase by MMOR are retained throughout the catalytic cycle. Several electron-transfer schemes are discussed with emphasis on those that invoke multiple interconverting MMOH populations. PMID:16332086

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

    PubMed

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

    2015-02-25

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

  20. 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

    are attracting considerable attention in many applications such as catalysts,1-3 solvents,4-6 electro-plating,7 purification media8 and others.9, 10 In many of these applications, the addition of water has little effect upon the chemical properties... with a diffusion probe capable of producing magnetic field gradient pulses up to 11.76 T m-1 in the z-direction and using a pulsed gradient stimulated echo (PGSTE) sequence with a homospoil gradient, which is usually preferred to the standard pulsed...

  1. Intermolecular interaction in solution—IV. The influence of solvent on the association of proton donors and acceptors1

    NASA Astrophysics Data System (ADS)

    Werner, R. L.; Quinn, J. M.; Haken, J. K.

    Infrared spectroscopic studies of indole, diphenylamine and tertiary butanol with proton acceptors, diethylacetamide and ethyl acetate show that the solvent used has a strong directive influence on the association. From a consideration of band frequencies and frequency shifts due to association the solvents were arranged according to the effects produced, while a linear correlation was not observed between the spectroscopic measurements on dilterent donor-acceptor systems and the solvents present.

  2. Mechanochemical mechanism for fast reaction of metastable intermolecular composites based on dispersion of liquid metal

    NASA Astrophysics Data System (ADS)

    Levitas, Valery I.; Asay, Blaine W.; Son, Steven F.; Pantoya, Michelle

    2007-04-01

    An unexpected mechanism for fast reaction of Al nanoparticles covered by a thin oxide shell during fast heating is proposed and justified theoretically and experimentally. For nanoparticles, the melting of Al occurs before the oxide fracture. The volume change due to melting induces pressures of 1-2 GPa and causes dynamic spallation of the shell. The unbalanced pressure between the Al core and the exposed surface creates an unloading wave with high tensile pressures resulting in dispersion of atomic scale liquid Al clusters. These clusters fly at high velocity and their reaction is not limited by diffusion (this is the opposite of traditional mechanisms for micron particles and for nanoparticles at slow heating). Physical parameters controlling the melt dispersion mechanism are found by our analysis. In addition to an explanation of the extremely short reaction time, the following correspondence between our theory and experiments are obtained: (a) For the particle radius below some critical value, the flame propagation rate and the ignition time delay are independent of the radius; (b) damage of the oxide shell suppresses the melt dispersion mechanism and promotes the traditional diffusive oxidation mechanism; (c) nanoflakes react more like micron size (rather than nanosize) spherical particles. The reasons why the melt dispersion mechanism cannot operate for the micron particles or slow heating of nanoparticles are determined. Methods to promote the melt dispersion mechanism, to expand it to micron particles, and to improve efficiency of energetic metastable intermolecular composites are formulated. In particular, the following could promote the melt dispersion mechanism in micron particles: (a) Increasing the temperature at which the initial oxide shell is formed; (b) creating initial porosity in the Al; (c) mixing of the Al with a material with a low (even negative) thermal expansion coefficient or with a phase transformation accompanied by a volume reduction; (d) alloying the Al to decrease the cavitation pressure; (e) mixing nano- and micron particles; and (f) introducing gasifying or explosive inclusions in any fuel and oxidizer. A similar mechanism is expected for nitridation and fluorination of Al and may also be tailored for Ti and Mg fuel.

  3. Hole - Nuclear Spin Interaction in Semiconductor Quantum Dots

    NASA Astrophysics Data System (ADS)

    Marie, Xavier

    2010-03-01

    Spins of localized electrons in semiconductor quantum dots (QDs) are attractive for future spintronic and quantum information devices since they are not subject to the classical spin relaxation mechanisms known for free carriers [1]. It is now well established that the main spin dephasing mechanism in QDs is due to the coupling of conduction electron spin with the randomly fluctuating nuclear spins (Fermi contact term) [2-5]. For a valence electron (or hole), this coupling is expected to be much weaker because of the p-symmetry of the valence band states and no experimental evidence of such a hole-nuclear spin interaction has been reported so far [6]. We have measured the carrier spin dynamics in p-doped InAs/GaAs quantum dots by pump probe and time-resolved photoluminescence experiments. We demonstrate that the hole spin dynamics in these QDs is governed by the interaction with randomly fluctuating nuclear spins [7]. Our calculations based on dipole-dipole coupling between the hole and the quantum dot nuclei lead to a hole spin dephasing time for an ensemble of dots of 15 ns in close agreement with experiments.[4pt] In collaboration with B. Eble, C. Testelin, F. Bernardot, and M. Chamarro, Institut des Nanosciences de Paris, Universit'e P. et M. Curie, CNRS, Paris, F-75015 France; A. Balocchi, T. Amand, and B. Urbaszek, Universit'e de Toulouse ; LPCNO, INSA-CNRS-UPS, 135 av. de Rangueil, 31077 Toulouse Cedex 4, France; and A. Lemaître, Laboratoire de Photonique et de Nanostructures, CNRS, Route de Nozay, F-91460, Marcoussis, France. [4pt] [1] Spin Physics in Semiconductors, edited by M. D'Yakonov (Springer, Berlin, 2008) [0pt] [2] I. Merkulov et al, Phys. Rev. B 65, 205309 (2002) [0pt] [3] P.-F. Braun, X. Marie et al, PRL 94, 116601 (2005) [0pt] [4] A. C. Johnson et al , Nature 435, 925 (2005) [0pt] [5] A. Greilich et al, Science 313, 341(2006) [0pt] [6] S. Laurent et al, Phys. Rev. Lett. 94, 147401 (2005) [0pt] [7] B. Eble et al, Phys. Rev. Lett. 102, 146601 (2009)

  4. Thioarsenides: A case for long-range Lewis acid-base-directed van der Waals interactions

    SciTech Connect

    Gibbs, Gerald V.; Wallace, Adam F.; Downs, R. T.; Ross, Nancy L.; Cox, David F.; Rosso, Kevin M.

