Science.gov

Sample records for intermolecular dipole-dipole interactions

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

    PubMed

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

    2016-03-31

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

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

    PubMed

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

    2015-02-01

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

  3. 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

    NASA Astrophysics Data System (ADS)

    Shimada, Rintaro; Hamaguchi, Hiro-o.

    2014-05-01

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-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 β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-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 β-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.

  4. 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.

    PubMed

    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-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-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 β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-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 β-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. PMID:24880300

  5. Mapping the dipole-dipole interaction among ultracold Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Fahey, Donald P.; Carroll, Thomas J.; Noel, Michael W.

    2014-05-01

    A long-range dipole-dipole interaction couples the atoms in an ultracold Rydberg gas. This can lead to changes in the spatial configuration of states over an extended region. We discuss the use of selective field ionization with a spatially sensitive ion detector to directly map dipole-dipole interaction induced level shifts and energy exchange over large distances in a MOT. Experimental and simulation results will be presented. This material is based upon work supported by the National Science Foundation under Grant No. 1205895.

  6. Observation of Stueckelberg oscillations in dipole-dipole interactions

    SciTech Connect

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

    2009-12-15

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

  7. 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.

  8. 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 π-π 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

  9. 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.

  10. Geometrical Simplification of the Dipole-Dipole Interaction Formula

    ERIC Educational Resources Information Center

    Kocbach, Ladislav; Lubbad, Suhail

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Khan, Salman; Jan, Munsif

    2016-03-01

    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.

  12. 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…

  13. 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

  14. Universal Behavior of Dielectric Responses of Glass Formers: Role of Dipole-Dipole Interactions.

    PubMed

    Paluch, M; Knapik, J; Wojnarowska, Z; Grzybowski, A; Ngai, K L

    2016-01-15

    From an exhaustive examination of the molecular dynamics in practically all van der Waals molecular glass formers ever probed by dielectric spectroscopy, we found that the width of the α-loss peak at or near the glass transition temperature T_{g} is strongly anticorrelated with the polarity of the molecule. The larger the dielectric relaxation strength Δε(T_{g}) of the system, the narrower is the α-loss peak. This remarkable property is explained by the contribution from the dipole-dipole interaction potential V_{dd}(r)=-Dr^{-6} to the attractive part of the intermolecular potential, making the resultant potential more harmonic, and the effect increases rapidly with the dipole moment μ and Δε(T_{g}) in view of the relation, D∝(μ^{4}/kT_{g})∝kT_{g}[Δε(T_{g})]^{2}. Since the novel correlation discovered encompasses practically all van der Waals molecular glass formers studied by dielectric spectroscopy, it impacts the large dielectric research community as well as those engaged in solving the glass transition problem. PMID:26824551

  15. 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-β-carotene (β-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute β-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 β-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of β-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 β-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.

  16. Droplet formation in a Bose-Einstein condensate with strong dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Xi, Kui-Tian; Saito, Hiroki

    2016-01-01

    Motivated by the recent experiment [H. Kadau et al., arXiv:1508.05007], we study roton instability and droplet formation in a Bose-Einstein condensate of 164Dy atoms with strong magnetic dipole-dipole interaction. We numerically solve the cubic-quintic Gross-Pitaevskii equation with dipole-dipole interaction, and show that the three-body interaction plays a significant role in the formation of droplet patterns. We numerically demonstrate the formation of droplet patterns and crystalline structures, decay of droplets, and hysteresis behavior, which are in good agreement with the experiment. Our numerical simulations provide the first prediction on the values of the three-body interaction in a 164Dy Bose-Einstein condensate. We also predict that the droplets remain stable during the time-of-flight expansion. From our results, further experiments investigating the three-body interaction in dipolar quantum gases are required.

  17. Observation of the dipole-dipole interaction between cold Rydberg atoms by microwave spectroscopy

    NASA Astrophysics Data System (ADS)

    Park, Hyunwook

    We measured the dipole-dipole interaction between nsnp pairs of atoms by the line broadening technique. The broadening rate relies on the atomic density, equivalently the average internuclear spacing Rav, and principal quantum number n. This measurement of the dipole-dipole broadening can be expressed in terms of n and provides a simple measure of line broadening due to increased atomic density in laboratory units. Calculation of the dipole-dipole interaction was compared to the observations. It was realized that the observations, which have smaller broadening rates than the calculation, stem from the spin-orbit coupling, which results in the shift-free and small-shift dipole-dipole energy levels as well as normal shift levels. As a result of the dipole-dipole interaction, the nsnp molecules form attractive and repulsive dipole-dipole potentials in which atoms are forced to move toward each other and farther apart, respectively. These motions of the atoms in the dipole potentials induce collisional ionization and trigger plasma formation from Rydberg atoms. The collisional ionization was systematically investigated by comparing the effects of the attractive, repulsive, and almost flat potentials. It turned out that atoms transferred to the attractive potential are ionized in a few microseconds, while those on the repulsive potential are not significantly ionized, similar to the flat potential case. Essentially the same result was observed again with an enhanced ion signal by extending the sampling to a broader range of internuclear separation via high microwave power. We also detected plasma fields by using the exaggerated property of Rydberg atoms responding to external electric fields. Rydberg atoms were injected into a plasma cloud, and the ns -- np microwave transition was driven to detect the plasma fields by measuring Stark shifts. We were able to measure a microscopic field as small as 0.1 V/cm. In the presence of a strong macroscopic field, the resonances are not only shifted but also double-peaked. The time evolution of the plasma. fields was also studied.

  18. BKT phase transition in a 2D system with long-range dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Fedichev, P. O.; Men'shikov, L. I.

    2012-01-01

    We consider phase transitions in 2D XY-like systems with long-range dipole-dipole interactions and demonstrate that BKT-type phase transition always occurs separating the ordered (ferroelectric) and the disordered (paraelectric) phases. The low-temperature phase corresponds to a thermal state with bound vortex-antivortex pairs characterized by linear attraction at large distances. Using the Maier-Schwabl topological charge model, we show that bound vortex pairs polarize and screen the vortex-antivortex interaction, leaving only the logarithmic attraction at sufficiently large separations between the vortices. At higher temperatures the pairs dissociate and the phase transition similar to BKT occurs, though at a larger temperature than in a system without the dipole-dipole interaction.

  19. Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

    NASA Astrophysics Data System (ADS)

    Mu, Yan; Gao, Yi Qin

    2007-09-01

    We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    SciTech Connect

    Gligoric, Goran; Hadzievski, Ljupco; Maluckov, Aleksandra; Malomed, Boris A.

    2009-05-15

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

  2. 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.

  3. 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.

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

    SciTech Connect

    Baudin, Emmanuel

    2014-08-07

    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 π/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.

  5. 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

  6. Microwave pump-probe spectroscopy of the dipole-dipole interaction in a cold Rydberg gas

    NASA Astrophysics Data System (ADS)

    Park, Hyunwook; Gallagher, T. F.; Pillet, P.

    2016-05-01

    Microwave pump-probe experiments starting with a cold gas of Rb 34 s atoms confirm that cusped line shapes observed in dipole-dipole broadened microwave transitions are due to atoms which are widely separated and exhibit small dipole-dipole energy shifts. When the experiments are interpreted in terms of a nearest-neighbor model, they demonstrate that it is possible to select pairs of atoms based on their separation and orientation.

  7. 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

  8. 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.

  9. Many particle magnetic dipole-dipole and hydrodynamic interactions in magnetizable stent assisted magnetic drug targeting

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    The implant assisted magnetic targeted drug delivery system of Avilés, Ebner and Ritter is considered both experimentally ( in vitro) and theoretically. The results of a 2D mathematical model are compared with 3D experimental results for a magnetizable wire stent. In this experiment a ferromagnetic, coiled wire stent is implanted to aid collection of particles which consist of single domain magnetic nanoparticles (radius ≈10 nm). In order to model the agglomeration of particles known to occur in this system, the magnetic dipole-dipole and hydrodynamic interactions for multiple particles are included. Simulations based on this mathematical model were performed using open source C++ code. Different initial positions are considered and the system performance is assessed in terms of collection efficiency. The results of this model show closer agreement with the measured in vitro experimental results and with the literature. The implications in nanotechnology and nanomedicine are based on the prediction of the particle efficiency, in conjunction with the magnetizable stent, for targeted drug delivery.

  10. 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.

  11. Exact solution of the Thomas-Fermi equation for a trapped Bose-Einstein condensate with dipole-dipole interactions

    SciTech Connect

    Eberlein, Claudia; O'Dell, Duncan H.J.; Giovanazzi, Stefano

    2005-03-01

    We derive an exact solution to the Thomas-Fermi equation for a Bose-Einstein condensate (BEC) which has dipole-dipole interactions as well as the usual s-wave contact interaction, in a harmonic trap. Remarkably, despite the nonlocal anisotropic nature of the dipolar interaction the solution is an inverted parabola, as in the pure s-wave case, but with a different aspect ratio. We explain in detail the mathematical tools necessary to describe dipolar BECs with or without cylindrical symmetry. Various properties such as electrostriction and stability are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    SciTech Connect

    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.

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

    NASA Astrophysics Data System (ADS)

    Saalwchter, Kay

    2014-08-01

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

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

    PubMed

    Saalwchter, 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. 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 β-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

  17. 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 cos2θ ) 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.

  18. 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

    2015-11-01

    We propose a novel low-frequency strategy to trap 10 μm 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

  19. Inter and intra macro-cell model for point dipoledipole energy calculations

    NASA Astrophysics Data System (ADS)

    Bowden, G. J.; Stenning, G. B. G.; van der Laan, G.

    2016-02-01

    In the field of micromagnetics, the calculation of long-range dipoledipole interactions in non-uniformly magnetized bodies has long posed computational problems. In this paper, we present an inter and intra macro-cell point-dipole model, which can be used to speed-up the determination of dipoledipole energies at the atomistic level. The model can be used to accurately compute the dipoledipole energy, using macro-cells of any shape or size.

  20. The effect of dipole-dipole interactions on coercivity, anisotropy constant, and blocking temperature of MnFe2O4 nanoparticles

    NASA Astrophysics Data System (ADS)

    Aslibeiki, B.; Kameli, P.; Salamati, H.

    2016-02-01

    Superparamagnetic manganese ferrite nanoparticles with mean size of = 6.5(±1.5) nm were synthesized through a solvothermal method using Tri-ethylene glycol as a solvent. The peak temperature of zero field cooled measurements of magnetization and AC magnetic susceptibility curves shifted toward higher temperatures by applying different pressures from 0 to 1 kbar and increasing the powders compaction. The frequency dependence of AC susceptibility measurements indicated the presence of weak dipole-dipole interactions between nanoparticles. By increasing the powders compaction and interactions strength, the coercive field (Hc) increased and squareness (Mr/Ms) decreased. The obtained effective anisotropy constant (Keff), by susceptibility measurements, was from 1.72 × 106 to 2.36 × 106 ergs/cm3 for pressure of 0 to 1 kbar. These values are larger than those obtained from hysteresis loops at 5 K (0.14 × 106 to 0.34 × 106 erg/cm3). Also, the Keff was two orders of magnitude greater than that of bulk MnFe2O4. Size, surface effects, and total energy barrier between equilibrium states were reported as the main causes of large anisotropy. Below 75 K, a signature of weak surface spin glass was observed. However, memory effect experiment indicated that there is no collective superspin glass state in the samples. This study suggests the role of powders compaction on properties of a magnetic nanoparticles system. Furthermore, the coercivity, the anisotropy constant, and the blocking temperature are affected by changing nanoparticles compaction.

  1. Quenching and dipole-dipole interactions in Sr2Al2SiO7:Ce3+ host lattice

    NASA Astrophysics Data System (ADS)

    Kolte, M.; Pawade, V. B.; Dhoble, S. J.

    2016-02-01

    This article reports novel results on the optical properties of Ce3+-doped Sr2Al2SiO7 host lattice which has been synthesized by the combustion method at 550 °C for the first time. Sr2Al2SiO7: Ce3+ phosphor shows the blue emission bands at 430 nm due to 5 d-4 f allowed transition of Ce3+ ion, keeping the excitation wavelength constant at 357 nm. Some theoretical study is carried out on the critical distance of energy transfer, concentration quenching and type of interaction in host and rare earth ion, and it is done by using the equation reported by Van Uiltert et al. Further phosphor is well characterized by XRD, SEM and EDS analysis to study phase purity, surface morphology and elemental analysis.

  2. Dipole-Dipole Interaction Driven Self-Assembly of Merocyanine Dyes: From Dimers to Nanoscale Objects and Supramolecular Materials.

    PubMed

    Würthner, Frank

    2016-05-17

    π-Conjugation between heterocyclic donor (D) and acceptor (A) groups via a polymethine chain leads to dyes with dipole moments greater than 10 D. These dipole moments direct the self-assembly of the dyes into antiparallel dimer aggregates, even in dilute solution, with binding strengths that are far beyond those observed for other π-scaffolds whose self-assembly is driven primarily by dispersion forces. The combination of directionality and exceptional binding strength of dipolar interactions between D-π-A dyes indeed resembles the situation of the hydrogen bond. Thus, similar to the latter, dipolar interactions between merocyanine dyes, a unique class of D-π-A chromophores, can be utilized to construct sophisticated supramolecular architectures of predictable geometry, particularly in low polarity environments. For bis(merocyanine) dyes it has been demonstrated that the self-assembly pathway is encoded in the tether between the two constituent merocyanine chromophores. If the tether enables the antiparallel stacking of the two appended dyes, folding takes place, which may be followed by further self-assembly into extended H-aggregate π-stacks at higher concentrations in solvents of low polarity. For tethers that do not support folding, the formation of bimolecular complexes of four merocyanine units, cyclic oligomers, and supramolecular polymers has been observed. For the former case, that is, formation of a bimolecular stack of four merocyanine units from tweezer-type molecules, association constants >10(9) M(-1) were measured in chloroform. On the other hand, because only one π-face is utilized in the formation of supramolecular polymers from bis(merocyanine) dyes, higher hierarchical structures typically originate in which the other π-face is surrounded by an antiparallel π-stacked neighbor molecule. Among the observed self-assembled structures, nanorods in particular have attracted considerable attention because their self-assembly into well-defined H-aggregates falls under kinetic control and is slowed tremendously with decreasing solvent polarity. Co-assembly of achiral and chiral merocyanine building blocks or two enantiomers of a chiral merocyanine in different ratios provided insight into "majority rules" and "sergeant-and-soldiers" effects as well as the autocatalytic fiber growth process. With regard to materials applications, it is important to note that the high propensity for dipolar aggregation was disadvantageous for many envisioned applications of these dyes in the area of nonlinear optics. However, this aggregation behavior proved to be advantageous for the recently demonstrated applications of D-π-A dyes, in particular, merocyanines as p-type organic semiconductors in organic electronics and photovoltaics. Thus, organic transistors with hole mobilities >0.5 cm(2)/(V s) and organic solar cells with power conversion efficiencies >6% could be achieved with merocyanine-based organic semiconductor molecules. PMID:27064423

  3. Dipole-Dipole Excitation and Ionization in an Ultracold Gas of Rydberg Atoms

    SciTech Connect

    Li Wenhui; Tanner, Paul J.; Gallagher, T. F.

    2005-05-06

    In cold dense Rydberg atom samples, the dipole-dipole interaction strength is effectively resonant at the typical interatomic spacing in the sample, and the interaction has a 1/R{sup 3} dependence on interatomic spacing R. The dipole-dipole attraction leads to ionizing collisions of initially stationary atoms, which produces hot atoms and ions and initiates the evolution of initially cold samples of neutral Rydberg atoms into plasmas. More generally, the strong dipole-dipole forces lead to motion, which must be considered in proposed applications.

  4. 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.

  5. 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…

  6. 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

  7. 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 πℏc | <= 1 . 5 × 10-3 and | gAegAe/4 πℏc | <= 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.

  8. 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.

  9. Rydberg-wave-packet evolution in a frozen gas of dipole-dipole-coupled atoms

    NASA Astrophysics Data System (ADS)

    Zhou, Tao; Li, Sha; Jones, R. R.

    2014-06-01

    We have studied the evolution of Rydberg wave packets in the presence of interatomic dipole-dipole interactions in a frozen Rb gas. Rb atoms in a magneto-optical trap (MOT) are first laser excited to ns Rydberg eigenstates. A picosecond THz pulse further excites them into coherent superposition states involving the initial-level and neighboring np states. A second, identical, time-delayed THz pulse probes the wave-packet dynamics. As the wave packets evolve they are influenced by dipole-dipole interactions, predominantly pairwise excitation-exchange processes of the form |s >|p>↔|p>|s>. The coherent electronic evolution of the ensemble dephases due to the variation in dipole-dipole coupling strength between atom pairs in the MOT. The experimental results are in good agreement with numerical calculations that simulate the interactions between nearest neighbors in a frozen gas.

  10. 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

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

    PubMed

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

    2012-03-22

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

  12. Influence of intermolecular interactions on magnetic observables

    NASA Astrophysics Data System (ADS)

    Schnack, Jürgen

    2016-02-01

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

  13. Dipole-dipole broadening of Rb ns-np microwave transitions

    SciTech Connect

    Park, Hyunwook; Tanner, P. J.; Claessens, B. J.; Shuman, E. S.; Gallagher, T. F.

    2011-08-15

    The dipole-dipole broadening of ns-np microwave transitions of cold Rb Rydberg atoms in a magneto-optical trap has been recorded for 28{<=}n{<=}51. Since the electric dipole transition matrix elements scale as n{sup 2}, a broadening rate scaling as n{sup 4} is expected and a broadening rate of 8.2x10{sup -15}n{sup 4} MHz cm{sup 3} is observed. The observed broadening is smaller than expected from a classical picture due to the spin-orbit interaction in the np atoms. The broadened resonances are asymmetric and cusp shaped, and their line shapes can be reproduced by a diatomic model which takes into account the dipole-dipole interaction, including the spin-orbit interaction, the strengths of the allowed microwave transitions, and the distribution of the atomic spacings in the trap.

  14. Computational studies on intermolecular interactions in solvation

    NASA Astrophysics Data System (ADS)

    Song, Weiping

    This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It was found that the geometric combining rule fails to predict the "weaker-than-expected" alkane-perfluoroalkane interactions, as illustrated by the systematic disagreements with experiment in the case of cross second pressure viral coefficients, gas solubilities, and liquid-liquid mixing properties. In Chapter 6, this study was extended to the investigation on combining rules and potential functions by looking extensively at the limit of accuracy of using some 2-parameter potential functions with some combining rules to represent a wide range of nonpolar interactions by fitting to experimental 2nd pressure virial coefficients. Overall, no pairing of potential function and any combining rules were found to represent simultaneously the intermolecular interactions within the provided experimental uncertainties for the range of molecules involved in the study. The limit of accuracy of representing the interactions using transferable parameters was found to be approximately 10--15%.

  15. 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.

  16. EPR line shifts and line shape changes due to Heisenberg spin exchange and dipole-dipole interactions of nitroxide free radicals in liquids: 9. An alternative method to separate the effects of the two interactions employing ¹⁵N and ¹⁴N.

    PubMed

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

    2014-08-14

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

  17. Learning about Intermolecular Interactions from the Cambridge Structural Database

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.

    2012-01-01

    A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the

  18. 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…

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

    NASA Astrophysics Data System (ADS)

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

    1998-07-01

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

  20. 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)/4πℏc|≤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

  1. 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 π ℏc | ≤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.