    2011-04-01

    Electron density distributions, bond paths, Laplacian and local energy density properties have been calculated for a number of As4Sn (n = 3,4,5) thioarsenide molecular crystals. On the basis of the distributions, the intramolecular As-S and As-As interactions classify as shared bonded interactions and the intermolecular As-S, As-As and S-S interactions classify as closed-shell van der Waals bonded interactions. The bulk of the intermolecular As-S bond paths link regions of locally concentrated electron density (Lewis base regions) with aligned regions of locally depleted electron density (Lewis acid regions) on adjacent molecules. The paths are comparable with intermolecular paths reported for several other molecular crystals that link aligned Lewis base and acid regions in a key-lock fashion, interactions that classified as long range Lewis acid-base directed van der Waals interactions. As the bulk of the intermolecular As-S bond paths (~70%) link Lewis acid-base regions on adjacent molecules, it appears that molecules adopt an arrangement that maximizes the number of As-S Lewis acid-base intermolecular bonded interactions. The maximization of the number of Lewis acid-base interactions appears to be connected with the close-packed array adopted by molecules: distorted cubic close-packed arrays are adopted for alacránite, pararealgar, uzonite, realgar and ?-AsS and the distorted hexagonal close-packed arrays adopted by ?- and ?-dimorphite. A growth mechanism is proposed for thioarsenide molecular crystals from aqueous species that maximizes the number of long range Lewis acid-base vdW As-S bonded interactions with the resulting directed bond paths structuralizing the molecules as a molecular crystal.

  5. 2004 Atomic and Molecular Interactions Gordon Research Conference

    SciTech Connect

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  6. Iron(II)-Catalyzed Intermolecular Amino-Oxygenation of Olefins through the N–O Bond Cleavage of Functionalized Hydroxylamines

    PubMed Central

    2015-01-01

    An iron-catalyzed diastereoselective intermolecular olefin amino-oxygenation reaction is reported, which proceeds via an iron-nitrenoid generated by the N–O bond cleavage of a functionalized hydroxylamine. In this reaction, a bench-stable hydroxylamine derivative is used as the amination reagent and oxidant. This method tolerates a range of synthetically valuable substrates that have been all incompatible with existing amino-oxygenation methods. It can also provide amino alcohol derivatives with regio- and stereochemical arrays complementary to known amino-oxygenation methods. PMID:25166591

  7. N-phosphino-p-tolylsulfinamide ligands: synthesis, stability, and application to the intermolecular Pauson-Khand reaction.

    PubMed

    Revés, Marc; Achard, Thierry; Solà, Jordi; Riera, Antoni; Verdaguer, Xavier

    2008-09-19

    Here we synthesized a family of racemic and optically pure N-phosphino-p-tolylsulfinamide (PNSO) ligands. Their stability and coordination behavior toward dicobalt-alkyne complexes was evaluated. Selectivities of up to 3:1 were achieved in the ligand exchange process with (mu-TMSC2H)Co2(CO)6. The resulting optically pure major complexes were tested in the asymmetric intermolecular Pauson-Khand reaction and yielded up to 94% ee. X-ray studies of the major complex 18a indicated that the presence of an aryl group on the sulfinamide reduces the hemilabile character of the PNSO ligands. PMID:18729408

  8. Palladium-catalyzed intermolecular oxyvinylcyclization of alkenes with alkynes: an approach to 3-methylene ?-lactones and tetrahydrofurans.

    PubMed

    Zhang, Zhenming; Ouyang, Lu; Wu, Wanqing; Li, Jianxiao; Zhang, Zhicai; Jiang, Huanfeng

    2014-11-21

    A novel chloropalladation-initiated intermolecular oxyvinylcyclization of alkenes with alkynoic acids or alkynols is developed. This protocol provides a series of 3-methylene ?-lactone and tetrahydrofuran derivatives in moderate to excellent yields with high stereoselectivities in the presence of PdCl2 and CuCl2 or CuCl2·2H2O. Besides a broad substrate scope, this method has the advantages of mild reaction conditions and easily accessible starting materials. Furthermore, the construction of C-Cl, C(sp(2))-C(sp(3)), and C-O bonds in one step was also achieved in this transformation. PMID:25215554

  9. Molecular structure and effects of intermolecular hydrogen bonding on the vibrational spectrum of trifluorothymine, an antitumor and antiviral agent.

    PubMed

    C?rak, Ca?r?; Koç, Nurettin

    2012-09-01

    In the present work, the experimental and the theoretical vibrational spectra of trifluorothymine were investigated. The FT-IR (400-4000 cm(-1)) and ?-Raman spectra (100-4000 cm(-1)) of trifluorothymine in the solid phase were recorded. The geometric parameters (bond lengths and bond angles) and vibrational frequencies of the title molecule in the ground state were calculated using ab initio Hartree-Fock (HF) method and density functional theory (B3LYP) method with the 6-31++G(d,p) and 6-311++G(d,p) basis sets for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with results found in the literature. Vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of trifluorothymine was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular N-H?O hydrogen bonds. PMID:22643971

  10. 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.