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

    SciTech Connect

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

    2002-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-08-01

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

  4. Direct observation of intermolecular interactions mediated by hydrogen bonding

    SciTech Connect

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

    2014-07-21

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

  5. Magnetic dipole-dipole sensing at atomic scale using electron spin resonance STM

    NASA Astrophysics Data System (ADS)

    Choi, T.; Paul, W.; Rolf-Pissarczyk, S.; MacDonald, A.; Yang, K.; Natterer, F. D.; Lutz, C. P.; Heinrich, A. J.

    Magnetometry having both high magnetic field sensitivity and atomic resolution has been an important goal for applications in diverse fields covering physics, material science, and biomedical science. Recent development of electron spin resonance STM (ESR-STM) promises coherent manipulation of spins and studies on magnetic interaction of artificially built nanostructures, leading toward quantum computation, simulation, and sensors In ESR-STM experiments, we find that the ESR signal from an Fe atom underneath a STM tip splits into two different frequencies when we position an additional Fe atom nearby. We measure an ESR energy splitting that decays as 1/r3 (r is the separation of the two Fe atoms), indicating that the atoms are coupled through magnetic dipole-dipole interaction. This energy and distance relation enables us to determine magnetic moments of atoms and molecules on a surface with high precision in energy. Unique and advantageous aspects of ESR-STM are the atom manipulation capabilities, which allow us to build atomically precise nanostructures and examine their interactions. For instance, we construct a dice cinque arrangement of five Fe atoms, and probe their interaction and energy degeneracy. We demonstrate the ESR-STM technique can be utilized for quantum magnetic sensors.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  7. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

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

    2015-01-01

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

  8. 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

  9. Dipole-dipole resonance line shapes in a cold Rydberg gas

    NASA Astrophysics Data System (ADS)

    Richards, B. G.; Jones, R. R.

    2016-04-01

    We have explored the dipole-dipole mediated, resonant energy transfer reaction, 32 p3 /2+32 p3 /2→32 s +33 s , in an ensemble of cold 85Rb Rydberg atoms. Stark tuning is employed to measure the population transfer probability as a function of the total electronic energy difference between the initial and final atom-pair states over a range of Rydberg densities, 2 ×108≤ρ ≤3 ×109 cm-3. The observed line shapes provide information on the role of beyond nearest-neighbor interactions, the range of Rydberg atom separations, and the electric field inhomogeneity in the sample. The widths of the resonance line shapes increase approximately linearly with the Rydberg density and are only a factor of 2 larger than expected for two-body, nearest-neighbor interactions alone. These results are in agreement with the prediction [B. Sun and F. Robicheaux, Phys. Rev. A 78, 040701(R) (2008), 10.1103/PhysRevA.78.040701] that beyond nearest-neighbor exchange interactions should not influence the population transfer process to the degree once thought. At low densities, Gaussian rather than Lorentzian line shapes are observed due to electric field inhomogeneities, allowing us to set an upper limit for the field variation across the Rydberg sample. At higher densities, non-Lorentzian, cusplike line shapes characterized by sharp central peaks and broad wings reflect the random distribution of interatomic distances within the magneto-optical trap (MOT). These line shapes are well reproduced by an analytic expression derived from a nearest-neighbor interaction model and may serve as a useful fingerprint for characterizing the position correlation function for atoms within the MOT.

  10. 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 β = 0.32. This provides an explanation for the terminal isobaric heat capacity maximum in supercritical fluids. PMID:23697423

  11. Lineshapes of Dipole-Dipole Resonances in a Cold Rydberg Gas

    NASA Astrophysics Data System (ADS)

    Richards, B. G.; Jones, R. R.

    2015-05-01

    We have examined the lineshapes associated with Stark tuned, dipole-dipole resonances involving Rydberg atoms in a cold gas. Rb atoms in a MOT are laser excited from the 5 p level to 32p3 / 2 in the presence of a weak electric field. A fast rising electric field pulse Stark tunes the total energy of two 32 p atom pairs so it is (nearly) degenerate with that of the 32s1 / 2+33s1 / 2 states. Because of the dipole-dipole coupling, atom pairs separated by a distance R, develop 32s1 / 2+33s1 / 2 character. The maximum probability for finding atoms in s-states depends on the detuning from degeneracy and on the dipole-dipole coupling. We obtain the ``resonance'' lineshape by measuring, via state-selective field ionization, the s-state population as a function of the tuning field. The resonance width decreases with density due to R-3 dependence of the dipole-dipole coupling. In principle, the lineshape provides information about the distribution of Rydberg atom spacings in the sample. For equally spaced atoms, the lineshape should be Lorentzian while for a random nearest neighbor distribution it appears as a cusp. At low densities nearly Gaussian lineshapes are observed with widths that are too large to be the result of inhomogeneous electric or magnetic fields. Supported by the NSF.

  12. 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.

  13. Influence of silver nanoparticles on relaxation processes and efficiency of dipole - dipole 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 dipole - dipole 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.

  14. Resonant intermolecular transfer of vibrational energy in liquid water

    NASA Astrophysics Data System (ADS)

    Woutersen, Sander; Bakker, Huib J.

    1999-12-01

    Many biological, chemical and physical processes involve the transfer of energy. In the case of electronic excitations, transfer between molecules is rapid, whereas for vibrations in the condensed phase, resonant energy transfer is an unlikely process because the typical timescale of vibrational relaxation (a few picoseconds) is much shorter than that of resonant intermolecular vibrational energy transfer. For the OH-stretch vibration in liquid water, which is of particular importance due to its coupling to the hydrogen bond, extensive investigations have shown that vibrational relaxation takes place with a time constant of 740 +/- 25 femtoseconds (ref. 7). So for resonant intermolecular energy transfer to occur in liquid water, the interaction between the OH-stretch modes of different water molecules needs to be extremely strong. Here we report time-resolved pump-probe laser spectroscopy measurements that reveal the occurrence of fast resonant intermolecular transfer of OH-stretch excitations over many water molecules before the excitation energy is dissipated. We find that the transfer process is mediated by dipole-dipole interactions (the Förster transfer mechanism) and additional mechanisms that are possibly based on intermolecular anharmonic interactions involving hydrogen bonds. Our findings suggest that liquid water may play an important role in transporting vibrational energy between OH groups located on either different biomolecules or along extended biological structures. OH groups in a hydrophobic environment should accordingly be able to remain in a vibrationally excited state longer than OH groups in a hydrophilic environment.

  15. Evolutionary meandering of intermolecular interactions along the drift barrier

    PubMed Central

    Lynch, Michael; Hagner, Kyle

    2015-01-01

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

  16. Ionization of Rb Rydberg atoms in the attractive nsnp dipole-dipole potential

    SciTech Connect

    Park, Hyunwook; Shuman, E. S.; Gallagher, T. F.

    2011-11-15

    We have observed the ionization of a cold gas of Rb Rydberg atoms which occurs when nsns van der Waals pairs of ns atoms of n{approx_equal} 40 on a weakly repulsive potential are transferred to an attractive dipole-dipole nsnp potential by a microwave transition. Comparing the measurements to a simple model shows that the initial 300-{mu}K thermal velocity of the atoms plays an important role. Excitation to a repulsive dipole-dipole potential does not lead to more ionization on a 15-{mu}s time scale than leaving the atoms in the weakly repulsive nsns state. This observation is slightly surprising since a radiative transition must occur to allow ionization in the latter case. Finally, by power broadening of the microwave transition, to allow transitions from the initial nsns state to the nsnp state over a broad range of internuclear spacings, it is possible to accelerate markedly the evolution to a plasma.

  17. Plasmon-Induced Resonant Energy Transfer: a coherent dipole-dipole coupling mechanism

    NASA Astrophysics Data System (ADS)

    Bristow, Alan D.; Cushing, Scott K.; Li, Jiangtian; Wu, Nianqiang

    Metal-insulator-semiconductor core-shell nanoparticles have been used to demonstrate a dipole-dipole coupling mechanism that is entirely dependent on the dephasing time of the localized plasmonic resonance. Consequently, the short-time scale of the plasmons leads to broad energy uncertainty that allows for excitation of charge carriers in the semiconductor via stimulation of photons with energies below the energy band gap. In addition, this coherent energy transfer process overcomes interfacial losses often associated with direct charge transfer. This work explores the efficiency of the energy transfer process, the dipole-dipole coupling strength with dipole separation, shell thickness and plasmonic resonance overlap. We demonstrate limits where the coherent nature of the coupling is switched off and charge transfer processes can dominate. Experiments are performed using transient absorption spectroscopy. Results are compared to calculations using a quantum master equation. These nanostructures show strong potential for improving solar light-harvesting for power and fuel generation.

  18. Near-field optical excitation as a dipole-dipole energy transfer process.

    PubMed

    Sekatskii, S K; Dietler, G

    1999-01-01

    The process of fluorescence excitation in the scanning near-field optical microscope (SNOM) is considered as a dipole-dipole resonance energy transfer process between a molecule under study and a SNOM aperture, which can be treated as a magnetic-type point dipole. It is shown that such an approach satisfactorily describes the conditions of the usual SNOM fluorescence experiments. Fluorescence excitation dependence on the polarization of the incident light and medium refraction index have been obtained. The equation to calculate the resonance dipole-dipole energy transfer radius (which is a natural unit of a SNOM's longitudinal resolution) is derived. Those cases where such a radius is of the order of the SNOM aperture, and thus single dipole, can strongly influence the radiation conditions are discussed briefly. PMID:11388248

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

    PubMed

    Remya, Karunakaran; Suresh, Cherumuttathu H

    2015-10-28

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

  20. Intermolecular interactions, nucleation, and thermodynamics of crystallization of hemoglobin C.

    PubMed

    Vekilov, Peter G; Feeling-Taylor, Angela R; Petsev, Dimiter N; Galkin, Oleg; Nagel, Ronald L; Hirsch, Rhoda Elison

    2002-08-01

    The mutated hemoglobin HbC (beta 6 Glu-->Lys), in the oxygenated (R) liganded state, forms crystals inside red blood cells of patients with CC and SC diseases. Static and dynamic light scattering characterization of the interactions between the R-state (CO) HbC, HbA, and HbS molecules in low-ionic-strength solutions showed that electrostatics is unimportant and that the interactions are dominated by the specific binding of solutions' ions to the proteins. Microscopic observations and determinations of the nucleation statistics showed that the crystals of HbC nucleate and grow by the attachment of native molecules from the solution and that concurrent amorphous phases, spherulites, and microfibers are not building blocks for the crystal. Using a novel miniaturized light-scintillation technique, we quantified a strong retrograde solubility dependence on temperature. Thermodynamic analyses of HbC crystallization yielded a high positive enthalpy of 155 kJ mol(-1), i.e., the specific interactions favor HbC molecules in the solute state. Then, HbC crystallization is only possible because of the huge entropy gain of 610 J mol(-1) K(-1), likely stemming from the release of up to 10 water molecules per protein intermolecular contact-hydrophobic interaction. Thus, the higher crystallization propensity of R-state HbC is attributable to increased hydrophobicity resulting from the conformational changes that accompany the HbC beta 6 mutation. PMID:12124294

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

    PubMed

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

    2016-01-01

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

  2. Problem-Based Learning in 9th Grade Chemistry Class: "Intermolecular Forces"

    ERIC Educational Resources Information Center

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

    2008-01-01

    This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students' understanding of intermolecular forces (dipole-dipole forces, London dispersion forces and hydrogen bonding). The student's alternate conceptions about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight…

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

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  5. Computer-graphics studies of dipole-dipole collisions - Evidence for neutral collision complexes.

    NASA Technical Reports Server (NTRS)

    Dugan, J. V., Jr.; Palmer, R. W.

    1972-01-01

    Extension of three-dimensional computer-graphics studies of orientation-dependent forces to multiple reflection behavior in dipole-dipole collisions. The collision pairs DCl-DCl and HCl-HCl are studied for rotational temperatures of 25, 77, and 300 K and translational temperatures of 77 and 300 K. The probability of a multiple reflection collision is a very sensitive inverse function of hard-core reflection distance for fixed temperatures. A brief comparison of the results is made with two-dimensional results of Clarke and Smith (1970) for CHF3-CHF3.

  6. Joint inversion of Wenner and dipole-dipole data to study a gasoline-contaminated soil

    NASA Astrophysics Data System (ADS)

    de la Vega, Matías; Osella, Ana; Lascano, Eugenia

    2003-11-01

    The goal of this work was to study a contaminated soil due to a gasoline spill produced by fissures in a concrete purge chamber located along a gas transmission line. A monitoring well drilled 16 m down gradient from the purge chamber revealed the presence of a gasoline layer of 0.5 m thick at 1.5 m depth, floating on top of the water table. A second well, drilled 30 m away from the first well, and in the same direction, did not show any evidence of contamination. To investigate this problem, a geoelectrical survey was conducted, combining dipole-dipole and Wenner arrays. First, four dipole-dipole profiles in a direction perpendicular to the longitudinal axis joining the wells were carried out. The electrical tomographies obtained from the 2D inversion of the data showed that the contaminated region was characterized by a resistive plume located at a depth between 1 to 2 m and had lateral extent of about 6-8 m. The longitudinal extension was less than 20 m, since the last profile located 30 m farther from the chamber did not show this kind of anomaly. To better determine the longitudinal extension, we performed a dipole-dipole profile along a line in this direction. The inverse model confirmed that the extension of the contaminated section was about 16 m. To complete the study of the deeper layer, we carried out Wenner soundings. The results of the inversion process indicated that to a depth of 20 m the soil was very conductive, because of the presence of clays as the main constituents, which confine the contaminant within this impermeable surrounding. To improve the inverse model, we performed a joint inversion of dipole-dipole and Wenner data. Analysis of the depth of penetration showed that it increased to 25 m and comparing the resulting model with the ones obtained from each array separately, we concluded that the joint inversion improves the depth obtained by the survey, while maintaining the shallow lateral resolution.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  8. Long-term dipole-dipole resistivity monitoring at the Cerro Prieto geothermal field

    SciTech Connect

    Wilt, M.; Goldstein, N.E.; Sasaki, Y.

    1984-04-01

    Dipole-dipole resistivity measurements for the combined purposes of reservoir delineation and reservoir monitoring were first made at Cerro Prieto in 1978 and have continued on approximately an annual basis since then. Two 20 km-long dipole-dipole lines with permanently emplaced electrodes at 1-km spacings were established over the field area. Resistivity remeasurements have been made on one line at 6- to 18-month intervals using a 25 kW generator capable of up to 80A output and a microprocessor-controlled signal-averaging receiver. This high-power, low-noise system provides highly accurate measurements even at large transmitter receiver separations. Standard error calculations for collected data indicate errors less than 5% for all points. Results from four years of monitoring (1979-1983) indicate a 5% average annual increase in apparent resistivity over the present production area, and larger decreases in apparent resistivity in the region to the east. The increase in resistivity in the production zone is most likely due to dilution of reservoir fluids with fresher water, as evidenced by a drop in chloride content of produced waters. The area of decreasing resistivity east of the reservoir is associated with a steeply dipping conductive body, a zone of higher thermal gradients and an increase in shale thickness in the section. Decreasing resistivity in this area may be caused by an influx of high temperature, saline water from depths of 3/sup +/ km through a sandy gap in the shales.

  9. 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)....

  10. X-ray Intermolecular Structure Factor (XISF): separation of intra- and intermolecular interactions from total X-ray scattering data

    SciTech Connect

    Mou, Q.; Benmore, C. J.; Yarger, J. L.

    2015-06-01

    XISF is a MATLAB program developed to separate intermolecular structure factors from total X-ray scattering structure factors for molecular liquids and amorphous solids. The program is built on a trust-region-reflective optimization routine with the r.m.s. deviations of atoms physically constrained. XISF has been optimized for performance and can separate intermolecular structure factors of complex molecules.

  11. Combined Electrostatics and Hydrogen Bonding Determine PIP2 Intermolecular Interactions

    PubMed Central

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

    2010-01-01

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

  12. 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

  13. 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

  14. Intermolecular interactions of the malate synthase of Paracoccidioides spp

    PubMed Central

    2013-01-01

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

  15. Solute-solvent intermolecular interactions in supercritical Xe, SF6, CO2, and CHF3 investigated by Raman spectroscopy: greatest attractive energy observed in supercritical Xe.

    PubMed

    Kajiya, Daisuke; Saitow, Ken-ichi

    2010-07-01

    Vibrational Raman spectra of the C=C stretching modes of cis- and trans-1,2-dichloroethylene (C(2)H(2)Cl(2)) were measured in supercritical Xe, SF(6), CO(2), and CHF(3). The spectra were collected over a wide range of densities of supercritical fluids at a fixed solute mole fraction and isotherm of T(r) = T/T(c) = 1.02. In all fluids, as the density increased, the peak frequencies of the C=C stretching modes shifted toward the low-energy side. By analyzing these density dependencies using the perturbed hard-sphere theory, the shifted amounts were characterized into attractive and repulsive components. The attractive shifts of both isomers were almost equivalent in supercritical CHF(3), CO(2), and SF(6), whereas they were significantly larger in supercritical Xe. The attractive shifts obtained experimentally were compared with the ones calculated on the basis of dispersion, dipole-dipole, dipole-induced-dipole, and dipole-quadrupole interactions between solute and solvent molecules. The experimental attractive shifts in supercritical Xe were 2-3 times greater than the calculated shifts. The large attractive shifts were ascribed to both an anisotropic solvation structure and to a strong interaction (charge transfer) between Xe and C(2)H(2)Cl(2) molecules. PMID:20540499

  16. 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...

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

    NASA Astrophysics Data System (ADS)

    Ayoub, Sarah; Lagowski, Jolanta B.

    2015-03-01

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

  18. Comparison of dipole-dipole resistivity and electromagnetic induction sounding over the Panther Canyon thermal anomaly, Grass Valley, Nevada

    SciTech Connect

    Wilt, M.; Beyer, J.H.; Goldstein, N.E.

    1980-05-01

    A comparison is made between the dipole-dipole resistivity method and electromagnetic sounding method based on surveys over a geothermal anomaly near Panther Canyon, Grass Valley, Nevada. Dipole-dipole data were taken in conjunction with large-scale geothermal studies in the area. Two orthogonal lines were measured over the heat flow anomaly and two-dimensional modeling was performed on the data. EM sounding data were taken with the Lawrence Berkeley Laboratory EM-60 system which is a large-moment, frequency-domain, horizontal-loop system. Relative to single 50-meter-radius transmitter coil, eight soundings were made with detectors at distances of 0.5 to 1.6 km from the loop. Interpreted results from the two surveys indicate substantial agreement in the depth to and thickness of a conductive zone that may be associated with the thermal anomaly. The dipole-dipole method is inherently better for resolving resistive basement beneath the conductive anomaly, and dc resistivity interpretation techniques are presently better to handle the complex two-dimensional geology. However, the EM method is far less labor intensive, requiring only one-third the field time for similar areal coverage.

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

    NASA Astrophysics Data System (ADS)

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

    2007-06-01

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

  20. The anisole--ammonia complex: Marks of the intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Piani, Giovanni; Pasquini, Massimiliano; Pietraperzia, Giangaetano; Becucci, Maurizio; Armentano, Antonio; Castellucci, Emilio

    2007-01-01

    We report an experimental study, supported by classical and quantum calculations, of the anisole-ammonia jet cooled complex. The origin band of the S 1 ← S 0 electronic transition is red shifted with respect to the corresponding band for the bare anisole molecule. From the simulation of the origin band rotational contour and the results of quantum mechanical calculations, we have been able to determine the non-planar structure of the complex. The ammonia molecule is bonded to anisole via two hydrogen bonds: one in which the nitrogen lone pair interacts with the hydrogen atoms of the methoxy group; the other involving the ammonia hydrogen atoms and the π-electron density of the aromatic ring.

  1. 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.

  2. 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.

  3. Cation-π 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

  4. Distinguishability and chiral stability in solution: effects of decoherence and intermolecular interactions.

    PubMed

    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. PMID:24880262

  5. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    NASA Astrophysics Data System (ADS)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  6. 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.

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

    PubMed

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

    2016-07-15

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

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

    SciTech Connect

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

    2013-08-15

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

  9. 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 π-π 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

  10. 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 (β), intermolecular free length ( L f), acoustical impedance ( Z), relative association ( R A), apparent molar compressibility (Φβ), and apparent molar volume (ΦV) 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.

  11. IPINV: a two-dimensional dipole-dipole resistivity modeling and inversion program. User's guide and documentation for Rev. 1

    SciTech Connect

    Tripp, A.C.; Killpack, T.J.

    1981-01-01

    IPINV.REV1 is a batch program that is capable of inverting resistivity data to two-dimensional models for a dipole-dipole array. The forward problem is computed using a transmission surface analogy. IPINV.REV1 is capable of inverting resistivity data to two-dimensional models of arbitrary complexity. The two-dimensional forward modeling routine is based on the transmission surface analogy (Madden, 1972). The inversion algorithm is a linearized least-squares technique. Step-size stabilization is provided by either the Box-Kanemaesu (1972) method or by using a Marquardt step. The program uses log derivatives to increase the rate of convergence.

  12. Studies of interdiffusion, chemical bonding, and intermolecular interactions in fiber-matrix adhesion

    SciTech Connect

    Chou, Chiate.

    1990-01-01

    A study of the key factors involved in adhesion was conducted to determine a quantitative relation between the underlying physicochemical mechanisms of adhesion and the adhesive performance at the fiber-matrix interface. Aramid fiber was modified by attaching pendent chains to its surface to change the nature of its interaction with matrix materials. The relative importance of the three fundamental factors of adhesion (interdiffusion, intermolecular interactions, and chemical bonding) was studied by evaluating the fiber-matrix adhesive performance of these modified fiber-matrix systems.

  13. Dipole-dipole interactions in the computational micromagnetism of iron (1955-2010) (invited)

    NASA Astrophysics Data System (ADS)

    Arrott, Anthony S.

    2011-04-01

    Basic treatment of magnetically soft ferromagnetic metals has been a long struggle during the 55 years of the MMM conferences. At the first conference, Charles Bean brought on stage a four-foot-long mechanical analog of a domain wall. Landau, twenty years earlier had shown that the wall exists to minimize the magnetostatic self-energy of the dipole moments that accompany the spins responsible for ferromagnetism, but no one could calculate the energy of the simple structure that Landau used to illustrate his conjecture. The structure itself was not adequately described. Today, computer programs use the full power of micromagnetics to properly describe the vortex structure that was hidden in Landau's model. Vortices terminate in swirls that can be manipulated by small bias fields (mT) or currents (mA). The swirls carry external fields of 0.5 T and can oscillate (driven or freely) over distances of tens of nm in times of tenths of ns, providing new tools for scientific and technical advances on the atomic scale. That this could have been overlooked for so long is evidence of the difficulty of visualizing the consequence of what for all these years has been called the pole-avoidance principle.

  14. Efficient dipole-dipole coupling of Mott-Wannier and Frenkel excitons in (Ga,In)N quantum well/polyfluorene semiconductor heterostructures

    NASA Astrophysics Data System (ADS)

    Itskos, G.; Heliotis, G.; Lagoudakis, P. G.; Lupton, J.; Barradas, N. P.; Alves, E.; Pereira, S.; Watson, I. M.; Dawson, M. D.; Feldmann, J.; Murray, R.; Bradley, D. D. C.

    2007-07-01

    We investigate interactions between Mott-Wannier (MW) and Frenkel excitons in a family of hybrid structures consisting of thin organic (polyfluorene) films placed in close proximity (systematically adjusted by GaN cap layer thickness) to single inorganic [(Ga,In)N/GaN] quantum wells (QWs). Characterization of the QW structures using Rutherford backscattering spectrometry and atomic force microscopy allows direct measurement of the thickness and the morphology of the GaN cap layers. Time-resolved photoluminescence experiments in the 8-75K temperature range confirm our earlier demonstration that nonradiative energy transfer can occur between inorganic and organic semiconductors. We assign the transfer mechanism to resonant Förster (dipole-dipole) coupling between MW exciton energy donors and Frenkel exciton energy acceptors and at 15K we find transfer efficiencies of up to 43%. The dependence of the energy transfer rate on the distance R between the inorganic QW donor dipole and organic film acceptor dipole indicates that a plane-plane interaction, characterized by a 1/R2 variation, best describes the situation found in our structures.

  15. Hierarchical intermolecular interaction models of N-heteroaromatic STM adlayer structures

    NASA Astrophysics Data System (ADS)

    Evans, Diane

    The molecular scale electronic device concept was initiated in 1974 with the semi-quantitative analysis of a hemiquinone molecule. Because of the molecule's electron donor and acceptor properties, and ability to transfer electrons along the pi-network, it was proposed that the molecule could perform as a circuit rectifier. Many investigations of molecular scale systems have occurred since then, in particular, of organic molecules with large, fused ring systems that spontaneously self-organize after deposition onto a substrate. The directionality and molecular specificity of hydrogen bonding differentiates it from the other weak interactions, driving molecules into specific arrangements and enabling spontaneous rearrangement after addition of only a small amount of enthalpic energy. A direct application of molecular recognition through self-assembly has been the design of patterned self-assembled monolayers (SAMs) for the construction of microelectrodes and supramolecular templates. However, the intermolecular interactions that drive ordered structures to form, including molecular chains and large aggregates, has not been well understood. To elucidate a quantitative description of the intermolecular forces of pi network systems of aromatics that control such features as packing density and porosity, two individual model heteroaromatic systems of 9-acridinecarboxylic acid and isonicotinic acid are investigated using both experimental and computational resources. Supported by scanning tunneling microscopy (STM) topographies, x-ray diffraction (XRD) data and x-ray photoelectron (XPS) spectra, this class of N-heteroaromatics adsorbed on Ag (111) serves as a model system to systematically investigate 2-dimensional intermolecular (2-D) interactions and their impact on forming different structural phases of molecular chain domains. To approach an understanding of the dynamics of N-heteroaromatic film growth, an intermolecular interaction model of 1-D single phase chains and clusters is performed. The model considers the anisotropy of the electrostatic force interactions to determine what charge arrangements (dipole, quadrupole, etc.) better characterize the molecular interactions. Furthermore, the competition between phase chain types is shown to be length dependent and in qualitative agreement with the coverage dependent STM structural phase composition.

  16. 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

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

    NASA Astrophysics Data System (ADS)

    Krummel, Amber

    2014-03-01

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

  18. Intermolecular interactions in solid-state metalloporphyrins and their impacts on crystal and molecular structures.

    PubMed

    Hunter, Seth C; Smith, Brenda A; Hoffmann, Christina M; Wang, Xiaoping; Chen, Yu-Sheng; McIntyre, Garry J; Xue, Zi-Ling

    2014-11-01

    A variable-temperature (VT) crystal structure study of [Fe(TPP)Cl] (TPP(2-) = meso-tetraphenylporphyrinate) and Hirshfeld surface analyses of its structures and previously reported structures of [M(TPP)(NO)] (M = Fe, Co) reveal that intermolecular interactions are a significant factor in structure disorder in the three metalloporphyrins and phase changes in the nitrosyl complexes. These interactions cause, for example, an 8-fold disorder in the crystal structures of [M(TPP)(NO)] at room temperature that obscures the M-NO binding. Hirshfeld analyses of the structure of [Co(TPP)(NO)] indicate that the phase change from I4/m to P1 leads to an increase in void-volume percentage, permitting additional structural compression through tilting of the phenyl rings to offset the close-packing interactions at the interlayer positions in the crystal structures with temperature decrease. X-ray and neutron structure studies of [Fe(TPP)Cl] at 293, 143, and 20 K reveal a tilting of the phenyl groups away from being perpendicular to the porphyrin ring as a result of intermolecular interactions. Structural similarities and differences among the three complexes are identified and described by Hirshfeld surface and void-volume calculations. PMID:25338536

  19. 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. PMID:26447810

  20. Intermolecular Interactions between Eosin Y and Caffeine Using 1H-NMR Spectroscopy

    PubMed Central

    Okuom, Macduff O.; Wilson, Mark V.; Jackson, Abby; Holmes, Andrea E.

    2014-01-01

    DETECHIP has been used in testing analytes including caffeine, cocaine, and tetrahydrocannabinol (THC) from marijuana, as well as date rape and club drugs such as flunitrazepam, gamma-hydroxybutyric acid (GHB), and methamphetamine. This study investigates the intermolecular interaction between DETECHIP sensor eosin Y (DC1) and the analyte (caffeine) that is responsible for the fluorescence and color changes observed in the actual array. Using 1H-NMR, 1H-COSY, and 1H-DOSY NMR methods, a proton exchange from C-8 of caffeine to eosin Y is proposed. PMID:25018772

  1. Electrostatic Domination of the Effect of Electron Correlation in Intermolecular Interactions.

    PubMed

    Thirman, Jonathan; Head-Gordon, Martin

    2014-04-17

    The electron-electron correlation energy is negative, and attractive dispersion interactions are entirely a correlation effect; therefore, the contribution of correlation to intermolecular binding is commonly assumed to be negative, or binding in nature. However, there are many cases where the long-range correlation binding energy is positive, with certain geometries of the water dimer as a prominent example. Geometries with dipoles misaligned can also have an electrostatically dominated, though negative, long-range correlation binding. In either case, the interaction decays as R(-3). This has its origin in the systematic overestimation of dipole moments by Hartree-Fock theory, leading to a reduction in the calculated electrostatic attraction upon inclusion of correlation. Thus, energy decomposition analyses that include correlation but do not correct mean field electrostatic terms are suboptimal. Attenuated second-order Møller-Plesset theory, which smoothly truncates long-range electron correlation effects to zero, can, paradoxically, have the correct long-range behavior for many intermolecular interactions. PMID:26269983

  2. Intermolecular potential energy surface for CS2 dimer.

    PubMed

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

    2011-04-15

    A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. PMID:20941736

  3. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    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.

  5. Intermolecular Interactions of Cardiac Transcription Factors NKX2.5 and TBX5.

    PubMed

    Pradhan, Lagnajeet; Gopal, Sunil; Li, Shichang; Ashur, Shayan; Suryanarayanan, Saai; Kasahara, Hideko; Nam, Hyun-Joo

    2016-03-29

    Heart development in mammalian systems is controlled by combinatorial interactions of master cardiac transcription factors such as TBX5 and NKX2.5. They bind to promoters/enhancers of downstream targets as homo- or heteromultimeric complexes. They physically interact and synergistically regulate their target genes. To elucidate the molecular basis of the intermolecular interactions, a heterodimer and a homodimer of NKX2.5 and TBX5 were studied using X-ray crystallography. Here we report a crystal structure of human NKX2.5 and TBX5 DNA binding domains in a complex with a 19 bp target DNA and a crystal structure of TBX5 homodimer. The ternary complex structure of NKX2.5 and TBX5 with the target DNA shows physical interactions between the two proteins through Lys158 (NKX2.5), Asp140 (TBX5), and Pro142 (TBX5), residues that are highly conserved in TBX and NKX families across species. Extensive homodimeric interactions were observed between the TBX5 proteins in both crystal structures. In particular, in the crystal structure of TBX5 protein that includes the N-terminal and DNA binding domains, intermolecular interactions were mediated by the N-terminal domain of the protein. The N-terminal domain of TBX5 was predicted to be "intrinsically unstructured", and in one of the two molecules in an asymmetric unit, the N-terminal domain assumes a β-strand conformation bridging two β-sheets from the two molecules. The structures reported here may represent general mechanisms for combinatorial interactions among transcription factors regulating developmental processes. PMID:26926761

  6. Intermolecular interactions during complex coacervation of pea protein isolate and gum arabic.

    PubMed

    Liu, Shuanghui; Cao, Yuan-Long; Ghosh, Supratim; Rousseau, Dérick; Low, Nicholas H; Nickerson, Michael T

    2010-01-13

    The nature of intermolecular interactions during complexation between pea protein isolate (PPI) and gum arabic (GA) was investigated as a function of pH (4.30-2.40) by turbidimetric analysis and confocal scanning microscopy in the presence of destabilizing agents (100 mM NaCl or 100 mM urea) and at different temperatures (6-60 degrees C). Complex formation followed two pH-dependent structure-forming events associated with the formation of soluble and insoluble complexes and involved interactions between GA and PPI aggregates. Complex formation was driven by electrostatic attractive forces between complementary charged biopolymers, with secondary stabilization by hydrogen bonding. Hydrophobic interactions were found to enhance complex stability at lower pH (pH 3.10), but not with its formation. PMID:19938857

  7. 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.

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

    PubMed Central

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

    2010-01-01

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

  9. Squeezing water clusters between graphene sheets: energetics, structure, and intermolecular interactions.

    PubMed

    McKenzie, S; Kang, H C

    2014-12-21

    The behavior of water confined at the nanoscale between graphene sheets has attracted much theoretical and experimental attention recently. However, the interactions, structure, and energy of water at the molecular scale underpinning the behavior of confined water have not been characterized by first-principles calculations. In this work we consider small water clusters up to the hexamer adsorbed between graphene sheets using density functional theory calculations with van der Waals corrections. We investigate the effects on structure, energy, and intermolecular interactions due to confinement between graphene sheets. For interlayer distances of about one nanometer or more, the cluster adsorption energy increases approximately linearly with the cluster size by 0.1 eV per molecule in the cluster. As the interlayer distance decreases, the cluster adsorption energy reaches a maximum at 6 to 7 Å with approximately 0.16 eV stabilization energy relative to large interlayer distances. This suggests the possibility of controlling the amount of adsorption in graphene nanomaterials by varying the interlayer distance. We also quantify the intermolecular hydrogen bonding in the clusters by calculating the dissociation energy required to remove one molecule from each cluster. For each cluster size, this is constant for interlayer distances larger than approximately 6 to 8 Å. For smaller distances the intermolecular interaction decreases rapidly thus leading to weaker cohesion between molecules in a squeezed cluster. We expect a mechanism of concerted motion for hydrogen-bonded water molecules confined between graphene sheets, as has been observed for water confined within the carbon nanotubes. Thus, the decrease in the dissociation energy we observed here is consistent with experimental results for water transport through graphene and related membranes that are of interest in nanofiltration. We also calculate the corrugation in the interaction potential between graphene sheets which suggests a switch from very small corrugation to stick-slip behavior at interlayer distances smaller than 6 Å. Our results for gas phase clusters agree reasonably with methods using more demanding quantum chemical methods to treat the van der Waals interactions, thus providing support for the relatively fast density functional theory methods used here for studying water-graphene interactions in nanoscale systems. PMID:25356833

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  11. Interionic and intermolecular interactions in ion-exchange and sorption systems involving physiologically active substances

    SciTech Connect

    Selemenev, V.F.; Chikin, G.A.; Khokhlov, V.J.

    1999-07-01

    This paper reviews the results obtained by studying the sorption of physiologically active substances (PAS) of different types such as, amino acids, nucleotides and melanoidins on ion exchangers and non-ionogenic sorbents. The review is mainly focused upon the mechanisms of interaction of PAS molecules in the sorbent phase. The contribution of ion-ionic, ion-molecular and intermolecular interactions to the overall sorption effect is discussed. The results of studying ion-exchange isothermal supersaturation of amino acid solutions on anion exchangers are reported and discussed. The mechanisms of aging of ion-exchange materials in the course of recovery of PAS from fermentation broths and hydrolysates are proposed. 48 refs.

  12. 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

  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-ζ and quadruple-ζ 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. Crowding, intermolecular interactions, and shear flow effects in the diffusion model of chemical reactions.

    PubMed

    Zaccone, Alessio; Dorsaz, Nicolas; Piazza, Francesco; De Michele, Cristiano; Morbidelli, Massimo; Foffi, Giuseppe

    2011-06-01

    In the diffusion model of chemical reactions, the encounter (reaction) rate between reactant particles is governed by the Smoluchowski equation, which is a diffusion equation in a field of forces. We consider crowded environments where the particles diffuse through a "liquid" of like particles. Assuming that the liquid-like short-range structure around the reactant gives rise to an effective (osmotic) barrier leads us to map a complicated many-body problem to a one-dimensional problem. This allows us to describe theoretically such complex systems that are encountered in many applications where crowding, intermolecular interactions, and flow are simultaneously present. A particularly important effect is discovered which is due to the interplay between shear and crowding. This effect is responsible for unexpected peaks in the reactivity at low flow intensity which may explain, among other things, the bizarre colloidal stability behavior of concentrated protein suspensions. PMID:21563752

  15. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    SciTech Connect

    Karayel, A. E-mail: yccaoh@hotmail.com; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-15

    The crystal structures of 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-(p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2, 4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  16. A structural study of the intermolecular interactions of tyramine in the solid state and in solution

    NASA Astrophysics Data System (ADS)

    Quevedo, Rodolfo; Nuñez-Dallos, Nelson; Wurst, Klaus; Duarte-Ruiz, Álvaro

    2012-12-01

    The nature of the interactions between tyramine units was investigated in the solid state and in solution. Crystals of tyramine in its free base form were analyzed by Fourier transform infrared (FT-IR) spectroscopy and single-crystal X-ray diffraction (XRD). The crystal structure shows a linear molecular organization held together by "head-to-tail" intermolecular hydrogen bonds between the amino groups and the phenolic hydroxyl groups. These chains are arranged in double layers that can geometrically favor the formation of templates in solution, which may facilitate macrocyclization reactions to form azacyclophane-type compounds. Computational calculations using the PM6-DH+ method and electrospray ionization mass spectrometry (ESI-HRMS) reveal that the formation of a hydrogen-bonded tyramine dimer is favored in solution.

  17. Crystal structures and intermolecular interactions of two novel antioxidant triazolyl-benzimidazole compounds

    NASA Astrophysics Data System (ADS)

    Karayel, A.; Özbey, S.; Ayhan-Kılcıgil, G.; Kuş, C.

    2015-12-01

    The crystal structures of 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(3-fluorophenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G6C) and 5-(2-( p-chlorophenylbenzimidazol-1-yl-methyl)-4-(2-methylphenyl)-2,4-dihydro-[1,2,4]-triazole-3-thione (G4C) have been determined by single-crystal X-ray diffraction. Benzimidazole ring systems in both molecules are planar. The triazole part is almost perpendicular to the phenyl and the benzimidazole parts of the molecules in order to avoid steric interactions between the rings. The crystal structures are stabilized by intermolecular hydrogen bonds between the amino group of the triazole and the nitrogen atom of benzimidazole of a neighboring molecule.

  18. Application of atomic force microscopy for characteristics of single intermolecular interactions.

    PubMed

    Safenkova, I V; Zherdev, A V; Dzantievf, B B

    2012-12-01

    Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions. PMID:23379527

  19. Theoretical studies on the optimal X (OH) 3-H 2O (X = N, P, Sb) complexes: Interaction energies and topological analysis of the electronic density

    NASA Astrophysics Data System (ADS)

    Ramírez-Solís, A.; Hô, M.; Hernández-Cobos, J.; Ortega-Blake, I.

    2012-02-01

    We study the interaction of N (OH)3, P (OH)3 and Sb (OH)3 with a water molecule for which triply hydrogen-bonded complexes have been found. We obtain interaction energies and analyze the electronic density through Atoms-in-Molecules approach. Including the recent result for As (OH)3, MP2 CBS extrapolated interaction energies are 9.37, 10.06, 10.67 and 10.72 kcal/mol for N (OH)3, P (OH)3, As (OH)3 and Sb (OH)3, respectively. CASSCF (6,6)+CASPT2 calculations reveal a multireference character for the complexes yielding interaction energies from 6.4 to 14 kcal/mol. AIM analysis shows three intermolecular bond critical points confirming the hydrogen bonds. NBO atomic charges show reveal the dominant dipole-dipole nature of the intermolecular interactions.