  11. To gel or not to gel: correlating molecular gelation with solvent parameters.

    PubMed

    Lan, Y; Corradini, M G; Weiss, R G; Raghavan, S R; Rogers, M A

    2015-10-01

    Rational design of small molecular gelators is an elusive and herculean task, despite the rapidly growing body of literature devoted to such gels over the past decade. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (log?P), to Henry's law constants (HLC), to solvatochromic parameters (ET(30)), and Kamlet-Taft parameters (?, ? and ?), and to Hansen solubility parameters (?p, ?d, ?h), are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries. These tools illustrate that the quest for the universal gelator should be left in the hands of Don Quixote and as researchers we must focus on identifying gelators capable of gelling classes of solvents as there is likely no one gelator capable of gelling all solvents. PMID:25941907

  12. Supramolecular solar cells

    NASA Astrophysics Data System (ADS)

    Subbaiyan, Navaneetha Krishnan

    Supramolecular chemistry - chemistry of non-covalent bonds including different type of intermolecular interactions viz., ion-pairing, ion-dipole, dipole-dipole, hydrogen bonding, cation-pi and Van der Waals forces. Applications based on supramolecular concepts for developing catalysts, molecular wires, rectifiers, photochemical sensors have been evolved during recent years. Mimicking natural photosynthesis to build energy harvesting devices has become important for generating energy and solar fuels that could be stored for future use. In this dissertation, supramolecular chemistry is being explored for creating light energy harvesting devices. Photosensitization of semiconductor metal oxide nanoparticles, such as titanium dioxide (TiO2) and tin oxide (SnO2,), via host-guest binding approach has been explored. In the first part, self-assembly of different porphyrin macrocyclic compounds on TiO2 layer using axial coordination approach is explored. Supramolecular dye sensitized solar cells built based on this approach exhibited Incident Photon Conversion Efficiency (IPCE) of 36% for a porphyrin-ferrocene dyad. In the second part, surface modification of SnO2 with water soluble porphyrins and phthalocyanine resulted in successful self-assembly of dimers on SnO2 surface. IPCE more than 50% from 400 - 700 nm is achieved for the supramolecular self-assembled heterodimer photocells is achieved. In summary, the axial ligation and ion-pairing method used as supramolecular tools to build photocells, exhibited highest quantum efficiency of light energy conversion with panchromatic spectral coverage. The reported findings could be applied to create interacting molecular systems for next generation of efficient solar energy harvesting devices.

  13. {pi}-{pi} Interactions and magnetic properties in a series of hybrid inorganic-organic crystals

    SciTech Connect

    Gonzalez, M.; Lemus-Santana, A.A.; Rodriguez-Hernandez, J.; Knobel, M.; Reguera, E.

    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.

  14. The impact of interactions between algal organic matter and humic substances on coagulation.

    PubMed

    Pivokonsky, Martin; Naceradska, Jana; Brabenec, Tomas; Novotna, Katerina; Baresova, Magdalena; Janda, Vaclav

    2015-11-01

    This study focuses on the effects of molecular interactions between two natural organic matter (NOM) fractions, peptides/proteins derived from cyanobacterium Microcystis aeruginosa (MA proteins) and peat humic substances (HS), on their removal by coagulation. Coagulation behaviour was studied by the jar tests with MA protein/HS mixtures and with single compounds (MA proteins or HS). Aluminium sulphate was used as a coagulant. Besides MA proteins, bovine serum albumin (BSA) was used as a model protein. For the MA protein/HS mixture, the removal rates were higher (80% versus 65%) and the dose of coagulant substantially lower (2.8 versus 5.5 mg L(-1) Al) than for coagulation of single HS, indicating the positive effect of protein-HS interactions on the coagulation process. The optimum coagulation pH was 5.2-6.7 for MA proteins and 5.5-6 for HS by alum. The optimum pH for the removal of MA protein/HS mixture ranged between pH 5.5-6.2, where the charge neutralization of negatively charged acidic functional groups of organic molecules by positively charged coagulant hydroxopolymers lead to coagulation. MA proteins interacted with HS, probably through hydrophobic, dipole-dipole and electrostatic interactions, even in the absence the coagulant. These interactions are likely to occur within a wide pH range, but they result in coagulation only at low pH values (pH < 4). At this pH, the negative charge of both MA proteins and HS was suppressed due to the protonation of acidic functional groups and thus the molecules could approach and combine forming aggregates. Virtually the same trends were observed in the experiments with HS and BSA, indicating that BSA is a suitable model for MA proteins under experimental conditions used in this study. The study showed that increases in organic content in source water due to the release of algae products may not necessarily entail deterioration of the coagulation process and a rise in coagulant demand. PMID:26255125

  15. Development of an Improved Intermolecular Model for MoS2 Adsorption Simulations

    NASA Astrophysics Data System (ADS)

    Leuty, Gary; Turner, Heath; Varshney, Vikas; Muratore, Christopher; Berry, Rajiv

    2015-03-01

    Molybdenum disulfide (MoS2), a transition metal dichalcogenide (TMD), has received much attention in electronics applications from transistors to sensors due to its layered nature and intrinsic, tunable band gap. In sensor applications, understanding molecular-level interactions with the MoS2 surface should be critical to superior device design, thus a detailed understanding of the dispersive interactions between surface and analyte during physisorption is required. Computational simulation offers numerous advantages in this regard, making accessible atomistic/molecular-level detail given an accurate force field; however, many force fields seem to focus on intra-layer covalent bonding interactions rather than adsorption-critical nonbonded interactions. In this work, we present a high-throughput screening method for nonbonded interaction parameters for all-atom molecular dynamics (MD) simulations of MoS2, combining DFT and MD analysis of structure and energetics with experimental characterization of adsorption in order to create a refined force field for TMDs to serve as a basis for exploration of the structure and energetics of adsorption on these novel materials. Supported by Research Associateship Program of the National Research Council.

  16. Photoinduced coupled twisted intramolecular charge transfer and excited-state proton transfer via intermolecular hydrogen bonding: A DFT/TD-DFT study

    NASA Astrophysics Data System (ADS)

    Wang, Dandan; Lü, Rui; Yuan, Minghu; Chen, Junsheng; Feng, Liqiang; Fu, Aiping; Tian, Fenghui; Varandas, António J. C.; Chu, Tianshu

    2014-08-01

    We discuss theoretically the geometric and electronic structure properties of the thiazolidinedione derivative A and its hydrogen-bonded complex in dimethylformamide (DMF) solution in the S0 and S1 states. To gain insight into the photoinduced coupled excited-state proton transfer (ESPT) and twisted intramolecular charge transfer (TICT) associated with intermolecular hydrogen bonding, the potential energy profiles are provided along the Osbnd H bond and the twisted angle. It is predicted that TICT in S1 can facilitate ESPT initiated by intermolecular hydrogen-bond strengthening in the S1 state. The coupling of ESPT and TICT is energetically preferable.

  17. A novel method for analyzing energy relaxation in condensed phases using nonequilibrium molecular dynamics simulations: Application to the energy relaxation of intermolecular motions in liquid water

    NASA Astrophysics Data System (ADS)

    Yagasaki, Takuma; Saito, Shinji

    2011-05-01

    We present a novel method to investigate energy relaxation processes in condensed phases using nonequilibrium molecular dynamics simulations. This method can reveal details of the time evolution of energy relaxation like two-color third-order IR spectroscopy. Nonetheless, the computational cost of this method is significantly lower than that of third-order response functions. We apply this method to the energy relaxation of intermolecular motions in liquid water. We show that the intermolecular energy relaxation in water is characterized by four energy transfer processes. The structural changes of the liquid associated with the energy relaxation are also analyzed by the nonequilibrium molecular dynamics technique.

  18. Switching Molecular Kondo Effect via Supramolecular Interaction.

    PubMed

    Zhang, Qiushi; Kuang, Guowen; Pang, Rui; Shi, Xingqiang; Lin, Nian

    2015-12-22

    We apply supramolecular assembly to control the adsorption configuration of Co-porphyrin molecules on Au(111) and Cu(111) surfaces. By means of cryogenic scanning tunneling microscopy, we reveal that the Kondo effect associated with the Co center is absent or present in different supramolecular systems. We perform first-principles calculations to obtain spin-polarized electronic structures and compute the Kondo temperatures using the Anderson impurity model. The switching behavior is traced to varied molecular adsorption heights in different supramolecular structures. These findings unravel that a competition between intermolecular interactions and molecule-substrate interactions subtly regulates the molecular Kondo effect in supramolecular systems. PMID:26568262

  19. Ab Initio Studies of the Interactions in Van der Waals Molecules

    E-print Network

    Ab Initio Studies of the Interactions in Van der Waals Molecules Ad van der Avoird, Paul E. S . . . . . . . . . . . . . . . . . . . . . . . . . . . 15 3 Quantitative Ab Initio Calculations . . . . . . . . . . . . . . . . . . . 16 3.1 Methods representation of the intermolecular potential; fitting of the ab initio results; atom-atom potentials

  20. Are Noncovalent Interactions an Achilles Heel in Chemistry Education? A Comparison of Instructional Approaches

    ERIC Educational Resources Information Center

    Williams, Leah C.; Underwood, Sonia M.; Klymkowsky, Michael W.; Cooper, Melanie M.

    2015-01-01

    Intermolecular forces (IMFs), or more broadly, noncovalent interactions either within or between molecules, are central to an understanding of a wide range of chemical and biological phenomena. In this study, we present a multiyear, multi-institutional, longitudinal comparison of how students enrolled in traditional general chemistry courses and…

  1. Intermolecular Paramagnetic Relaxation Enhancement (PRE) Studies of Transient Complexes in Intrinsically Disordered Proteins.