  20. Biaxial Dielectrophoresis Force Spectroscopy: A Stoichiometric Approach for Examining Intermolecular Weak Binding Interactions.

    PubMed

    Park, In Soo; Kwak, Tae Joon; Lee, Gyudo; Son, Myeonggu; Choi, Jeong Woo; Choi, Seungyeop; Nam, Kihwan; Lee, Sei-Young; Chang, Woo-Jin; Eom, Kilho; Yoon, Dae Sung; Lee, Sangyoup; Bashir, Rashid; Lee, Sang Woo

    2016-04-26

    The direct quantification of weak intermolecular binding interactions is very important for many applications in biology and medicine. Techniques that can be used to investigate such interactions under a controlled environment, while varying different parameters such as loading rate, pulling direction, rupture event measurements, and the use of different functionalized probes, are still lacking. Herein, we demonstrate a biaxial dielectrophoresis force spectroscopy (BDFS) method that can be used to investigate weak unbinding events in a high-throughput manner under controlled environments and by varying the pulling direction (i.e., transverse and/or vertical axes) as well as the loading rate. With the BDFS system, we can quantitatively analyze binding interactions related to hydrogen bonding or ionic attractions between functionalized microbeads and a surface within a microfluidic device. Our BDFS system allowed for the characterization of the number of bonds involved in an interaction, bond affinity, kinetic rates, and energy barrier heights and widths from different regimes of the energy landscape. PMID:27007455

  1. Intermolecular interactions and 3D structure in cellulose-NaOH-urea aqueous system.

    PubMed

    Jiang, Zhiwei; Fang, Yan; Xiang, Junfeng; Ma, Yanping; Lu, Ang; Kang, Hongliang; Huang, Yong; Guo, Hongxia; Liu, Ruigang; Zhang, Lina

    2014-08-28

    The dissolution of cellulose in NaOH/urea aqueous solution at low temperature is a key finding in cellulose science and technology. In this paper, (15)N and (23)Na NMR experiments were carried out to clarify the intermolecular interactions in cellulose/NaOH/urea aqueous solution. It was found that there are direct interactions between OH(-) anions and amino groups of urea through hydrogen bonds and no direct interaction between urea and cellulose. Moreover, Na(+) ions can interact with both cellulose and urea in an aqueous system. These interactions lead to the formation of cellulose-NaOH-urea-H2O inclusion complexes (ICs). (23)Na relaxation results confirmed that the formation of urea-OH(-) clusters can effectively enhance the stability of Na(+) ions that attracted to cellulose chains. Low temperature can enhance the hydrogen bonding interaction between OH(-) ions and urea and improve the binding ability of the NaOH/urea/H2O clusters that attached to cellulose chains. Cryo-TEM observation confirmed the formation of cellulose-NaOH-urea-H2O ICs, which is in extended conformation with mean diameter of about 3.6 nm and mean length of about 300 nm. Possible 3D structure of the ICs was proposed by the M06-2X/6-31+G(d) theoretical calculation, revealing the O3H···O5 intramolecular hydrogen bonds could remain in the ICs. This work clarified the interactions in cellulose/NaOH/urea aqueous solution and the 3D structure of the cellulose chain in dilute cellulose/NaOH/urea aqueous solution. PMID:25111839

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

    SciTech Connect

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

    2011-12-21

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

  3. Intermolecular interactions in binary mixtures of 2-Chloroethanol with 2-Dimethylaminoethanol and 2-Diethylaminoethanol at different temperatures

    NASA Astrophysics Data System (ADS)

    Pandey, Puneet Kumar; Awasthi, Anjali; Awasthi, Aashees

    2013-09-01

    The ultrasonic velocity (u) and density (ρ) of binary mixtures of 2-Chloroethanol (2-CletOH) with 2-Dimethylaminoethanol (DMAE) and 2-Diethylaminoethanol (DEAE) have been measured over the entire concentration range at temperatures 293.15, 303.15 and 313.15 K. The ultrasonic velocity and density data are used to estimate adiabatic compressibility (βS), intermolecular free length (Lf), molar sound velocity (R), molar compressibility (B) and specific acoustic impedance (Z) along with excess values of ultrasonic velocity (uE), adiabatic compressibility (βSE), intermolecular free length (LfE), acoustic impedance (ZE) and molar volume (VmE). The infrared spectra of both of the systems, 2-CletOH + DMAE and 2-CletOH + DEAE, have also been recorded at room temperature (298.15 K). The observed variations of these parameters, with concentration and temperature, are discussed in terms of the intermolecular interactions between the unlike molecules of the binary mixtures.

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

    NASA Astrophysics Data System (ADS)

    Brinck, Nils Tore

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

  5. Effect of polar intermolecular interactions on the elastic constants of bent-core nematics and the origin of the twist-bend phase.

    PubMed

    Osipov, M A; Pajak, G

    2016-04-01

    A molecular theory of both elastic constants and the flexoelectric coefficients of bent-core nematic liquid crystals has been developed taking into account dipole-dipole interactions as well as polar interactions determined by the bent molecular shape. It has been shown that if polar interactions are neglected, the elastic constants are increasing monotonically with the decreasing temperature. On the other hand, dipolar interactions between bent-core molecules may result in a dramatic increase of the bend flexocoefficient. As a result, the flexoelectric contribution to the bend elastic constant increases significantly, and the bend elastic constant appears to be very small throughout the nematic range and may vanish at a certain temperature. This temperature may then be identified as a temperature of the elastic instability of the bent-core nematic phase which induces a transition into the modulated phases with bend deformations like recently reported twist-bend phase. The temperature variation of the elastic constants is qualitatively similar to the typical experimental data for bent-core nematics. PMID:27118535

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

    PubMed

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

    2011-08-01

    The cytoskeletal proteins talin and vinculin are localized at cell-matrix junctions and are key regulators of cell signaling, adhesion, and migration. Talin couples integrins via its FERM domain to F-actin and is an important regulator of integrin activation and clustering. The 220 kDa talin rod domain comprises several four- and five-helix bundles that harbor amphipathic α-helical vinculin binding sites (VBSs). In its inactive state, the hydrophobic VBS residues involved in binding to vinculin are buried within these helix bundles, and the mechanical force emanating from bound integrin receptors is thought necessary for their release and binding to vinculin. The crystal structure of a four-helix bundle of talin that harbors one of these VBSs, coined VBS33, was recently determined. Here we report the crystal structure of VBS33 in complex with vinculin at 2 Å resolution. Notably, comparison of the apo and vinculin bound structures shows that intermolecular interactions of the VBS33 α-helix with vinculin are more extensive than the intramolecular interactions of the VBS33 within the talin four-helix bundle. PMID:21648001

  7. Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

    PubMed

    Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

    2014-03-01

    The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. PMID:24361848

  8. 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.

  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 π-π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which was actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  11. Hydrogen versus fluorine: effects on molecular structure and intermolecular interactions in a platinum isocyanate complex.

    PubMed

    Raven, William; Joschko, Thomas; Kalf, Irmgard; Englert, Ulli

    2016-03-01

    At the molecular level, the enantiomerically pure square-planar organoplatinum complex (SP-4-4)-(R)-[2-(1-aminoethyl)-5-fluorophenyl-κ(2)C(1),N][(R)-1-(4-fluorophenyl)ethylamine-κN](isocyanato-κN)platinum(II), [Pt(C8H9FN)(NCO)(C8H10FN)], and its congener without fluorine substituents on the aryl rings adopt the same structure within error. The similarities between the compounds extend to the most relevant intermolecular interactions, i.e. N-H...O and N-H...N hydrogen bonds link neighbouring molecules into chains along the shortest lattice parameter in each structure. Differences between the crystal structures of the fluoro-substituted and parent complex become obvious with respect to secondary interactions perpendicular to the classical hydrogen bonds; the fluorinated compound features short C-H...F contacts with an F...H distance of ca 2.6 Å. The fluorine substitution is also reflected in reduced backbonding from the metal cation to the isocyanate ligand. PMID:26942427

  12. Very low frequency magnetotelluric and dipole-dipole responses of three-dimensional thin-layer resistivity structure modeled using finite elements

    SciTech Connect

    Wannamaker, P.E.

    1985-09-01

    An algorithm to simulate the very low frequency magnetotelluric and dipole-dipole responses of three-dimensional thin-layer inhomogeneity has been developed from an existing finite element program used to simulate resistivity/IP signatures of 2-D earth sections. The 3-D body is confined to and extends uniformly across a thin layer overlain by air and underlain by infinite resistivity. Electric fields are obtained through differentiation of piecewise parabolas fit to nodal voltages while magnetic fields arise from integration of the free-space Green's tensor over secondary current perturbations throughout the thin layer. Dipole-dipole apparent resistivities arise through application to nodal voltages of the logarithmic geometric factors appropriate to continuously grounded line sources of current. Checks on accuracy of the simulation utilize analytic solutions, 2-D AC plane-wave results using finite elements, and a surface integral equations technique. 18 refs., 14 figs.

  13. Molecular packing and intermolecular interactions in N-acylethanolamines: crystal structure of N-myristoylethanolamine.

    PubMed

    Ramakrishnan, M; Swamy, M J

    1999-05-12

    N-Acylethanolamines elicited much interest in recent years owing to their occurrence in biological membranes under conditions of stress as well as under normal conditions. The molecular conformation, packing properties and intermolecular interactions of N-myristoylethanolamine (NMEA) have been determined by single crystal X-ray diffraction analysis. The lipid crystallized in the space group P21/a with unit cell dimensions: a=9.001, b=4.8761, c=39. 080. There are four symmetry-related molecules in the monoclinic unit cell. The molecules are organized in a tail-to-tail fashion, similar to the arrangement in a bilayer membrane. The hydrophobic acyl chain of the NMEA molecule is tilted with respect to the bilayer normal by an angle of 37 degrees. Each hydroxy group forms two hydrogen bonds, one as a donor and the other as an acceptor, with the hydroxy groups of molecules in the opposing leaflet. These O-H...O hydrogen bonds form an extended, zig-zag type network along the b-axis. In addition, the N-H and C=O groups of adjacent molecules are involved in N-H...O hydrogen bonds, which also connect adjacent molecules along the b-axis. PMID:10320678

  14. Polarization contributions to intermolecular interactions revisited with fragment electric-field response functions.

    PubMed

    Horn, Paul R; Head-Gordon, Martin

    2015-09-21

    The polarization energy in intermolecular interactions treated by self-consistent field electronic structure theory is often evaluated using a constraint that the atomic orbital (AO) to molecular orbital transformation is blocked by fragments. This approach is tied to AO basis sets, overestimates polarization energies in the overlapping regime, particularly in large AO basis sets, and lacks a useful complete basis set limit. These problems are addressed by the construction of polarization subspaces based on the responses of isolated fragments to weak electric fields. These subspaces are spanned by fragment electric-field response functions, which can capture effects up to the dipole (D), or quadrupole (DQ) level, or beyond. Schemes are presented for the creation of both non-orthogonal and orthogonal fragment subspaces, and the basis set convergence of the polarization energies computed using these spaces is assessed. Numerical calculations for the water dimer, water-Na(+), water-Mg(2+), water-F(-), and water-Cl(-) show that the non-orthogonal DQ model is very satisfactory, with small differences relative to the orthogonalized model. Additionally, we prove a fundamental difference between the polarization degrees of freedom in the fragment-blocked approaches and in constrained density schemes. Only the former are capable of properly prohibiting charge delocalization during polarization. PMID:26395691

  15. 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

  16. Thermal dissociation of protein-oligosaccharide complexes in the gas phase: mapping the intrinsic intermolecular interactions.

    PubMed

    Kitova, Elena N; Bundle, David R; Klassen, John S

    2002-05-22

    Blackbody infrared radiative dissociation (BIRD) and functional group replacement are used to map the location and strength of hydrogen bonds between an antibody single chain fragment (scFv) and its natural trisaccharide receptor, alpha-D-Galp (1-->2)[alpha-D-Abep (1-->3)]alpha-D-Manp1-->OMe (1), in the gaseous, multiply protonated complex. Arrhenius activation parameters (E(a) and A) are reported for the loss of 1 and a series of monodeoxy trisaccharide congeners (5-8 identical with tri) from the (scFv + tri + 10H)(+10) complex. The energetic contribution of the specific oligosaccharide OH groups to the stability of the (scFv + 1 + 10H)(+10) complex is determined from the differences in E(a) measured for the trisaccharide analogues and 1 (55.2 kcal/mol). A decrease of 6 to 11 kcal/mol in E(a), measured for the monodeoxy trisaccharides, indicates that the deleted OH groups interact strongly with the scFv and that they account for a majority of the stabilizing intermolecular interactions. A partial map of the hydrogen bond donor/acceptor groups of 1 and the strength of the interactions is presented for the protonated +10 complex. A comparison of the gas-phase map with the crystal structure indicates that significant structural differences exist. The hydroxyl groups located outside of the binding pocket, and exposed to solvent in solution, participate in new protein-oligosaccharide hydrogen bonds in the gas phase. The decrease in kinetic and energetic stability of the (scFv + 2 + nH)(n)()(+) complex with increasing charge-state is attributed to conformational differences in the binding region induced by electrostatic repulsion. The similarity in the Arrhenius parameters for the +9 and +10 charge states suggests that repulsion effects on the structure of the binding region are negligible below +11. PMID:12010066

  17. Using electronic polarization from the internal continuum (EPIC) for intermolecular interactions

    PubMed Central

    Truchon, Jean-François; Nicholl's, Anthony; Grant, J. Andrew; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    Recently, the vacuum-phase molecular polarizability tensor of various molecules has been accurately modeled (Truchon, J.-F. et al, J Chem Theory and Comput 2008, 4, 1480) with an intra-molecular continuum dielectric model. This preliminary study showed that electronic polarization can be accurately modeled when combined with appropriate dielectric constants and atomic radii. In this article, using the parameters developed to reproduce ab initio Quantum molecular polarizabilities, we extend the application of the "electronic polarization from internal continuum" (EPIC) approach to intermolecular interactions. We first derive a dielectric-adapted least-square-fit procedure similar to RESP, called DRESP, to generate atomic partial charges based on a fit to a Quantum ab initio electrostatic potential. We also outline a procedure to adapt any existing charge model to EPIC. The ability of this to reproduce local polarization, as opposed to uniform polarization, is also examined leading to an induced electrostatic potential relative root mean square deviation of 1%, relative to ab initio, when averaged over 37 molecules including aromatics and alkanes. The advantage of using a continuum model as opposed to an atom-centered polarizable potential is illustrated with a symmetrically perturbed atom and benzene. We apply EPIC to a cation-π binding system formed by an atomic cation and benzene and show that the EPIC approach can accurately account for the induction energy. Finally, this article shows that the ab initio electrostatic component in the difficult case of the H-bonded 4-pyridone dimer, a highly polar and polarized interaction, is well reproduced without parameter adjustment. PMID:19598266

  18. 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.

  19. Effect of intermolecular interactions on the nucleation, growth, and propagation of like-spin domains in spin-crossover materials

    NASA Astrophysics Data System (ADS)

    Slimani, A.; Boukheddaden, K.; Yamashita, K.

    2015-07-01

    The nucleation, growth, and propagation of like-spin domains in spin-crossover materials was investigated during the relaxation process of a metastable HS state at low temperature using an electroelastic model running on a deformable two-dimensional square lattice. We distinguish the onset of patterns formation of low-spin domain as the intermolecular interaction is increased, passing successively through random dispersion to clustering pattern and ending up with an impressive single macroscopic domain growth. Attaining and maintaining a single-domain configuration through the transition is attributed to the long-range character of interactions. Qualitative investigation of the elastic energy, of the propagation of the low-spin domain, and of the displacement field are presented. We demonstrate that as the intermolecular interaction increases the propagation of the like-spin domain slowdown. The deformations are believed as the prolonged effect of the intermolecular interactions that are at the origin of the onset of dispersed, poly-, and single-domain nucleation. Spatial autocorrelation of the deformations analysis based on Moran's I index is used. We demonstrate that at short distance significant spatially autocorrelated patterns are detected, and the extent of the autocorrelation decreases with the distance.

  20. 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.

  1. 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 Lwdin 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.

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

    PubMed

    Azar, Richard Julian; Head-Gordon, Martin

    2015-05-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    We perform an ab initio computational study of molecular complexes with the general formula CF3X—B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  4. Subunit–subunit interactions are critical for proton sensitivity of ROMK: Evidence in support of an intermolecular gating mechanism

    PubMed Central

    Leng, Qiang; MacGregor, Gordon G.; Dong, Ke; Giebisch, Gerhard; Hebert, Steven C.

    2006-01-01

    The tetrameric K channel ROMK provides an important pathway for K secretion by the mammalian kidney, and the gating of this channel is highly sensitive to changes in cytosolic pH. Although charge–charge interactions have been implicated in pH sensing by this K channel tetramer, the molecular mechanism linking pH sensing and the gating of ion channels is poorly understood. The x-ray crystal structure KirBac1.1, a prokaryotic ortholog of ROMK, has suggested that channel gating involves intermolecular interactions of the N- and C-terminal domains of adjacent subunits. Here we studied channel gating behavior to changes in pH using giant patch clamping of Xenopus laevis oocytes expressing WT or mutant ROMK, and we present evidence that no single charged residue provides the pH sensor. Instead, we show that N–C- and C–C-terminal subunit–subunit interactions form salt bridges, which function to stabilize ROMK in the open state and which are modified by protons. We identify a highly conserved C–C-terminal arginine–glutamate (R-E) ion pair that forms an intermolecular salt bridge and responds to changes in proton concentration. Our results support the intermolecular model for pH gating of inward rectifier K channels. PMID:16446432

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

    NASA Astrophysics Data System (ADS)

    Karst, David T.

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

  6. Noncovalent intermolecular interactions between dehydroepiandrosterone and the active site of human dehydroepiandrosterone sulphotransferase: A density functional theory based treatment

    NASA Astrophysics Data System (ADS)

    Astani, Elahe; Heshmati, Emran; Chen, Chun-Jung; Hadipour, Nasser L.; Shekarsaraei, Setareh

    2016-04-01

    A theoretical study was performed to characterize noncovalent intermolecular interactions, especially hydrogen bond (HB), in the active site of enzyme human dehydroepiandrosterone sulphotransferase (SULT2A1/DHEA) using the local (M06-L) and hybrid (M06, M06-2X) meta-GGA functionals of density functional theory (DFT). Results revealed that DHEA is able to form HBs with residues His99, Tyr231, Met137 and Met16 in the active site of the SULT2A1/DHEA. It was found that DHEA interacts with the other residues through electrostatic and Van der Waals interactions.

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

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

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

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

    SciTech Connect

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

    2014-10-07

    We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pair (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  10. 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 χ2 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, ε), structure (equilibrium distance, rm) and spectroscopy (anharmonic frequency, ν):€ν = A⋅ (ε /μ)1/ 2 /rm + B⋅ε /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.

  11. Basis set effects on the intermolecular interaction energies of methane dimers obtained by the Moeller-Plesset perturbation theory calculation

    SciTech Connect

    Tsuzuki, Seiji; Tanabe, Kazutoshi )

    1991-03-21

    Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.