    PubMed

    Janowska, Maria K; Baum, Jean

    2016-01-01

    NMR interchain paramagnetic relaxation enhancement (PRE) techniques are a very powerful approach for detecting transient interchain interactions between intrinsically disordered proteins. These experiments, requiring a mixed sample containing a 1:1 ratio of isotope-labeled (15)N protein and natural abundance (14)N protein with a paramagnetic spin label, provide data that is limited to interchain interactions only. Application of these experiments to weakly associated transient species such as those that are present in the very early stages of self-assembly processes will aid our understanding of protein aggregation or fibril formation processes. PMID:26453204

  2. From intra- to inter-molecular hydrogen bonds with the surroundings: steady-state and time-resolved behaviours.

    PubMed

    Alarcos, Noemí; Gutiérrez, Mario; Liras, Marta; Sánchez, Félix; Douhal, Abderrazzak

    2015-07-01

    We report on the photodynamics of 2-(2'-hydroxyphenyl)benzoxazole (HBO), compared to its amino derivatives, 6-amino-2-(2'-hydroxypheny)benzoxazole (6A-HBO) and 5-amino-2-(2'-hydroxypheny)benzoxazole (5A-HBO) in N,N-dimethylformamide (DMF) solutions. HBO at S0 shows a reversible deprotonation reaction leading to the production of anionic forms. However, for 6A-HBO and 5A-HBO, DMF containing KOH is necessary to produce the anions. Excited HBO in DMF exhibits intra- as well as inter-molecular proton transfer (ESIPT and ESPT) reactions. With excitation at 330 nm, we observed the open-enol, anti-enol and keto forms with different emission and lifetimes (620 ps, 1.5 ns, and 74 ps, respectively), while with the excitation at 433 nm, only the anionic species emission was detected (3.7 ns). Contrary to HBO, 6A-HBO and 5A-HBO do not exhibit any proton transfer process, and only the emissions of the open-enol charge-transferred forms (open-ECT) were observed, which are comparable to those of their methylated derivatives (6A-MBO and 5A-MBO). Femtosecond studies of 6A-MBO and 6A-HBO in DMF indicate that an intramolecular charge-transfer (ICT) reaction (?80 fs) and solvent relaxation process (2 ps) take place at S1. Remarkably, the photoinduced breaking of the intramolecular hydrogen bond of 6A-HBO and the formation of an intermolecular hydrogen bond with DMF molecules occurs in 80 ps, while for 5A-HBO, this process occurs in less than 10 ps. In this study, we have demonstrated that the presence and position of the amino group in the HBO framework change both the S0 and S1 behaviours of the intramolecular H-bonds; a result which might be useful for the design and better understanding of supramolecular systems based on intra- and intermolecular H-bonds. PMID:26066612

  3. Specific features of the extra strong intermolecular hydrogen bonds in crystals: Insights from the theoretical charge density analysis

    NASA Astrophysics Data System (ADS)

    Vener, M. V.; Levina, E. O.; Astakhov, A. A.; Tsirelson, V. G.

    2015-10-01

    Specific features of extra strong intermolecular hydrogen bonds (H-bonds) are the electron density varying from 0.12 to 0.19 a.u. and the negative Laplacian values at the bond critical point. The Kirzhnitz approximation, widely used for estimation of the kinetic energy density from the crystalline electron density, leads to rather large errors (?15%) for these bonds. The border between the extra strong and strong H-bonds locates at the O⋯O distance around 2.45 Å for crystals with the quasi-linear Osbnd H⋯O moiety. The simple dependence between the H-bond energy and the O⋯O distance is suggested.

  4. Activity-Directed Synthesis with Intermolecular Reactions: Development of a Fragment into a Range of Androgen Receptor Agonists

    PubMed Central

    Karageorgis, George; Dow, Mark; Aimon, Anthony; Warriner, Stuart; Nelson, Adam

    2015-01-01

    Activity-directed synthesis (ADS), a novel discovery approach in which bioactive molecules emerge in parallel with associated syntheses, was exploited to develop a weakly binding fragment into novel androgen receptor agonists. Harnessing promiscuous intermolecular reactions of carbenoid compounds enabled highly efficient exploration of chemical space. Four substrates were prepared, yet exploited in 326 reactions to explore diverse chemical space; guided by bioactivity alone, the products of just nine of the reactions were purified to reveal diverse novel agonists with up to 125-fold improved activity. Remarkably, one agonist stemmed from a novel enantioselective transformation; this is the first time that an asymmetric reaction has been discovered solely on the basis of the biological activity of the product. It was shown that ADS is a significant addition to the lead generation toolkit, enabling the efficient and rapid discovery of novel, yet synthetically accessible, bioactive chemotypes. PMID:26358926

  5. Dipolar field effects described by boson operators techniques: The case of intermolecular multiple-quantum coherences in liquids

    NASA Astrophysics Data System (ADS)

    Nosel, W.; Gili, T.; Capuani, S.; Maraviglia, B.

    2005-05-01

    Dipolar couplings between macroscopically distant spins in solution nuclear magnetic resonance (NMR) are treated. We propose a novel technique to calculate the intermolecular multiple-quantum coherences (iMQCs) based on a boson operators approach. The choice of an annihilation and creation operator basis set allows us to produce a general expression of the NMR signal depending on local inhomogeneities of magnetic field. The general expression we derive fits into the well known background of iMQCs signal descriptions [J. Jeener, J. Chem. Phys. 112 (2000) 5091] and turns into the conventional quantum-mechanical Warren formulation [S. Lee, W. Richter, S. Vathyam, W.S. Warren, J. Chem. Phys. 105 (1996) 874] by means of appropriate approximations.

  6. Transformations of PTCDA structures on rutile TiO2 induced by thermal annealing and intermolecular forces

    PubMed Central

    Godlewski, Szymon; Glatzel, Thilo; Meyer, Ernst; Szymo?ski, Marek

    2015-01-01

    Summary Transformations of molecular structures formed by perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA) molecules on a rutile TiO2(110) surface are studied with low-temperature scanning tunnelling microscopy. We demonstrate that metastable molecular assemblies transform into differently ordered structures either due to additional energy provided by thermal annealing or when the influence of intermolecular forces is increased by the enlarged amount of deposited molecules. Proper adjustment of molecular coverage and substrate temperature during deposition allows for fabrication of desired assemblies. Differences between PTCDA/TiO2(110) and PTCDA/TiO2(011) systems obtained through identical experimental procedures are discussed. PMID:26199854

  7. Activity-Directed Synthesis with Intermolecular Reactions: Development of a Fragment into a Range of Androgen Receptor Agonists.

    PubMed

    Karageorgis, George; Dow, Mark; Aimon, Anthony; Warriner, Stuart; Nelson, Adam

    2015-11-01

    Activity-directed synthesis (ADS), a novel discovery approach in which bioactive molecules emerge in parallel with associated syntheses, was exploited to develop a weakly binding fragment into novel androgen receptor agonists. Harnessing promiscuous intermolecular reactions of carbenoid compounds enabled highly efficient exploration of chemical space. Four substrates were prepared, yet exploited in 326 reactions to explore diverse chemical space; guided by bioactivity alone, the products of just nine of the reactions were purified to reveal diverse novel agonists with up to 125-fold improved activity. Remarkably, one agonist stemmed from a novel enantioselective transformation; this is the first time that an asymmetric reaction has been discovered solely on the basis of the biological activity of the product. It was shown that ADS is a significant addition to the lead generation toolkit, enabling the efficient and rapid discovery of novel, yet synthetically accessible, bioactive chemotypes. PMID:26358926

  8. Symmetric bi-pyridyl banana-shaped molecule and its intermolecular hydrogen bonding liquid-crystalline complexes

    NASA Astrophysics Data System (ADS)

    Sui, Dan; Hou, Qiufei; Chai, Jia; Ye, Ling; Zhao, Liyan; Li, Min; Jiang, Shimei

    2008-11-01

    A new symmetric bi-pyridyl banana-shaped molecule 1,3-phenylene diisonicotinate (PDI) was designed and synthesized. Its molecular structure was confirmed by FTIR, Elemental analysis and 1H NMR. X-ray crystallographic study reveals that there is an angle of approximate 118° among the centroids of the three rings (pyridyl-phenyl-pyridyl) in each PDI molecule indicating a desired banana shape. In addition, a series of liquid crystal complexes nBA:PDI:nBA induced by intermolecular hydrogen bonding between PDI (proton acceptor) and 4-alkoxybenzoic acids (nBA, proton donor) were synthesized and characterized. The mesomorphism properties and optical textures of the complex of nBA:PDI:nBA were investigated by differential scanning calorimetry, polarizing optical microscope and X-ray diffraction.

  9. Coarse-Grained Intermolecular Potentials Derived From The Effective Fragment Potential: Application To Water, Benzene, And Carbon Tetrachloride

    NASA Astrophysics Data System (ADS)

    Pranami, Gaurav; Slipchenko, Lyudmila; Lamm, Monica H.; Gordon, Mark S.

    A force matching technique based on previous work by Voth and co-workers is developed and employed to coarse grain intermolecular potentials for three common solvents: carbon tetrachloride, benzene, and water. The accuracy of the force-matching approach is tested by comparing radial distribution functions (RDF) obtained from simulations using the atomistic and coarse-grained potentials. Atomistic molecular dynamics simulations were performed using the effective fragment potential method (EFP). The RDFs obtained from molecular dynamics simulations of EFPs for carbon tetrachloride, benzene and water are in a good agreement with the corresponding experimental data. The coarse-grained potentials reproduce the EFP molecular dynamics center-of-mass RDFs with reasonable accuracy. The biggest discrepancies are observed for benzene, while the coarse-graining of water and spherically symmetric carbon tetrachloride is of better quality.

  10. Zirconium complexes stabilized by amine-bridged bis(phenolato) ligands as precatalysts for intermolecular hydroamination reactions.

    PubMed

    Sun, Qiu; Wang, Yaorong; Yuan, Dan; Yao, Yingming; Shen, Qi

    2015-12-21

    A series of zirconium complexes bearing amine-bridged bis(phenolato) ligands of different steric and electronic properties have been synthesized, and their activities in catalyzing intermolecular hydroamination reactions have been studied and compared. In general, hexacoordinate zirconium dibenzyl complexes 1-4 stabilized by [ONNO]- or [ONOO]-type ligands were found to be less active than pentacoordinate complexes 5 and 7 that carry [ONO]-type ligands, which clearly imply that amine-bridged bis(phenolato) ligands play crucial roles in influencing catalytic activities. Complex 5 showed good activities and regioselectivities in catalysing reactions of various primary amines and alkynes. Moreover, reactions of challenging substrates, including secondary amines, internal alkynes, and hydrazines, were achieved with in situ generated cationic species from complex 5 and [Ph3C][B(C6F5)4]. PMID:26459787

  11. Multidimensional network structures and versatile magnetic properties of intermolecular compounds of a radical-anion ligand, [1,2,5]thiadiazolo[3,4-f][1,10]phenanthroline 1,1-dioxide.