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

    PubMed

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

    2015-06-21

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

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

    PubMed

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

    2015-06-01

    Three new data sets for intermolecular interactions, AHB21 for anion-neutral dimers, CHB6 for cation-neutral dimers, and IL16 for ion pairs, are assembled here, with complete-basis CCSD(T) results for each. These benchmarks are then used to evaluate the accuracy of the single-exchange approximation that is used for exchange energies in symmetry-adapted perturbation theory (SAPT), and the accuracy of SAPT based on wave function and density-functional descriptions of the monomers is evaluated. High-level SAPT calculations afford poor results for these data sets, and this includes the recently proposed "gold", "silver", and "bronze standards" of SAPT, namely, SAPT2+(3)-δMP2/aug-cc-pVTZ, SAPT2+/aug-cc-pVDZ, and sSAPT0/jun-cc-pVDZ, respectively [ Parker , T. M. , et al. , J. Chem. Phys. 2014 , 140 , 094106 ]. Especially poor results are obtained for symmetric shared-proton systems of the form X(-)···H(+)···X(-), for X = F, Cl, or OH. For the anionic data set, the SAPT2+(CCD)-δMP2/aug-cc-pVTZ method exhibits the best performance, with a mean absolute error (MAE) of 0.3 kcal/mol and a maximum error of 0.7 kcal/mol. For the cationic data set, the highest-level SAPT method, SAPT2+3-δMP2/aug-cc-pVQZ, outperforms the rest of the SAPT methods, with a MAE of 0.2 kcal/mol and a maximum error of 0.4 kcal/mol. For the ion-pair data set, the SAPT2+3-δMP2/aug-cc-pVTZ performs the best among all SAPT methods with a MAE of 0.3 kcal/mol and a maximum error of 0.9 kcal/mol. Overall, SAPT2+3-δMP2/aug-cc-pVTZ affords a small and balanced MAE (<0.5 kcal/mol) for all three data sets, with an overall MAE of 0.4 kcal/mol. Despite the breakdown of perturbation theory for ionic systems at short-range, SAPT can still be saved given two corrections: a "δHF" correction, which requires a supermolecular Hartree-Fock calculation to incorporate polarization effects beyond second order, and a "δMP2" correction, which requires a supermolecular MP2 calculation to account for higher-order induction-dispersion coupling. These corrections serve to remove artifacts introduced by the single exchange approximation in the exchange-induction and exchange-dispersion interactions, and obviate the need for ad hoc scaling of the first- and second-order exchange energies. Finally, some density-functional and MP2-based electronic structure methods are assessed as well, and we find that the best density-functional method for computing binding energies in these data sets is B97M-V/aug-cc-pVTZ, which affords a MAE of 0.4 kcal/mol, whereas complete-basis MP2 affords an MAE of 0.3 kcal/mol. PMID:26575547

  14. Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures.

    PubMed

    Odahara, Takayuki; Odahara, Koji

    2016-04-01

    Mixtures of neutral salts and polyethylene glycol are used for various purposes in biological studies. Although the effects of each component of the mixtures are theoretically well investigated, comprehension of their integrated effects remains insufficient. In this work, their roles and effects as a precipitant were clarified by studying dependence of precipitation curves on salt concentration for integral membrane protein/detergent particles of different physicochemical properties. The dependence of precipitation curves was reasonably related to intermolecular interactions among relevant molecules such as protein, detergent and polyethylene glycol by considering their physicochemical properties. The obtained relationships are useful as basic information to learn the early stage of biological macromolecular associations. PMID:26705098

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

    NASA Astrophysics Data System (ADS)

    Korlyukov, A. A.

    2015-04-01

    The review is devoted to analysis and generalization of the results of (i) quantum chemical studies on the structure, chemical bonding and intermolecular interactions in coordination compounds of tetravalent silicon, germanium and tin in crystals, in solutions and in the gas phase and (ii) experimental investigations of the electron density distribution in these systems. The bibliography includes 147 references. In memoriam of Corresponding Member of the Russian Academy of Sciences M Yu Antipin (1951 - 2013), Academician of the Russian Academy of Sciences M G Voronkov (1921 - 2014) and Dr. S P Knyazev, Lomonosov Moscow University of Fine Chemical Technology (1949 - 2012).

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

    PubMed

    Rezler, Mateusz; Żołek, Teresa; Wolska, Irena; Maciejewska, Dorota

    2014-10-01

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

  17. Contributions of intermolecular interactions between constitutive arabinoxylans to the flaxseeds mucilage properties.

    PubMed

    Warrand, J; Michaud, P; Picton, L; Muller, G; Courtois, B; Ralainirina, R; Courtois, J

    2005-01-01

    The main fraction (about 75%) of the mucilage extracted from seeds of Linum usitatissimum which consists of arabino-xylans (AX) has been studied in dilute and semidilute regimes by SEC/MALLS analysis and rheology, respectively. It has been found that AX contains 3 populations of about 5 000 000 g mol(-1) (less than 10%), 1 000 000 g mol(-1) (about 40%), and 200 000 g mol(-1) (about 50%). We have also observed a great retention of polymer during the filtration procedure, which is much pronounced as the AX concentration increases. This evidences the presence of large aggregates in the solution. The retention can be greatly diminished if the filtration is conducted under higher temperature. Aggregation could result from the establishment of intermolecular associations via hydrogen bonds. This hypothesis seems to be confirmed by the two higher populations in molar masses which present a random coil conformation consistent with a low degree of branching. Rheological measurements, conducted at 20 g L(-1), have confirmed the association tendency leading to pseudo gels behavior. Viscoelastic properties have been evidenced by time-temperature master curves of dynamic spectra. Such master curves have also been established with addition of chaotropic (i.e., KSCN) and lyotropic (i.e., NaCl) salts. It has been shown that intermolecular associations are greatly diminished under chaotropic salts influence. This has been also confirmed by SEC/MALLS analysis. These results point out the role of hydrogen bonds in the organization of the AX system. PMID:16004423

  18. Physical nature of intermolecular interactions inside Sir2 homolog active site: molecular dynamics and ab initio study.

    PubMed

    Czeleń, Przemysław; Czyżnikowska, Żaneta

    2016-06-01

    In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used as a starting point for molecular dynamics simulation. The intermolecular interaction energy partitioning was performed for protein-ADP-HPD complex resulting from molecular dynamics simulation. The analysis was performed for ADP-HPD and 15 amino acids forming a deacetylase binding pocket. Although the results indicate that the first-order electrostatic interaction energy is substantial, the presence of multiple hydrogen bonds in investigated complexes can lead to significant value of induction component. PMID:27154340

  19. Investigation on Intermolecular Interaction in Supersaturation State of Cadmium Sulphate Mixed Zinc tris-THIOUREA Sulphate Solutions

    NASA Astrophysics Data System (ADS)

    Muley, G. G.; Naik, A. B.; Gambhire, A. B.

    2014-06-01

    Zinc tris-thiourea sulphate (ZTS) is a well known nonlinear optical (NLO) crystal widely used for various NLO applications. The NLO, physical and chemical properties can be modified by adding impurities and/or modifying crystal growth conditions. The impurities present in the growth solution and growth conditions can affect the crystal growth parameters at great extent. Thus, the study on the nature of intermolecular interaction with the dopant in the solution during crystal growth process becomes important. In the present investigation, the ultrasonic velocity was measured in the aqueous solutions of pure and cadmium sulphate mixed ZTS in the supersaturation state at 313.15 K. The thermodynamic parameters such as adiabatic compressibility, inter molecular free length, acoustic impedance and relative associations have been calculated from the ultrasonic data and densities of water and solutions at 313.15 K, and the nature of intermolecular interaction has been discussed. FT-IR spectra of all mixtures in the solid form at room temperature were recorded and the shifts in the absorption peaks corresponding to the functional groups of ZTS have been reported.

  20. Method for Slater-Type Density Fitting for Intermolecular Electrostatic Interactions with Charge Overlap. I. The Model.

    PubMed

    Öhrn, Anders; Hermida-Ramon, Jose M; Karlström, Gunnar

    2016-05-10

    The effects of charge overlap, or charge penetration, are neglected in most force fields and interaction terms in QM/MM methods. The effects are however significant at intermolecular distances near the van der Waals minimum. In the present study, we propose a method to evaluate the intermolecular Coloumb interaction using Slater-type functions, thus explicitly modeling the charge overlap. The computational cost of the method is low, which allows it to be used in large systems with most force fields as well as in QM/MM schemes. The charge distribution is modeled as a distributed multipole expansion up to quadrupole and Slater-type functions of angular momentum up to L = 1. The exponents of the Slater-type functions are obtained using a divide-and-conquer method to avoid the curse of dimensionality that otherwise is present for large nonlinear optimizations. A Levenberg-Marquardt algorithm is applied in the fitting process. A set of parameters is obtained for each molecule, and the process is fully automated. Calculations have been performed in the carbon monoxide and the water dimers to illustrate the model. Results show a very good accuracy of the model with relative errors in the electrostatic potential lower than 3% over all reasonable separations. At very short distances where the charge overlaps is the most significant, errors are lower than 8% and lower than 3.5% at distances near the van der Waals minimum. PMID:27015000

  1. [Structural and functional bases of the intermolecular interaction of calix[4]arene C-97 with myosin subfragment-1 of myometrium].

    PubMed

    Labyntseva, R D; Bevza, A A; Bevza, O V; Cherenok, S O; Kal'chenko, V I; Kosterin, S O

    2012-01-01

    Calix[4]arene C-97 (code is shown) is the macrocyclic compound which has lipophilic intramolecular higly-structured cavity formed by four aromatic cycles, one of which on the upper rim is modified by methylene bisphosphonic group. It was shown that calix[4]arene C-97 (100 microM) efficiently inhibits ATPase activity of myosin subfragment-1 from pig myometrium, the inhibition coefficient I(0.5) being 83 +/- 7 microM. At the same time, this compound at 100 microM concentration significantly increases the effective hydrodynamic diameter of myosin subfragment-1, that may be indicative of intermolecular complexation between the calix[4]arene and myosin head. Computer simulation methods (docking, molecular dynamics, involving the Grid) have been used to clarify structural basis of the intermolecular interaction of calix[4]arene C-97 with myosin subfragment-1 of the myometrium; participation of hydrophobic, electrostatic and pi-pi (stacking) interactions between calix[4]arene C-97 and amino acid residues of myosin subfragment-1, some of them being located near the active site of the ATPase has been found out. PMID:22679756

  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. Calculation of intermolecular interaction strengths in the P beta' phase in lipid bilayers. Implications for theoretical models.

    PubMed Central

    Scott, H L; Pearce, P A

    1989-01-01

    The existence of the P beta' phase in certain lipid bilayers is evidence that molecular interactions between lipids are capable of producing unusual large-scale structures at or near biological conditions. The problem of identifying the specific intermolecular interactions responsible for the structures requires construction of theoretical models capable of clear predictions of the observable consequences of postulated intermolecular interactions. To this end we have carried out a twofold modeling effort aimed at understanding the ripple phase. First, we have performed detailed numerical calculations of potential energies of interaction between pairs and triplets of lipid molecules having different chain tilt angles and relative vertical alignments. The calculations support the notion that chain tilting in the gel phase is a result of successive 3-5-A displacements of neighboring molecules perpendicular to the bilayer plane rather than long-range cooperative chain tilting. Secondly, we have used these results as a guide to formulate a new lattice model for lipid bilayer condensed phases. The new model is less complex than our earlier model and it includes interactions which are, based on the energy calculations, more likely to be responsible for the ripple phase. In a certain limit the model maps onto the chiral clock model, a model of much interest in condensed matter theory. In this limit the model exhibits a chain-tilted ordered phase followed by (as temperature increases) a modulated phase followed by a disordered phase. Within this limit we discuss the properties of the model and compare structures of the modulated phase exhibited by the model with experimental data for the P beta' phase in lipid bilayers. PMID:2713447

  4. Intermolecular structure and collective dynamics of supercritical fluoroform studied by molecular dynamics simulations.

    PubMed

    Ingrosso, Francesca; Ladanyi, Branka M

    2013-01-17

    The density dependence of the local structure and of collective dynamics of a polar fluid fluoroform along an isotherm at a temperature of 1.03 T(c), in the near-critical (NC) region, were studied by classical molecular dynamics (MD) simulations. In the case of local structure we focus on local density inhomogeneities and on orientational pair correlations that are relevant to dielectric properties and light scattering intensities. Our results show that the density dependence of the frequency shifts of fluoroform ?(2) and ?(3) modes correlates well with that of intermolecular dipole-dipole interactions. Our study of collective dynamics deals with dipole and polarizability anisotropy relaxation, experimentally accessible through far-infrared absorption, depolarized light scattering, and optical Kerr effect. Our MD simulations were performed using an all-atom nonpolarizable potential model of fluoroform. Contributions of induced dipoles to dielectric properties were included using first-order perturbation theory, and this approach was also used to include interaction-induced contributions to polarizability anisotropy relaxation. For interactions involving induced dipoles, we calculated and compared the results of a distributed polarizability model to a model with a single polarizable site located at the center-of-mass. Using a projection scheme that allows us to identify the contributions from different relaxation mechanisms, we found that dipole relaxation is dominated by collective reorientation, while in the case of polarizability anisotropy, relaxation processes related to translational dynamics make a major contribution over most of the fluid density range. The dielectric properties of fluoroform in the NC region were calculated and compared to the corresponding measurements. We found the dielectric constant and the far-infrared absorption spectrum to be in good agreement with experiments. PMID:23259748

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

    PubMed

    Raimondo, Corinna; Kenens, Bart; Reinders, Federica; Mayor, Marcel; Uji-i, Hiroshi; Samor, Paolo

    2015-09-01

    ?-? 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. PMID:26234482

  6. Gold behaves as hydrogen in the intermolecular self-interaction of metal aurides MAu4 (M = Ti, Zr, and Hf).

    PubMed

    Jung, Jaehoon; Kim, Hyemi; Kim, Jong Chan; Park, Min Hee; Han, Young-Kyu

    2011-03-01

    We performed density functional calculations to examine the intermolecular self-interaction of metal tetraauride MAu(4) (M = Ti, Zr, and Hf) clusters. We found that the metal auride clusters have strong dimeric interactions (2.8-3.1 eV) and are similar to the metal hydride analogues with respect to structure and bonding nature. Similarly to (MH(4))(2), the (μ-Au)(3) C(s) structures with three three-center two-electron (3c-2e) bonds were found to be the most stable. Natural orbital analysis showed that greater than 96 % of the Au 6s orbital contributes to the 3c-2e bonds, and this predominant s orbital is responsible for the similarity between metal aurides and metal hydrides (>99 % H 1s). The favorable orbital interaction between occupied Au 6s and unoccupied metal d orbitals leads to a stronger dimeric interaction for MAu(4)-MAu(4) than the interaction for MH(4)-MH(4). There is a strong relationship between the dimeric interaction energy and the chemical hardness of its monomer for (MAu(4))(2) and (MH(4))(2). PMID:21225974

  7. 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.

  8. 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

  9. 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

  10. On intermolecular dipolar coupling in two strongly polar liquids: dimethyl sulfoxide and acetonitrile.

    PubMed

    Jadzyn, Jan; Swiergiel, Jolanta

    2011-05-26

    The paper presents the results of studies of the electric and dielectric properties of dimethyl sulfoxide (DMSO) and acetonitrile (ACN), two strongly polar liquids composed of the molecules of the same dipole moment value (? ? 4 D) but of a quite different static dielectric permittivity (?(S)(DMSO) > ?(S)(ACN)). It was shown that the activation energies for both the dc ionic conductivity (?(DC)) and the viscosity (?) are two times higher for DMSO than for ACN; however, for both of the liquids, the temperature dependence of the product ?(DC)? is quite close to the prediction of the Stokes-Einstein relation. The dielectric results are interpreted in terms of the intermolecular dipole-dipole coupling. An exceptional behavior of DMSO most certainly results from its "monomolecularity", i.e., from the lack of the dipolar coupling in that strongly polar liquid. The effect is a consequence of a very specific structure of the DMSO molecule where its rotational dynamics makes the intermolecular dipole-dipole coupling very unfavorable, in contrast to the ACN molecules. PMID:21528869

  11. An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin.

    PubMed

    Wade, Kristin R; Hotze, Eileen M; Kuiper, Michael J; Morton, Craig J; Parker, Michael W; Tweten, Rodney K

    2015-02-17

    β-Barrel pore-forming toxins (βPFTs) form an obligatory oligomeric prepore intermediate before the formation of the β-barrel pore. The molecular components that control the critical prepore-to-pore transition remain unknown for βPFTs. Using the archetype βPFT perfringolysin O, we show that E183 of each monomer within the prepore complex forms an intermolecular electrostatic interaction with K336 of the adjacent monomer on completion of the prepore complex. The signal generated throughout the prepore complex by this interaction irrevocably commits it to the formation of the membrane-inserted giant β-barrel pore. This interaction supplies the free energy to overcome the energy barrier (determined here to be ∼ 19 kcal/mol) to the prepore-to-pore transition by the coordinated disruption of a critical interface within each monomer. These studies provide the first insight to our knowledge into the molecular mechanism that controls the prepore-to-pore transition for a βPFT. PMID:25646411

  12. Investigation of intermolecular interactions between single walled nanotubes and conjugated oligomers using the dispersion-corrected DFT methods

    NASA Astrophysics Data System (ADS)

    Lagowski, Jolanta B.; Aljohani, Suad; Khan, M. Zahidul H.; Zhao, Yuming

    The area of carbon nanotubes (CNT)-polymer composites has been progressing rapidly in recent years. Pure CNT and CNT-polymer composites have many useful (industry related) properties: ranging from electronic electrical conductivity to superior strength. However the full potential of using CNTs as reinforcements (in say a polymer matrix) has been severely limited because of complications associated with the dispersion of CNTs. CNTs tend to entangle with each other forming materials that have properties that fall short of the expectations. The goal of this work is to identify the type of conjugated oligomers that are best suited for the dispersion of single walled CNT (SWCNT). For this purpose, various methods of dispersion corrected density functional theory (DFT-D/B97D, /WB97XD, /CAM-B3LYP) have been used to investigate the interaction between the SWCNT and the organic conjugated oligomers with different end groups (aldehyde (ALD) and dithiafulvenyl (DTF)). We investigate the effect of intermolecular interactions on the structure, polarity and energetics of the oligomers and SWCNT combinations. The comparison of results obtained using different DFT approximations is made. Our results show that DFT-endcapped oligomer interact more strongly with CNT than ALD-endcapped oligomer. The financial support from NSERC, SACBC and Memorial University and the computational resources from Compute Canada were received.

  13. 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).

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

    PubMed

    Huang, Yuanhang; Beran, Gregory J O

    2015-07-28

    Three-body and higher intermolecular interactions can play an important role in molecular condensed phases. Recent benchmark calculations found problematic behavior for many widely used density functional approximations in treating 3-body intermolecular interactions. Here, we demonstrate that the combination of second-order Møller-Plesset (MP2) perturbation theory plus short-range damped Axilrod-Teller-Muto (ATM) dispersion accurately describes 3-body interactions with reasonable computational cost. The empirical damping function used in the ATM dispersion term compensates both for the absence of higher-order dispersion contributions beyond the triple-dipole ATM term and non-additive short-range exchange terms which arise in third-order perturbation theory and beyond. Empirical damping enables this simple model to out-perform a non-expanded coupled Kohn-Sham dispersion correction for 3-body intermolecular dispersion. The MP2 plus ATM dispersion model approaches the accuracy of O(N(6)) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N(5)) computational cost. PMID:26233113

  15. 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.

  16. [Noncovalent cation-π interactions--their role in nature].