    PubMed

    Shuku, Yoshiaki; Suizu, Rie; Domingo, Alex; Calzado, Carmen J; Robert, Vincent; Awaga, Kunio

    2013-09-01

    The crystal structures and magnetic properties of seven kinds of [1,2,5]thiadiazolo[3,4-f][1,10]phenanthroline 1,1-dioxide (tdapO2) radical-anion salts, namely, K·tdapO2, K·tdapO2·0.5MeCN, K·(tdapO2)2, Rb·(tdapO2)2, Cs7·(tdapO2)6·ClO4, (NH4)2·tdapO2·I, and Hppda·tdapO2·MeCN, were investigated. Single-crystal X-ray analyses of these radical-anion salts revealed formation of ?-stacking columns and the presence of intercolumnar coordination bonding or hydrogen bonding. The intermolecular magnetic coupling constants in these salts range from strong antiferromagnetic (J/kB = -310 K) to ferromagnetic (J/kB = 24 K). Ab initio calculations performed on the nearest-neighbor radical pairs in the ?-stacking columns suggested that the magnetic interactions are strongly governed by the overlap between the two anionic radical species and well explain the observed ferromagnetic and antiferromagnetic interactions. In addition, calculations of a hypothetical oxygen-less tdap analogue suggested that the presence of oxygen in tdapO2 significantly reduces the hopping integral and enhances the probability of ferromagnetic interaction. PMID:23937243

  12. Density functional investigation of intermolecular effects on {sup 13}C NMR chemical-shielding tensors modeled with molecular clusters

    SciTech Connect

    Holmes, Sean T.; Dybowski, Cecil; Iuliucci, Robbie J.; Mueller, Karl T.

    2014-10-28

    A quantum-chemical method for modeling solid-state nuclear magnetic resonance chemical-shift tensors by calculations on large symmetry-adapted clusters of molecules is demonstrated. Four hundred sixty five principal components of the {sup 13}C chemical-shielding tensors of 24 organic materials are analyzed. The comparison of calculations on isolated molecules with molecules in clusters demonstrates that intermolecular effects can be successfully modeled using a cluster that represents a local portion of the lattice structure, without the need to use periodic-boundary conditions (PBCs). The accuracy of calculations which model the solid state using a cluster rivals the accuracy of calculations which model the solid state using PBCs, provided the cluster preserves the symmetry properties of the crystalline space group. The size and symmetry conditions that the model cluster must satisfy to obtain significant agreement with experimental chemical-shift values are discussed. The symmetry constraints described in the paper provide a systematic approach for incorporating intermolecular effects into chemical-shielding calculations performed at a level of theory that is more advanced than the generalized gradient approximation. Specifically, NMR parameters are calculated using the hybrid exchange-correlation functional B3PW91, which is not available in periodic codes. Calculations on structures of four molecules refined with density plane waves yield chemical-shielding values that are essentially in agreement with calculations on clusters where only the hydrogen sites are optimized and are used to provide insight into the inherent sensitivity of chemical shielding to lattice structure, including the role of rovibrational effects.

  13. Lateral Intermolecular Self-Exchange Reactions for Hole and Energy Transport on Mesoporous Metal Oxide Thin Films.

    PubMed

    Hu, Ke; Meyer, Gerald J

    2015-10-20

    Intermolecular self-exchange energy and electron-transfer reactions occur without a loss of free energy. This behavior can be exploited for energy-transport applications when molecules that undergo self-exchange transfer reactions are immobilized on a solid support. This Article focuses upon lateral self-exchange reactions and the relevant interfacial chemistry that occurs on the mesoporous nanocrystalline (anatase) TiO2 thin films that are commonly used in dye-sensitized solar cells. It has been known for some time that all of the dye molecules (termed sensitizers) within such thin films can be reversibly oxidized and reduced by lateral self-exchange electron transfer provided that the sensitizer surface coverage exceeds a percolation threshold. Under conditions where excited-state electron injection into TiO2 is unfavored, lateral intermolecular energy-transfer reactions are also known to occur. The self-exchange rate constants have been quantified by electrochemical, absorption, and/or time-resolved anisotropy techniques and understood within the framework of Marcus theory. Such analysis reveals that the reorganization energy and the electronic coupling are sensitive to the identity of the molecular compound. Time-resolved anisotropy measurements have shown that lateral charge and energy-transfer reactions across the TiO2 surface occur in kinetic competition with charge recombination and excited-state relaxation, respectively. The extent to which lateral self-exchange reactions might be exploited for solar energy conversion applications is discussed, as are critical fundamental issues that remain unresolved. PMID:26223263

  14. Nanomechanics and intermolecular forces of amyloid revealed by four-dimensional electron microscopy

    PubMed Central

    Fitzpatrick, Anthony W. P.; Vanacore, Giovanni M.; Zewail, Ahmed H.

    2015-01-01

    The amyloid state of polypeptides is a stable, highly organized structural form consisting of laterally associated ?-sheet protofilaments that may be adopted as an alternative to the functional, native state. Identifying the balance of forces stabilizing amyloid is fundamental to understanding the wide accessibility of this state to peptides and proteins with unrelated primary sequences, various chain lengths, and widely differing native structures. Here, we use four-dimensional electron microscopy to demonstrate that the forces acting to stabilize amyloid at the atomic level are highly anisotropic, that an optimized interbackbone hydrogen-bonding network within ?-sheets confers 20 times more rigidity on the structure than sequence-specific sidechain interactions between sheets, and that electrostatic attraction of protofilaments is only slightly stronger than these weak amphiphilic interactions. The potential biological relevance of the deposition of such a highly anisotropic biomaterial in vivo is discussed. PMID:25733888

  15. A matrix partitioning approach to the calculation of intermolecular potentials. General theory and some examples

    NASA Astrophysics Data System (ADS)