    PubMed

    Fink, Krzysztof; Boratyński, Janusz

    2014-01-01

    Non-covalent interactions play an extremely important role in organisms. The main non-covalent interactions in nature are: ion-ion interactions, dipole-dipole interactions, hydrogen bonds, and van der Waals interactions. A new kind of intermolecular interactions--cation-π interactions--is gaining increasing attention. These interactions occur between a cation and a π system. The main contributors to cation-π interactions are electrostatic, polarization and, to a lesser extent, dispersion interactions. At first, cation-π interactions were studied in a gas phase, with metal cation-aromatic system complexes. The characteristics of these complexes are as follows: an increase of cation atomic number leads to a decrease of interaction energy, and an increase of cation charge leads to an increase of interaction energy. Aromatic amino acids bind with metal cations mainly through interactions with their main chain. Nevertheless, cation-π interaction with a hydrophobic side chain significantly enhances binding energy. In water solutions most cations preferentially interact with water molecules rather than aromatic systems. Cation-π interactions occur in environments with lower accessibility to a polar solvent. Cation-π interactions can have a stabilizing role on the secondary, tertiary and quaternary structure of proteins. These interactions play an important role in substrate or ligand binding sites in many proteins, which should be taken into consideration when the screening of effective inhibitors for these proteins is carried out. Cation-π interactions are abundant and play an important role in many biological processes. PMID:25380210

  17. 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.

  18. 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.

  19. 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; Şahin, 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.

  20. 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

  1. Intermolecular and Intramolecular Interactions Regulate Catalytic Activity of Myotonic Dystrophy Kinase-Related Cdc42-Binding Kinase??

    PubMed Central

    Tan, Ivan; Seow, Kah Tong; Lim, Louis; Leung, Thomas

    2001-01-01

    Myotonic dystrophy kinase-related Cdc42-binding kinase (MRCK) is a Cdc42-binding serine/threonine kinase with multiple functional domains. We had previously shown MRCK? to be implicated in Cdc42-mediated peripheral actin formation and neurite outgrowth in HeLa and PC12 cells, respectively. Here we demonstrate that native MRCK exists in high-molecular-weight complexes. We further show that the three independent coiled-coil (CC) domains and the N-terminal region preceding the kinase domain are responsible for intermolecular interactions leading to MRCK? multimerization. N terminus-mediated dimerization and consequent transautophosphorylation are critical processes regulating MRCK? catalytic activities. A region containing the two distal CC domains (CC2 and CC3; residues 658 to 930) was found to interact intramolecularly with the kinase domain and negatively regulates its activity. Its deletion also resulted in an active kinase, confirming a negative autoregulatory role. We provide evidence that the N terminus-mediated dimerization and activation of MRCK and the negative autoregulatory kinasedistal CC interaction are two mutually exclusive events that tightly regulate the catalytic state of the kinase. Disruption of this interaction by a mutant kinase domain resulted in increased kinase activity. MRCK kinase activity was also elevated when cells were treated with phorbol ester, which can interact directly with a cysteine-rich domain next to the distal CC domain. We therefore suggest that binding of phorbol ester to MRCK releases its autoinhibition, allowing N-terminal dimerization and subsequent kinase activation. PMID:11283256

  2. 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.

  3. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism

    PubMed Central

    Kieslich, Chris A.; Tamamis, Phanourios; Guzman, Yannis A.; Onel, Melis; Floudas, Christodoulos A.

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389

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

    ERIC Educational Resources Information Center

    Pullman, David; Peterson, Karen I.

    2004-01-01

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

  5. Highly Accurate Structure-Based Prediction of HIV-1 Coreceptor Usage Suggests Intermolecular Interactions Driving Tropism.

    PubMed

    Kieslich, Chris A; Tamamis, Phanourios; Guzman, Yannis A; Onel, Melis; Floudas, Christodoulos A

    2016-01-01

    HIV-1 entry into host cells is mediated by interactions between the V3-loop of viral glycoprotein gp120 and chemokine receptor CCR5 or CXCR4, collectively known as HIV-1 coreceptors. Accurate genotypic prediction of coreceptor usage is of significant clinical interest and determination of the factors driving tropism has been the focus of extensive study. We have developed a method based on nonlinear support vector machines to elucidate the interacting residue pairs driving coreceptor usage and provide highly accurate coreceptor usage predictions. Our models utilize centroid-centroid interaction energies from computationally derived structures of the V3-loop:coreceptor complexes as primary features, while additional features based on established rules regarding V3-loop sequences are also investigated. We tested our method on 2455 V3-loop sequences of various lengths and subtypes, and produce a median area under the receiver operator curve of 0.977 based on 500 runs of 10-fold cross validation. Our study is the first to elucidate a small set of specific interacting residue pairs between the V3-loop and coreceptors capable of predicting coreceptor usage with high accuracy across major HIV-1 subtypes. The developed method has been implemented as a web tool named CRUSH, CoReceptor USage prediction for HIV-1, which is available at http://ares.tamu.edu/CRUSH/. PMID:26859389

  6. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    PubMed

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. PMID:26867971

  7. Weak intra- and intermolecular interactions in a binaphthol imine: an experimental charge-density study on (+/-)-8'-benzhydrylideneamino-1,1'-binaphthyl-2-ol.

    PubMed

    Farrugia, Louis J; Kocovsk, Pavel; Senn, Hans Martin; Vyskocil, Stepn

    2009-12-01

    The charge density in (+/-)-8'-benzhydrylideneamino-1,1'-binaphthyl-2-ol (1) has been studied experimentally using Mo Kalpha X-ray diffraction at 100 K, and by theory using density-functional thoery (DFT) calculations at the B3LYP/6-311++G** level. The nature of the weak intramolecular peri-C...N, CH...pi, H...H and C(pi)...C(pi) interactions has been examined by topological analysis using the Quantum Theory of Atoms in Molecules (QTAIM) approach. An analysis of the density rho(r), the Laplacian of the density inverted Delta(2)rho(r(b)) and other topological properties at the bond-critical points were used to classify these interactions. The study confirms the presence of the intramolecular CH...pi interaction in (1), which was previously suspected on geometrical grounds. An analysis of the ellipticity profiles along the bond paths unambiguously shows the pi-delocalization between the imine unit and one N-phenyl group. The weak intermolecular interactions in the crystal of (1) were examined experimentally and theoretically through the pairwise interactions of the seven independent dimeric pairs of (1) responsible for the set of unique intermolecular interactions, and also through examination of the Hirshfeld surface d(norm) property. The theoretical dimeric-pair calculations used the BLYP-D functional which supplements the exchange-correlational functional with an empirical dispersion term to provide a more accurate determination of the energies for the weak intermolecular interactions. PMID:19923704

  8. 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.

  9. Intermolecular Contact Potentials for Protein-Protein Interactions Extracted from Binding Free Energy Changes upon Mutation.

    PubMed

    Moal, Iain H; Fernandez-Recio, Juan

    2013-08-13

    Understanding and predicting the energetics of protein-protein interactions is fundamental to the structural modeling of protein complexes. Binding free energy can be approximated as a sum of pairwise atomic or residue contact energies, which are commonly inferred from contact frequencies observed in experimental protein structures. However, such statistically inferred potentials require certain assumptions and approximation. Here, we explore the possibility of deriving atomic and residue contact potentials directly from experimental binding free energy changes following mutation and present a number of such potentials. The first set of potentials is obtained by unweighted least-squares fitting and bootsrap aggregating. The second set is calculated using a weighting scheme optimized against absolute binding affinity data, so as to account for the over-representation of certain complexes, residues, and families of interactions. The congruence of the potentials with known physical chemistry is investigated. The potentials are further validated by ranking and clustering protein-protein docking poses. PMID:26584123

  10. Intramolecular and Intermolecular Interactions of Protein Kinase B Define Its Activation In Vivo

    PubMed Central

    Laguerre, Michel; Park, Jongsun; Vojnovic, Borivoj; Hemmings, Brian A; Downward, Julian; Parker, Peter J; Larijani, Banafshé

    2007-01-01

    Protein kinase B (PKB/Akt) is a pivotal regulator of diverse metabolic, phenotypic, and antiapoptotic cellular controls and has been shown to be a key player in cancer progression. Here, using fluorescent reporters, we shown in cells that, contrary to in vitro analyses, 3-phosphoinositide–dependent protein kinase 1 (PDK1) is complexed to its substrate, PKB. The use of Förster resonance energy transfer detected by both frequency domain and two-photon time domain fluorescence lifetime imaging microscopy has lead to novel in vivo findings. The preactivation complex of PKB and PDK1 is maintained in an inactive state through a PKB intramolecular interaction between its pleckstrin homology (PH) and kinase domains, in a “PH-in” conformer. This domain–domain interaction prevents the PKB activation loop from being phosphorylated by PDK1. The interactive regions for this intramolecular PKB interaction were predicted through molecular modeling and tested through mutagenesis, supporting the derived model. Physiologically, agonist-induced phosphorylation of PKB by PDK1 occurs coincident to plasma membrane recruitment, and we further shown here that this process is associated with a conformational change in PKB at the membrane, producing a “PH-out” conformer and enabling PDK1 access the activation loop. The active, phosphorylated, “PH-out” conformer can dissociate from the membrane and retain this conformation to phosphorylate substrates distal to the membrane. These in vivo studies provide a new model for the mechanism of activation of PKB. This study takes a crucial widely studied regulator (physiology and pathology) and addresses the fundamental question of the dynamic in vivo behaviour of PKB with a detailed molecular mechanism. This has important implications not only in extending our understanding of this oncogenic protein kinase but also in opening up distinct opportunities for therapeutic intervention. PMID:17407381

  11. Synovial fluid response to extensional flow: effects of dilution and intermolecular interactions.

    PubMed

    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

  12. 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

  13. Role of intermolecular interactions in fabricating hardened electro-optic materials

    NASA Astrophysics Data System (ADS)

    Dalton, Larry R.; Harper, Aaron W.; Chen, Jinghong; Sun, Shajing; Mao, Shane S.; Garner, Sean; Chen, Antao; Steier, William H.

    1997-07-01

    Until recently, the product of chromophore dipole moment, (mu) , and molecular first hyperpolarizability, (beta) , divided by chromophore molecular weight was considered to be an appropriate chromophore figure of merit. Substantial progress has been made designing and synthesizing chromophores characterized by large (mu) (beta) values. If such high (mu) (beta) chromophores could be translated to hardened acentric polymer lattices with the same efficiency achieved for disperse red (azobenzene) chromophores then optical nonlinearities in excess of 50 pm/V could be expected. Although high (mu) (beta) chromophores have been available for several years, such macroscopic optical nonlinearities have only been recently realized. We demonstrated that the problem of translating microscopic to macroscopic optical nonlinearity can be traced to the attenuation of electric field poling-induced order by chromophore-chromophore electrostatic interactions. Such interactions are frequently treated within the approximations of London theory. We extend theoretical analysis to take into account the size and shapes of chromophores; such theory permits essentially quantitative prediction of variation of electro-optic coefficient with chromophore loading. Theory also suggests structural modification of chromophores to improve the maximum realizable optical nonlinearity as a function of chromophore loading and theoretical predictions have been experimentally realized in a number of cases leading to doubling and tripling of previously realized maximum electro-optic coefficient values. Chromophore-chromophore electrostatic interactions also contribute to aggregation and phase-separation which result in unacceptably high values of optical loss. Such interactions can also inhibit lattice hardening (e.g., thermosetting) reactions. A systematic analysis of such effects is presented.

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

    PubMed

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

    2016-02-17

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

  15. Intermolecular Interaction Effects on the Ultrafast Depolarization of the Optical Emission from Conjugated Polymers

    NASA Astrophysics Data System (ADS)

    Chang, M. H.; Frampton, M. J.; Anderson, H. L.; Herz, L. M.

    2007-01-01

    We have investigated the effect of interchain interactions on the ultrafast depolarization of the photoluminescence from solid films of a conjugated polymer. Accurate control was exercised over the interchain separation by threading of the conjugated chains with insulating macrocycles or complexation with an inert host polymer. Our measurements indicate that excitation into the higher electronic states of a chain aggregate is followed by a fast (<100fs) relaxation into lower excited states with an associated rotation of the transition dipole moment. These findings emphasize the need for consideration of initial excitonic delocalization across more than one polymeric chain.

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

    SciTech Connect

    Leszczynski, Jerzy; Sponer, Judit; Sponer, Jiri; Sumpter, Bobby G; Fuentes-Cabrera, Miguel A; Vazquez-Mayagoitia, Alvaro

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Czy?nikowska, ?aneta; Gra, 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.

  18. Unconditionally stable indole-derived glass blends having very high photorefractive gain: the role of intermolecular interactions.

    PubMed

    Angelone, Rocco; Ciardelli, Francesco; Colligiani, Arturo; Greco, Francesco; Masi, Paolo; Romano, Annalisa; Ruggeri, Giacomo; Stehlé, Jean-Louis

    2008-12-20

    The photorefractivity of an indole derivative and of its polymer blends has been studied at room temperature. The indole derivative 3-[2-(4-nitrophenyl)ethenyl]-1-(2-ethylhexyl)-2-methylindole (NPEMI-E) is a typical low-molecular-weight glass-forming molecule having peculiar nonlinear optics characteristics. It is unconditionally soluble in the photoconductive poly-(N-vinyl-2,3-dimethylindole) so that all the possible blends can be studied for a weight percent (wt. %) content of NPEMI-E ranging from zero to 100. A very high and sharp maximum of the photorefractive optical gain Gamma(2) approximately 2000 cm(-1) was obtained for a NPEMI-E wt. % content of about 90. On the basis of recently published theoretical calculations, we have made the hypothesis that the rapid change of Gamma(2) can also be ascribed to a correspondingly quick variation of the molecular electro-optic parameters of the dissolved chromophore for some well distinguished values of its concentration in the polymer matrix. Differential scanning calorimetry measurements were made and the results carefully analyzed with the aim of obtaining information on the intermolecular interactions. These last measurements also allowed rationalizing the unconditionally stable glass appearance of the obtained blends. Measurements of spectroscopic ellipsometry were also made on blends with different NPEMI-E content. PMID:19104520

  19. 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.

  20. Weak interactions in barbituric acid derivatives. Unusually steady intermolecular organic “sandwich” complexes. π π Stacking versus hydrogen bonding interactions

    NASA Astrophysics Data System (ADS)

    Khrustalev, Victor N.; Krasnov, Konstantin A.; Timofeeva, Tatiana V.

    2008-04-01

    The 4-methoxy-6,6-dimethyl-5,6,7,8-tetrahydro[1,3]dioxolo[4,5- g]isoquinolin-6-ium ( 1) and 2-(1 H-indol-3-yl)-1-ethanaminium (tryptaminium) ( 2) salts of 1,3-dimethyl-2,4,6-trioxoperhydro-pyrimidine-5-spiro-6'-{4'-methoxy-7'-(1,3-dimethyl-2,4,6-trioxoper-hydropyrimidin-5-yl)-5',6',7',8'-tetrahydro[1,3]dioxolo[4,5- g]naphthalene} ( 3) have been prepared and their structures have been investigated by single-crystal X-ray diffraction analysis. It has been found on the basis of the crystal packing arrangement as well as physical and chemical properties that derivatives 1 and 2 form unusually steady intermolecular sandwich-like complexes both in the crystal and in solution, which are stabilized by weak C sbnd H… n(O dbnd C) hydrogen bonds and π-π stacking. The interplay between the intermolecular π-π stacking and strong N sbnd H…O hydrogen bond interactions and its influence on the "sandwich" structures of 1 and 2 are discussed.

  1. 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

  2. Conformations, conformational preferences, and conformational exchange of N'-substituted N-acylguanidines: intermolecular interactions hold the key.

    PubMed

    Kleinmaier, Roland; Keller, Max; Igel, Patrick; Buschauer, Armin; Gschwind, Ruth M

    2010-08-18

    Guanidine and acylguanidine groups are crucial structural features of numerous biologically active compounds. Depending on the biological target, acylguanidines may be considered as considerably less basic bioisosteres of guanidines with improved pharmacokinetics and pharmacodynamics, as recently reported for N'-monoalkylated N-acylguanidines as ligands of G-protein-coupled receptors (GPCRs). The molecular basis for enhanced ligand-receptor interactions of acylguanidines is far from being understood. So far, only a few and contradictory results about their conformational preferences have been reported. In this study, the conformations, conformational preferences, and conformational exchange of four unprotonated and seven protonated monoalkylated acylguanidines with up to six anions and with bisphosphonate tweezers are investigated by NMR. Furthermore, the effects of the acceptor properties in acylguanidine salts, of microsolvation by dimethylsulfoxide, and of varying acyl and alkyl substituents are studied. Throughout the whole study, exclusively two out of eight possible acylguanidine conformations were detected, independent of the compound, the anion, or the solvent used. For the first time, it is shown that the strength and number of intermolecular interactions with anions, solvent molecules, or biomimetic receptors decide the conformational preferences and exchange rates. One recently presented and two new crystal structures resemble the conformational preferences observed in solution. Thus, consistent conformational trends are found throughout the structurally diverse compound pool, including two potent GPCR ligands, different anions, and receptors. The presented results may contribute to a better understanding of the mechanism of action at the molecular level and to the prediction and rational design of these biologically active compounds. PMID:20698689

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

    NASA Astrophysics Data System (ADS)

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

    2003-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Konno, Kohzo; Shiina, Isamu; Yui, Hiroharu

    2013-03-01

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

  5. A quantum chemical insight to intermolecular hydrogen bonding interaction between cytosine and nitrosamine: Structural and energetic investigations

    NASA Astrophysics Data System (ADS)

    Khalili, Behzad

    2016-03-01

    Hydrogen bond interactions which are formed during complex formation between cytosine and nitrosamine have been fully investigated using B3LYP, B3PW91 and MP2 methods in conjunction with various basis sets including 6-311++G (d,p), 6-311++G (2d,2p), 6-311++G (df,pd) and AUG-cc-pVDZ. Three regions around the most stable conformer of cytosine in the gas phase with six possible double H-bonded interactions were considered. Two intermolecular hydrogen bonds of type NC-N-HNA and O-H(N-H)C-ONA were found on the potential energy surface in a cyclic system with 8-member in CN1, CN3, CN5 and 7-member in CN2, CN4, CN6 systems. Results of binding energy calculation at all applied methods reveal that the CN1 structure is the most stable one which is formed by interaction of nitrosamine with cytosine in S1 region. The BSSE-corrected binding energy for six complex system is ranging from -23.8 to -43.6 kJ/mol at MP2/6-311++G (df,pd) level and the stability order is as CN1 > CN2 > CN3 > CN4 > CN5 > CN6 in all studied levels of theories. The NBO results reveal that the charge transfer occurred from cytosine to nitrosamine in CN1, CN3, CN5 and CN6 whereas this matter in the case of CN2 and CN4 was reversed. The relationship between BEs with red shift of H-bond involved bonds vibrational frequencies, charge transfer energies during complex formation and electron densities at H-bond BCPs were discussed. In addition activation energetic properties related to the proton transfer process between cytosine and nitrosamine have been calculated at MP2/6-311++G (df,pd) level. AIM results imply that H-bond interactions are electrostatic with partially covalent characteristic in nature.

  6. Interplay between Intrinsic Conformational Propensities and Intermolecular Interactions in the Self-Assembly of Short Surfactant-like Peptides Composed of Leucine/Isoleucine.