    Amovilli, Claudio; McWeeny, Roy

    1990-02-01

    A general expression for the interaction energy of two molecules is obtained by using a matrix partitioning method. The wavefunction of the whole system is expanded in terms of antisymmetrized products of free-molecule functions and using a matrix perturbation scheme it is possible to describe the interaction energy in terms of free-molecule quantities (like frequency-dependent polarizabilities and density or spin density matrices) that, in principle, can be evaluated at any level of approximation. By way of example, the interaction potentials are calculated for (N 2) 2 and Ne 2 using wavefunctions of HF and TDHF form. The results are in substantial accord with those available in the literature. Application of these potentials to the calculation of macroscopic properties, however, leads to considerable errors. From the analysis of our results it appears that the dispersion energy is underestimated, probably on account of the neglect of intrasystem correlation energy in the TDHF approximation. The use of more sophisticated methods of evaluation of dynamic polarizabilities will not involve any extension of the approach presented in this work.

  16. A Closer Look at Trends in Boiling Points of Hydrides: Using an Inquiry-Based Approach to Teach Intermolecular Forces of Attraction

    ERIC Educational Resources Information Center

    Glazier, Samantha; Marano, Nadia; Eisen, Laura

    2010-01-01

    We describe how we use boiling-point trends of group IV-VII hydrides to introduce intermolecular forces in our first-year general chemistry classes. Starting with the idea that molecules in the liquid state are held together by some kind of force that must be overcome for boiling to take place, students use data analysis and critical reasoning to…

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

    EPA Science Inventory

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

  18. Synthesis, crystal growth and physicochemical studies on a novel organic inter-molecular compound; 3,5-dinitrobenzoic acid and salicylamide system

    NASA Astrophysics Data System (ADS)

    Singh, Manjeet; Rai, R. N.; Rai, U. S.

    2015-06-01

    The phase diagram of salicylamide (SAM) and 3,5-dinitrobenzoic acid (DNBA) system was determined by the thaw-melt method. Results show the formation of an inter-molecular compound and two eutectics. The values of heat of mixing, entropy of fusion, roughness parameter, interfacial energy, and the excess thermodynamic functions were calculated from the enthalpy of fusion data determined by the differential scanning calorimetric (DSC) method. The spectroscopic investigations (IR and NMR) suggest the presence of hydrogen bonding between the components of the compound. A single crystal of the inter-molecular compound was grown using slow cooling technique from the mixed solvent of ethanol and triple distilled water in 2:1 volume ratio. The single crystal analysis and the atomic packing pattern of the grown crystal confirm the monoclinic crystal structure with P21/c space group. The solubility of the inter-molecular compound was determined in the mixed solvent at different temperatures. Using solubility and entropy of fusion data, the entropy of dissolution and heat of mixing were calculated. The optical transmittance spectra of the crystal of the inter-molecular compound show 75% transmittance and the band gap of the crystal was found to be 3.00 eV. The refractive index of the crystal was computed to be 2.50 at the cut off wavelength.

  19. Ultra-violet and visible absorption characterization of explosives by differential reflectometry

    NASA Astrophysics Data System (ADS)

    Dubroca, Thierry; Moyant, Kyle; Hummel, Rolf E.

    2013-03-01

    This study presents some optical properties of TNT (2,4,6-trinitrotoluene), RDX, HMX and tetryl, specifically their absorption spectra as a function of concentration in various solvents in the ultraviolet and visible portion of the electromagnetic spectrum. We utilize a standoff explosives detection method, called differential reflectometry (DR). TNT was diluted in six different solvents (acetone, acetonitrile, ethanol, ethyl acetate, methanol, and toluene), which allowed for a direct comparison of absorption features over a wide range of concentrations. A line-shape analysis was adopted with great accuracy (R2 > 0.99) to model the absorption features of TNT in differential reflectivity spectra. We observed a blue shift in the pertinent absorption band with decreasing TNT concentration for all solvents. Moreover, using this technique, it was found that for all utilized solvents the concentration of TNT as well as of RDX, HMX, and tetryl, measured as a function of the transition wavelength of the ultra-violet absorption edge in differential reflectivity spectra shows three distinct regions. A model is presented to explain this behavior which is based on intermolecular hydrogen bonding of explosives molecules with themselves (or lack thereof) at different concentrations. Other intermolecular forces such as dipole-dipole interactions, London dispersion forces and ?-stacking contribute to slight variations in the resulting spectra, which were determined to be rather insignificant in comparison to hydrogen bonding. The results are aimed towards a better understanding of the DR spectra of explosives energetic materials.

  20. Inter- and intramolecular dispersion interactions.

    PubMed

    Swart, Marcel; Solà, Miquel; Bickelhaupt, F Matthias

    2011-04-30

    We have investigated the performance of a variety of density functional methods for weak intra- and intermolecular dispersion interactions. Grimme's empirical dispersion correction method is shown to give a good description for these interactions and helps to improve the description of water-hexamer isomers, noble-gas dimers, hydrocarbon C(12)H(12) isomers, branching energy of linear versus branched octane, dissociation of the covalently bound anthracene dimer, and stacking within the adenine dimer. However, the dispersion correction does not correct all shortcomings of the different density functionals, which leads to sizeable differences compared to ab initio CCSD(T) and experimental reference data. The only exception is shown to be our recently presented SSB-D functional that works well for all systems studied here. PMID:21387338