    PubMed

    Zhou, Peng; Deng, Li; Wang, Yanting; Lu, Jian R; Xu, Hai

    2016-05-10

    To study how the conformational propensities of individual amino acid residues, primary structures (i.e., adjacent residues and molecular lengths), and intermolecular interactions of peptides affect their self-assembly properties, we report the use of replica exchange molecular dynamics (REMD) to investigate the monomers, dimers, and trimers of a series of short surfactant-like peptides (I3K, L3K, L4K, and L5K). For four-residue peptides X3K (I3K and L3K), the results show that their different aggregation behaviors arise from the different intrinsic conformational propensities of isoleucine and leucine. For LmK peptides (L3K, L4K, and L5K), the molecular length is found to dictate their aggregation via primarily modulating intermolecular interactions. Increasing the number of hydrophobic amino acid residues of LmK peptides enhances their intermolecular H-bonding and promotes the formation of β-strands in dimer and trimer aggregates, overwhelming the intrinsic preference of Leu for helical structures. Thus, the interplay between the conformational propensities of individual amino acid residues for secondary structures and molecular interactions determines the self-assembly properties of the peptides, and the competition between intramolecular and intermolecular H-bonding interactions determines the probability of β-sheet alignment of peptide molecules. These results are validated by comparing simulated and experimental CD spectra of the peptides. This study will aid the design of short peptide amphiphiles and improve the mechanistic understanding of their self-assembly behavior. PMID:27088564

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  9. The different biological effects of telomestatin and TMPyP4 can be attributed to their selectivity for interaction with intramolecular or intermolecular G-quadruplex structures.

    PubMed

    Kim, Mu-Yong; Gleason-Guzman, Mary; Izbicka, Elzbieta; Nishioka, David; Hurley, Laurence H

    2003-06-15

    Demonstration of the existence of G-quadruplex structures in telomeres of Stylonychia macronuclei and in the promoter of c-myc in human cells has validated these secondary DNA structures as potential targets for drug design. The next important issue is the selectivity of G-quadruplex-interactive agents for the different types of G-quadruplex structures. In this study, we have taken an important step in associating specific biological effects of these drugs with selective interaction with either intermolecular or intramolecular G-quadruplex structures formed in telomeres. Telomestatin is a natural product isolated from Streptomyces anulatus 3533-SV4 and has been shown to be a very potent telomerase inhibitor through its G-quadruplex interaction. We have demonstrated that telomestatin interacts preferentially with intramolecular versus intermolecular G-quadruplex structures and also has a 70-fold selectivity for intramolecular G-quadruplex structures over duplex DNA. Telomestatin is able to stabilize G-quadruplex structures that are formed from duplex human telomeric DNA as well as from single-stranded DNA. Importantly, telomestatin stabilizes these G-quadruplex structures in the absence of monovalent cations, which is a unique characteristic among G-quadruplex-interactive compounds. At noncytotoxic concentrations, telomestatin suppresses the proliferation of telomerase-positive cells within several weeks. In contrast, TMPyP4, a compound that preferentially facilitates the formation of intermolecular G-quadruplex structures, suppresses the proliferation of alternative lengthening of telomeres (ALT)-positive cells as well as telomerase-positive cells. We have also demonstrated that TMPyP4 induces anaphase bridges in sea urchin embryos, whereas telomestatin did not have this effect, leading us to conclude that the selectivity of telomestatin for intramolecular G-quadruplex structures and TMPyP4 for intermolecular G-quadruplex structures is important in mediating different biological effects: stabilization of intramolecular G-quadruplex structures produces telomerase inhibition and accelerated telomere shortening, whereas facilitation of the formation of intermolecular G-quadruplex structures induces the formation of anaphase bridges. PMID:12810655

  10. 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

    2015-10-26

    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

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

    PubMed

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

    2014-01-21

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

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

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-01

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the Cs-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

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

    PubMed

    Azar, R Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C(s)-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible. PMID:22260560

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

    SciTech Connect

    Azar, R. Julian; Head-Gordon, Martin

    2012-01-14

    We propose a wave function-based method for the decomposition of intermolecular interaction energies into chemically-intuitive components, isolating both mean-field- and explicit correlation-level contributions. We begin by solving the locally-projected self-consistent field for molecular interactions equations for a molecular complex, obtaining an intramolecularly polarized reference of self-consistently optimized, absolutely-localized molecular orbitals (ALMOs), determined with the constraint that each fragment MO be composed only of atomic basis functions belonging to its own fragment. As explicit inter-electronic correlation is integral to an accurate description of weak forces underlying intermolecular interaction potentials, namely, coordinated fluctuations in weakly interacting electronic densities, we add dynamical correlation to the ALMO polarized reference at the coupled-cluster singles and doubles level, accounting for explicit dispersion and charge-transfer effects, which map naturally onto the cluster operator. We demonstrate the stability of energy components with basis set extension, follow the hydrogen bond-breaking coordinate in the C{sub s}-symmetry water dimer, decompose the interaction energies of dispersion-bound rare gas dimers and other van der Waals complexes, and examine charge transfer-dominated donor-acceptor interactions in borane adducts. We compare our results with high-level calculations and experiment when possible.

  15. Theoretical analysis of intermolecular interactions of selected residues of triosephosphate isomerase from Trypanosoma cruzi with its inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid.

    PubMed

    Chávez-Calvillo, Rodrigo; Costas, Miguel; Hernández-Trujillo, Jesús

    2010-03-01

    The interaction between selected amino acid residues of the homodimeric enzyme triosephosphate isomerase from Trypanosoma cruzi with the inhibitor 3-(2-benzothiazolylthio)-1-propanesulfonic acid (BTT) was investigated by means of high level quantum chemical methods. The amino acids phe75A, arg71A and tyr102B from the enzyme monomers A and B were selected using experimental X-ray structural data. The ab initio intermolecular energies for the association of the inhibitor with the individual amino acids were calculated in two forms, namely, with a supermolecular approach and using the symmetry adapted perturbation theory. The latter also provided the contributions to the interaction energies, which were interpreted in terms of the usual van der Waals forces. The electron density for the specific interactions between BTT and the amino acids and the charge redistribution due to complex formation were also analyzed. It was found that for phe75A and tyr102B the dispersion energy is the dominant contribution to the complex stabilization followed by the induction and electrostatic energies. In addition, whereas the face-edge complex of BTT with phe75A exhibits a C-H pi bond similar to that observed for the benzene dimer, the complex with arg71A shows an important charge redistribution on the amino acid in regions far removed from those where the intermolecular specific interactions occur. PMID:20165754

  16. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: the interplay between hydrophobic interactions and formation of intermolecular disulfide bonds.

    PubMed

    Xie, Jinbing; Qin, Meng; Cao, Yi; Wang, Wei

    2011-08-01

    Recently, it was reported that ultraviolet (UV) illumination could trigger the unfolding of proteins by disrupting the buried disulfide bonds. However, the consequence of such unfolding has not been adequately evaluated. Here, we report that unfolded chicken egg white lysozyme (CEWL) triggered by UV illumination can form uniform globular aggregates as confirmed by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The assembling process of such aggregates was also monitored by several other methods, such as circular dichroism, fluorescence spectroscopy, mass spectrometry based on chymotrypsin digestion, ANS-binding assay, Ellman essay, and SDS-PAGE. Our finding is that due to the dissociation of the native disulfide bonds by UV illumination, CEWL undergoes drastic conformational changes resulting in the exposure of some hydrophobic residues and free thiols. Subsequently, these partially unfolded molecules self-assemble into small granules driven by intermolecular hydrophobic interaction. With longer UV illumination or longer incubation time, these granules can further self-assemble into larger globular aggregates. The combined effects from both the hydrophobic interaction and the formation of intermolecular disulfide bonds dominate this process. Additionally, similar aggregation behavior can also be found in other three typical disulfide-bonded proteins, that is, α-lactalbumin, RNase A, and bovine serum albumin. Thus, we propose that such aggregation behavior might be a general mechanism for some disulfide-bonded proteins under UV irradiation. PMID:21661057

  17. 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

  18. 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.

  19. New aspects of weak CH⋯π bonds: intermolecular interactions between alicyclic and aromatic rings in crystals of small compounds, peptides and proteins

    NASA Astrophysics Data System (ADS)

    Ciunik, Z.; Berski, S.; Latajka, Z.; Leszczyński, J.

    1998-02-01

    The geometry of intermolecular contacts between alicyclic and aromatic rings in a number of crystal structures suggests an attractive interaction between the rings. An analysis of molecular packing of 444 different crystal structures collected in the Cambridge Structural Database shows that phenyl…cyclohexanonyl, cyclohexyl, and/or cyclopentyl ring interactions occur in 59-82% of studied crystals. Similar interactions are observed between aromatic rings and heterocyclic pyrrolidine rings of proline in peptides and proteins. An analysis of data collected in the Brookhaven Protein Data Bank reveals that interactions between proline CH groups and aromatic rings of phenylalanine, tyrosine, and tryptophan as acceptors are frequently observed in proteins. Based on these results, several geometric models of these interactions are proposed. Two of these models are fully optimized using quantum chemical calculations at the density functional theory level. Calculated energies suggest that the most important interaction between the cyclohexanone and benzene rings is described by the face-to-face model, in which three axial hydrogen atoms are directed toward the aromatic partner.

  20. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures.

    PubMed

    Odahara, Takayuki; Odahara, Koji

    2016-06-01

    The data provide information in support of the research article, "Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures" [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt-PEG phase separation. PMID:27135050

  1. 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.

  2. Intermolecular interactions and high dielectric energy storage density in poly(vinylidene fluoride-hexafluoropropylene)/poly(vinylidene fluoride) blend thin films

    NASA Astrophysics Data System (ADS)

    Rahimabady, Mojtaba; Yao, Kui; Arabnejad, Saeid; Lu, Li; Shim, Victor P. W.; Cheong Wun Chet, Davy

    2012-06-01

    Homogeneous poly(vinylidene fluoride-hexafluoropropylene) and poly (vinylidene fluoride) (P(VDF-HFP)/PVDF) blend films were prepared via a chemical solution approach, followed by quenching, annealing, and hot pressing. The intermolecular interactions of the blends were investigated through atomic simulation. Higher melting temperature, higher crystallinity, larger elastic modulus, and improved breakdown strength (>850 MV/m) were observed in the optimized polymer blends, in comparison with either of the two constituent polymers, PVDF or P(VDF-HFP). In addition, the P(VDF-HFP)/PVDF blend film also showed larger dielectric constant. As a result, an extremely high energy density of 30.1 J/cm3 was achieved in P(VDF-HFP)/PVDF (50:50 by weight) blend films.

  3. Data in support of intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures

    PubMed Central

    Odahara, Takayuki; Odahara, Koji

    2016-01-01

    The data provide information in support of the research article, “Intermolecular interactions at early stage of protein/detergent particle association induced by salt/polyethylene glycol mixtures” [1]. The data regarding variation of absorption spectra is used as an indicator of the duration of Rp. viridis PRU and RC, Rb. sphaeroides RC and LH2, and Rb. capsulatus LH2 in the native state in the presence of NaCl/polyethylene glycol (PEG) mixture. The data about minimum concentrations of salt and PEG whose aqueous phases are mutually separated presents information on additional influence of Tris buffer and N-octyl-β-d-glucoside on the salt–PEG phase separation. PMID:27135050

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

    SciTech Connect

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

    2015-02-15

    A new spin crossover coordination polymer (SCO-CPs) of Fe(II)-4,4′-bipyridine (4,4′-bipy) family: (Fe(4,4′-bipy){sub 2}(H{sub 2}O){sub 2})·(4,4′-bipy)· 8(H{sub 2}O)·2(ClO{sub 4}) (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 π…π 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) (H{sub 2}O){sub 2} (NCS){sub 2})·4,4′-bipy, 1 and (Fe(4,4′-bipy){sub 2}(NCS){sub 2})·mSolv, 2) through Hirshfeld surfaces analysis, which revealed that the low ligand field strength (NCS{sup −}) 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 π…π packing interactions) make for the LS (low-spin) state. - Highlights: ●A new member of Fe(||)-4,4′-bipy family has been prepared. ●It displays half spin transitions tuned by ligand field and intermolecular interactions. ●We have made a detailed comparison of this new member with two other analogous complexes.

  5. The effect of deformation and intermolecular interaction on the absorption spectrum of 5-aminotetrazole and hydrazine: A computational molecular spectroscopy study on hydrazinium 5-aminotetrazolate

    NASA Astrophysics Data System (ADS)

    Farrokhpour, H.; Dehbozorgi, A.; Manassir, M.; Najafi Chermahini, A.

    2016-03-01

    In the present work, the UV absorption spectra of seven complexes of hydrazinium 5-aminotetrazolate (HY-5AT), in the range of 4-12 eV, were calculated in both gas and water. The UV absorption spectra of the selected HY-5AT complexes were also calculated in the absence of the intermolecular interaction between 5-aminotetrazole (5AT) and hydrazine (HY) and compared with the calculated UV absorption spectra of isolated HY and 5AT in the gas phase to see the effect of deformation on the electronic structures of the fragments. In addition, the calculated spectra of HY-5AT complexes were compared with the corresponding calculated spectra of HY-5AT complexes in the absence of the interaction between HY and 5AT to see the effect of interaction between two fragments on the absorption spectra of the complexes. Similar studies were performed on the most stable structure of HY-5AT complex in water and different trend was observed for the effect of deformation and interaction on the absorption spectrum of complex compared to the gas phase.

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

    PubMed

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

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

    The Merlin/MCL optimization environment and the GAMESS-US package were combined so as to offer an extended and efficient quantum chemistry optimization system, capable of implementing complex optimization strategies for generic molecular modeling problems. A communication and data exchange interface was established between the two packages exploiting all Merlin features such as multiple optimizers, box constraints, user extensions and a high level programming language. An important feature of the interface is its ability to perform dimer computations by eliminating the basis set superposition error using the counterpoise (CP) method of Boys and Bernardi. Furthermore it offers CP-corrected geometry optimizations using analytic derivatives. The unified optimization environment was applied to construct portions of the intermolecular potential energy surface of the weakly bound H-bonded complex C 6H 6-H 2O by utilizing the high level Merlin Control Language. The H-bonded dimer HF-H 2O was also studied by CP-corrected geometry optimization. The ab initio electronic structure energies were calculated using the 6-31G ** basis set at the Restricted Hartree-Fock and second-order Moller-Plesset levels, while all geometry optimizations were carried out using a quasi-Newton algorithm provided by Merlin. Program summaryTitle of program: MERGAM Catalogue identifier:ADYB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYB_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: The program is designed for machines running the UNIX operating system. It has been tested on the following architectures: IA32 (Linux with gcc/g77 v.3.2.3), AMD64 (Linux with the Portland group compilers v.6.0), SUN64 (SunOS 5.8 with the Sun Workshop compilers v.5.2) and SGI64 (IRIX 6.5 with the MIPSpro compilers v.7.4) Installations: University of Ioannina, Greece Operating systems or monitors under which the program has been tested: UNIX Programming language used: ANSI C, ANSI Fortran-77 No. of lines in distributed program, including test data, etc.:11 282 No. of bytes in distributed program, including test data, etc.: 49 458 Distribution format: tar.gz Memory required to execute with typical data: Memory requirements mainly depend on the selection of a GAMESS-US basis set and the number of atoms No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: no Nature of physical problem: Multidimensional geometry optimization is of great importance in any ab initio calculation since it usually is one of the most CPU-intensive tasks, especially on large molecular systems. For example, the geometric and energetic description of van der Waals and weakly bound H-bonded complexes requires the construction of related important portions of the multidimensional intermolecular potential energy surface (IPES). So the various held views about the nature of these bonds can be quantitatively tested. Method of solution: The Merlin/MCL optimization environment was interconnected with the GAMESS-US package to facilitate geometry optimization in quantum chemistry problems. The important portions of the IPES require the capability to program optimization strategies. The Merlin/MCL environment was used for the implementation of such strategies. In this work, a CP-corrected geometry optimization was performed on the HF-H 2O complex and an MCL program was developed to study portions of the potential energy surface of the C 6H 6-H 2O complex. Restrictions on the complexity of the problem: The Merlin optimization environment and the GAMESS-US package must be installed. The MERGAM interface requires GAMESS-US input files that have been constructed in Cartesian coordinates. This restriction occurs from a design-time requirement to not allow reorientation of atomic coordinates; this rule holds always true when applying the COORD = UNIQUE keyword in a GAMESS-US input file. Typical running time: It depends on the size of the molecular system, the size of the basis set and the method of electron correlation. Execution of the test run took approximately 5 min on a 2.8 GHz Intel Pentium CPU.

  8. Toward more efficient CCSD(T) calculations of intermolecular interactions in model hydrogen-bonded and stacked dimers.

    PubMed

    Dedíková, Pavlína; Pitonák, Michal; Neogrády, Pavel; Cernusák, Ivan; Urban, Miroslav

    2008-07-31

    Interaction energies of the model H-bonded complexes, the formamide and formamidine dimers, as well as the stacked formaldehyde and ethylene dimers are calculated by the coupled cluster CCSD(T) method. These systems serve as a model for H-bonded and stacking interactions, typical in molecules participating in biological systems. We use the optimized virtual orbital space (OVOS) technique, by which the dimension of the space of virtual orbitals in coupled cluster CCSD(T) calculations can be significantly reduced. We demonstrate that when the space of virtual orbitals is reduced to 50% of the full space, which means reducing computational demands by 1 order of magnitude, the interaction energies for both H-bonded and stacked dimers are affected by no more than 0.1 kcal/mol. This error is much smaller than the error when interaction energies are calculated using limited basis sets. PMID:18593134

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  11. Useful lower limits to polarization contributions to intermolecular interactions using a minimal basis of localized orthogonal orbitals: Theory and analysis of the water dimer

    NASA Astrophysics Data System (ADS)

    Azar, R. Julian; Horn, Paul Richard; Sundstrom, Eric Jon; Head-Gordon, Martin

    2013-02-01

    The problem of describing the energy-lowering associated with polarization of interacting molecules is considered in the overlapping regime for self-consistent field wavefunctions. The existing approach of solving for absolutely localized molecular orbital (ALMO) coefficients that are block-diagonal in the fragments is shown based on formal grounds and practical calculations to often overestimate the strength of polarization effects. A new approach using a minimal basis of polarized orthogonal local MOs (polMOs) is developed as an alternative. The polMO basis is minimal in the sense that one polarization function is provided for each unpolarized orbital that is occupied; such an approach is exact in second-order perturbation theory. Based on formal grounds and practical calculations, the polMO approach is shown to underestimate the strength of polarization effects. In contrast to the ALMO method, however, the polMO approach yields results that are very stable to improvements in the underlying AO basis expansion. Combining the ALMO and polMO approaches allows an estimate of the range of energy-lowering due to polarization. Extensive numerical calculations on the water dimer using a large range of basis sets with Hartree-Fock theory and a variety of different density functionals illustrate the key considerations. Results are also presented for the polarization-dominated Na+CH4 complex. Implications for energy decomposition analysis of intermolecular interactions are discussed.

  12. 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

  13. 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), β = 128.123°, V = 4.4797 nm3, empirical formula: C52H44Mn2N4O8, Mr = 962.79, Z = 4, Dc = 1.428 g/cm3, μ = 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), β = 92.02°, V = 4.660 nm3, empirical formula: C26H22MnN2O4, Mr = 481.40, Z = 8, Dc = 1.372 g/cm3, μ = 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, π-π stacking and Csbnd H⋯π 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.

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

    PubMed

    Baranowska-Łączkowska, Angelika; Fernández, Berta

    2014-01-30

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-05-01

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

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

    SciTech Connect

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

    2013-08-29

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

  17. Studies on the electronic structure and intermolecular interactions of diacetyl-, and methylglyoxal- bis(thiosemicarbazone)copper(II) complexes

    NASA Astrophysics Data System (ADS)

    Yordanov, N. D.; Batchvarova, M. T.

    1984-03-01

    The electronic structure of the title complexes are studied by e.p.r. and electronic spectra in DMF solution (300 and 100 K) as well as in magnetically diluted powder sample. It is found that the electronic structure is determined mainly by the unit CuN 2S 2 of the complex. The interaction of the complexes with some Lewis acids is also studied. The formation of D-A complex with relatively weak acids is observed. The strong Lewis acids destroy the complexes.

  18. Mixed layers of β-lactoglobulin and SDS at air-water interfaces with tunable intermolecular interactions.

    PubMed

    Engelhardt, Kathrin; Weichsel, Ulrike; Kraft, Elena; Segets, Doris; Peukert, Wolfgang; Braunschweig, Björn

    2014-04-17

    Mixtures of β-lactoglobulin (BLG) and sodium dodecyl sulfate (SDS) were studied at pH 3.8 and 6.7 under equilibrium conditions. At these pH conditions, BLG carries either a positive or a negative net charge, respectively, which enables tunable electrostatic interactions between anionic SDS surfactants and BLG proteins. For pH 3.8, vibrational sum-frequency generation (SFG) and ellipsometry indicate strong BLG-SDS complex formation at air-water interfaces that is caused by attractive electrostatic interactions. The latter complexes are already formed in the bulk solution which was confirmed by a thermodynamic study of BLG-SDS mixtures using isothermal titration calorimetry (ITC). For acidic conditions we determine from our ITC data an exothermal binding enthalpy of -40 kJ mol(-1). Increasing SDS/BLG molar ratios above 10 leads to a surface excess of SDS and thus to a charge reversal from a positive net charge with BLG as the dominating surface adsorbed species to a negatively charged layer with SDS as the dominating surface species. The latter is evidenced by a pronounced minimum in SFG intensities that is also accompanied by a phase change of O-H stretching bands due to a reorientation of H2O within the local electric field. This phase change which occurs at SDS/BLG molar ratio between 1 and 10 causes a polarity change in SFG intensities from BLG aromatic C-H stretching vibrations. Conclusions from SFG spectra are corroborated by ellipsometry which shows a dramatic increase in layer thicknesses at molar ratios where a charge reversal occurs. The formation of interfacial multilayers comprising SDS-BLG complexes is, thus, caused by cancellation of electrostatic interactions which leads to agglomeration at the interface. In contrast to pH 3.8, behavior of BLG-SDS mixtures at pH 6.7 is different due to repulsive electrostatic interactions between SDS and BLG which lead to a significantly reduced binding enthalpy of -17 kJ mol(-1). Finally, it has to be mentioned that SFG spectra show a coexistence of BLG and SDS molecules at the interface for BLG-SDS molar ratios > 2. PMID:24678897

  19. Evidence for intermolecular interaction as a necessary step for pore-formation activity and toxicity of Bacillus thuringiensis Cry1Ab toxin.

    PubMed

    Soberón, M; Pérez, R V; Nuñez-Valdéz, M E; Lorence, A; Gómez, I; Sánchez, J; Bravo, A

    2000-10-15

    Based on the observation of large conductance states formed by Bacillus thuringiensis Cry toxins in synthetic planar lipid bilayers and the estimation of a pore size of 10-20 A, it has been proposed that the pore could be formed by an oligomer containing four to six Cry toxin monomers. However, there is a lack of information regarding the insertion of Cry toxins into the membrane and oligomer formation. Here we provide direct evidence showing that the intermolecular interaction between Cry1Ab toxin monomers is a necessary step for pore formation and toxicity. Two Cry1Ab mutant proteins affected in different steps of their mode of action (F371A in receptor binding and H168F in pore formation) were affected in toxicity against Manduca sexta larvae. Binding analysis showed that F371A protein bound more efficiently to M. sexta brush border membrane vesicles when mixed with H168F in a one to one ratio. These mutant proteins also recovered pore-formation activity, measured with a fluorescent dye with isolated brush border membrane vesicles, and toxicity against M. sexta larvae when mixed, showing that monomers affected in different steps of their mode of action can form functional hetero-oligomers. PMID:11024267

  20. 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

  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 (η) 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. Networks of intermolecular interactions involving nitro groups in the crystals of three polymorphs of 9-aminoacridinium 2,4-dinitrobenzoate ṡ 2,4-dinitrobenzoic acid

    NASA Astrophysics Data System (ADS)

    Sikorski, Artur; Trzybiński, Damian

    2013-10-01

    We report on the crystal structures of three polymorphs of 9-aminoacridinium 2,4-dinitrobenzoate ṡ 2,4-dinitrobenzoic acid (I, II and III). Single-crystal X-ray diffraction measurements show that the title compound forms three polymorphs with the space groups P21/n (I) and P1¯ (II and III). The asymmetric units of all the polymorphs consist of 9-aminoacridinium cation, the 2,4-dinitrobenzoate anion and the 2,4-dinitrobenzoic acid molecule. The neutral and ionic forms of 2,4-dinitrobenzoic acid are linked via O-H⋯O hydrogen bonds with a D graph-set motif, forming monoanionic dimers. The amine and carboxylic acid moieties are linked via N-H⋯O, O-H⋯O and C-H⋯O hydrogen bonds. The acridinium skeletons in the crystal packing form π-stacked columns, whereas the monoanionic dimers of 2,4-dinitrobenzoic acid are linked by different types of intermolecular interactions, especially those involving nitro groups. To the best of our knowledge, the crystal structure of 9-aminoacridinium 2,4-dinitrobenzoate ṡ 2,4-dinitrobenzoic acid is the first in which the appearance of monoanionic dimers of 2,4-dinitrobenzoic acid has been documented.

  3. 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 ℓ} clusters (n going from 6 to 10 and ℓ 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.

  4. Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies.

    PubMed

    Horn, Paul R; Mao, Yuezhi; Head-Gordon, Martin

    2016-03-21

    In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na(+), water-Cl(-), and the naphthalene dimer. PMID:27004862

  5. Defining the contributions of permanent electrostatics, Pauli repulsion, and dispersion in density functional theory calculations of intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Mao, Yuezhi; Head-Gordon, Martin

    2016-03-01

    In energy decomposition analysis of Kohn-Sham density functional theory calculations, the so-called frozen (or pre-polarization) interaction energy contains contributions from permanent electrostatics, dispersion, and Pauli repulsion. The standard classical approach to separate them suffers from several well-known limitations. We introduce an alternative scheme that employs valid antisymmetric electronic wavefunctions throughout and is based on the identification of individual fragment contributions to the initial supersystem wavefunction as determined by an energetic optimality criterion. The density deformations identified with individual fragments upon formation of the initial supersystem wavefunction are analyzed along with the distance dependence of the new and classical terms for test cases that include the neon dimer, ammonia borane, water-Na+, water-Cl-, and the naphthalene dimer.

  6. Glycoprotein B of herpes simplex virus type 1 oligomerizes through the intermolecular interaction of a 28-amino-acid domain.

    PubMed Central

    Laquerre, S; Person, S; Glorioso, J C

    1996-01-01

    Herpes simplex virus type 1 glycoprotein B (gB) is an envelope component that plays an essential role in virus infection. The biologically active form of gB is an oligomer that contributes to the process of viral envelope fusion with the cell surface membrane, resulting in viral penetration and initiation of the replication cycle. In previous studies, two discontinuous sites for oligomer formation were identified: a nonessential upstream site located between residues 93 and 282 and an essential downstream site located between residues 596 and 711. In this study, in vitro-transcribed and -translated gB test molecules were used to characterize the more active essential membrane-proximal domain. A series of gB test polypeptides mutated in this downstream oligomerization domain were assayed for their abilities to form oligomers with a mutant gB capture polypeptide containing the analogous wild-type domain. Detection of oligomers was achieved by coimmunoprecipitation of two gB mutant molecules by using a monoclonal antibody specific for a hemagglutinin epitope tag introduced into the coding sequence of the capture polypeptide. Analysis of the immune-precipitated products by sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated that the downstream oligomerization domain resided within residues 626 to 676. This region was further resolved into two segments, residues 626 to 653 and 653 to 675, each of which was independently sufficient to form oligomers. However, residues 626 to 653 provided for a stronger interaction between gB monomers. Moreover, this stretch of 28 amino acids was shown to form oligomers when introduced into the carboxy-terminal region of gB monomers lacking this domain at the normal site, thus indicating that this domain was functionally independent of its natural location within the gB molecule. Further analysis of the sequence within residues 596 to 653 by using mutant test polypeptides altered in individual amino acids revealed that cysteines 9 and 10 located at positions 596 and 633, respectively, were not required for oligomer formation but contributed to dimer formation and/or stabilization. The results of this study suggest that oligomerization of gB monomers is induced by interactions between contiguous residues localized within the ectodomain near the site of molecule insertion into the viral envelope membrane. PMID:8627685

  7. 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.

  8. 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

  9. Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory.

    PubMed

    Witte, Jonathon; Neaton, Jeffrey B; Head-Gordon, Martin

    2016-05-21

    With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems. PMID:27208948

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

    PubMed Central

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

    1992-01-01

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

  11. 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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    We develop the method proposed by Chernyshuk and Lev [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 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→∞.

  13. 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.

  14. 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

  15. Calculating intermolecular potentials with SIMPER

    NASA Astrophysics Data System (ADS)

    Wheatley, Richard J.; Lillestolen, Timothy C.

    Recent theoretical studies of the van der Waals complexes formed between water and the two main components of air, nitrogen and oxygen, are reviewed. Combined with previous work on the water-argon complex, the results allow non-ideal thermodynamic properties of water-air mixtures to be calculated. The intermolecular potential energy surfaces for these complexes have been calculated using a combination of supermolecule methods and perturbation theory, as described in a previous review. Theoretical techniques introduced since this previous work include the extension of the intermolecular perturbation theory to open-shell electronic species, as required for the water-oxygen complex, and new and more accurate calculations of dispersion energy coefficients. Spin-unrestricted, time-dependent coupled cluster theory has been used for calculating dispersion energy coefficients for the water-oxygen complex, and this method is described and compared with other accurate methods, and a possible alternative method is suggested for future work. The results obtained for the water-nitrogen complex are highly satisfactory. With little more computational effort than is required to produce a second-order Moller-Plesset supermolecule potential energy surface, the intermolecular potential is calculated to an accuracy which appears to be comparable to coupled-cluster calculations with perturbative triple excitations. For the water-oxygen complex, the different theoretical methods produce potential energy surfaces with larger discrepancies than for water-nitrogen, although they predict the main features of the potential energy surface better than calculations in the literature. Although few experimental measurements of water-oxygen virial coefficients are available, the agreement of theoretical predictions with these is reasonable, and the agreement with the better characterized water-air virial coefficients is very good. The review concludes with a forward look to work on larger molecules. Increasing the size of the interacting molecules creates a number of practical problems. Some problems, including the steep scaling of computation time with system size, are common to all methods. The use in the current work of a damped multipole expansion about the molecular centres also causes problems when larger molecules are considered. The review therefore considers methods that can be used to reduce the unfavourable size scaling, to reduce the size of the basis set, and to use damped atomic multipole expansions, which are centred on the nuclei of the interacting molecules.

  16. Transition temperature of the interacting dipolar Bose gas

    SciTech Connect

    Kao, Yee-Mou; Jiang, T. F.

    2007-03-15

    We investigate the effects of long-ranged dipole-dipole potential on the transition temperature of a weakly interacting Bose gas. We apply the two-fluid model to derive the energy spectra of the thermal and the condensate parts. From the interaction modified spectra of the system, the formula for the shift of transition temperature was derived. Compared to the conventional weakly interacting Bose system with contact potential only where thermal effect is larger, we find that the condensate effect is about two times that of the thermal part in the dipolar system. Due to the relative smallness of dipole-dipole interaction with respect to the contact interaction in current dipolar Bose-Einstein condensation, we suggest to measure the dipolar effect by tuning the scattering length to negligible small by the Feshbach resonance technique.

  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 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.

  19. C-NOT gate based on ultracold Rydberg atom interactions

    NASA Astrophysics Data System (ADS)

    Rashid, Muhammad; Maarten, Hoogerland; Yasir, Jamil

    2013-11-01

    The Rydberg states of neutral atoms are strongly polarisable and possess long lifetimes because of high energies which can lead to strong and long range dipole-dipole interactions. The energy levels corresponding to these states are shifted because of dipole-dipole interactions and can be used to block transitions of more than one excitation in the Rydberg regime. This reputed Rydberg blockade is obtained when the excitation is shifted out of resonance by these interactions. Electromagnetically induced transparency (EIT) is sensitive to a small detuning. At large distances, up to several micrometers, the interactions can interrupt the EIT consequence. Herein we investigate a novel scheme based on EIT and Rydberg blockade and performed a simulation of a controlled-NOT (C-NOT) quantum gate which is critical for quantum computation by using neutral atoms.

  20. Desensitization of metastable intermolecular composites

    SciTech Connect

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

    2011-04-26

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

  1. 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

    NASA Astrophysics Data System (ADS)

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

    A newly synthesized chalcone, Ethyl 4-[3-(2-chloro-phenyl)-acryloyl]-3,5-dimethyl-1H-pyrrole-2-carboxylate (ECPADMPC) has been characterized by 1H NMR, 13C 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 (ρBCP), Laplacian of electron density (▿2ρBCP), energetic parameters-kinetic electron energy density (GBCP), potential electron density (VBCP) and the total electron energy density (HBCP) 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 -12.3 kcal/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.

  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. Analysis of transition state stabilization by non-covalent interactions in the Houk-List model of organocatalyzed intermolecular Aldol additions using functional-group symmetry-adapted perturbation theory.

    PubMed

    Bakr, Brandon W; Sherrill, C David

    2016-04-21

    Rational design of catalysts would be aided by a better understanding of how non-covalent interactions stabilize transition states. Here, we apply the newly-developed Functional-Group Symmetry-Adapted Perturbation Theory (F-SAPT) to quantify non-covalent interactions in transition states of the proline-catalyzed intermolecular aldol reaction between benzaldehyde and cyclohexanone, according to the Houk-List mechanism [Bahmanyar et al., J. Am. Chem. Soc., 2003, 125, 2475]. A recent re-examination of this organocatalytic reaction by Rzepa and co-workers [Armstrong et al., Chem. Sci., 2014, 5, 2057] used electron density analysis to identify three key non-covalent interactions thought to influence stereoselectivity: (1) a favorable electrostatic interaction (originally identified by Houk and List) between the NCH(δ+) group of the enamine intermediate and the (δ-)O[double bond, length as m-dash]C of benzaldehyde; (2) a C-H/π interaction between the cyclohexene group of the enamine intermediate and the benzaldehyde phenyl ring; (3) a stabilizing contact between an ortho-hydrogen of the phenyl and an oxygen of the carboxylic acid group of the enamine. These three interactions have been directly computed using F-SAPT, which confirms the stabilizing interaction between an ortho-hydrogen and the carboxylic acid in the (S,S) and (R,S) transition state stereoisomers. F-SAPT analysis also finds stabilizing dispersion and electrostatic interactions due to a C-H/π interaction between the cyclohexene and phenyl groups in the (S,S) and (R,R) transition states. However, unfavorable exchange-repulsion cancels the attractive terms that favor these stereoisomers. Surprisingly, the interaction thought to be most important for stereoselectivity, the NCH(δ+)(δ-)O[double bond, length as m-dash]C interaction, is actually found to be repulsive due to the negative charge on the nitrogen. Hence, our results indicate that geometric analysis and/or density-based analysis does not necessarily produce a reliable picture of non-covalent stabilization. As confirmed by high-level coupled-cluster computations, intermolecular interaction energies are strongest for the (R,R) transition states, which are not the experimentally favored products. This suggests that at least for this reaction, stereoselectivity is also strongly dependent on the energy required to distort the reacting molecules into the transition state geometry. PMID:27020417

  4. Intermolecular electrostatic energies using density fitting.

    PubMed

    Cisneros, G Andrs; Piquemal, Jean-Philip; Darden, Thomas A

    2005-07-22

    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

  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. 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

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

    PubMed

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

    2015-12-21

    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. Impact of protein/protein interactions on global intermolecular translocation rates of the transcription factors Sox2 and Oct1 between DNA cognate sites analyzed by z-exchange NMR spectroscopy.

    PubMed

    Takayama, Yuki; Clore, G Marius

    2012-08-01

    Oct1 and Sox2 synergistically regulate developmental genes by binding to adjacent sites within promoters. We have investigated the kinetics of global intermolecular translocation of Sox2 and Oct1 between cognate sites located on different DNA molecules by z-exchange NMR spectroscopy. In the Hoxb1 promoter, the Sox2 and Oct1 sites are immediately adjacent to one another, and the intermolecular translocation rates are too slow to be measured by z-exchange spectroscopy. By introducing a 3-bp insertion between the Sox2 and Oct1 sites to mimic the spacing in the FGF4 enhancer, the interprotein contact surface is reduced, and the translocation rates are increased. Interaction between Sox2 and the POU-specific domain (POU(S)) of Oct1 does not affect the translocation mechanism but modulates the rates. Translocation involves only jumping (dissociation and reassociation) for Sox2, but both jumping and direct intersegment transfer (no dissociation into free solution) for Oct1. The dissociation (k(off) ∼1.5 s(-1)) and association (k(on) ∼5.1 × 10(9) m(-1)s(-1)) rate constants for Sox2 are reduced 4-fold and increased 5-fold, respectively, in the presence of Oct1. k(off) (∼3.5 s(-1)) for Oct1 is unaffected by Sox2, whereas k(on) (∼1.3 × 10(9) m(-1)s(-1)) is increased ∼13-fold. The direct intermolecular translocation rate (k(inter) ∼1.8 × 10(4) m(-1)s(-1)) for the POU(S) domain of Oct1 is reduced 2-fold by Sox2, whereas that for the POU homeodomain (POU(HD)) of Oct1 (k(inter) ∼ 1.7 × 10(4) m(-1)s(-1)) remains unaltered, consistent with the absence of contacts between Sox2 and POU(HD). The data suggest a model for the sequence of binding events involved in synergistic gene regulation by Sox2 and Oct1. PMID:22718759

  9. Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111)

    NASA Astrophysics Data System (ADS)

    Müller, Moritz; Diller, Katharina; Maurer, Reinhard J.; Reuter, Karsten

    2016-01-01

    We employ dispersion-corrected density-functional theory to study the adsorption of tetrapyrrole 2H-porphine (2H-P) at Cu(111) and Ag(111). Various contributions to adsorbate-substrate and adsorbate-adsorbate interactions are systematically extracted to analyze the self-assembly behavior of this basic building block to porphyrin-based metal-organic nanostructures. This analysis reveals a surprising importance of substrate-mediated van der Waals interactions between 2H-P molecules, in contrast to negligible direct dispersive interactions. The resulting net repulsive interactions rationalize the experimentally observed tendency for single molecule adsorption.

  10. Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111).

    PubMed

    Müller, Moritz; Diller, Katharina; Maurer, Reinhard J; Reuter, Karsten

    2016-01-14

    We employ dispersion-corrected density-functional theory to study the adsorption of tetrapyrrole 2H-porphine (2H-P) at Cu(111) and Ag(111). Various contributions to adsorbate-substrate and adsorbate-adsorbate interactions are systematically extracted to analyze the self-assembly behavior of this basic building block to porphyrin-based metal-organic nanostructures. This analysis reveals a surprising importance of substrate-mediated van der Waals interactions between 2H-P molecules, in contrast to negligible direct dispersive interactions. The resulting net repulsive interactions rationalize the experimentally observed tendency for single molecule adsorption. PMID:26772581

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

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-01

    We report numerical simulations based on a non-Markovian density matrix propagation scheme of singlet fission (SF) in molecular crystals. Ab initio electronic structure calculations were used to parametrize the exciton and phonon Hamiltonian as well as the interactions between the exciton and the intramolecular and intermolecular vibrational modes. We demonstrate that the interactions of the exciton with intermolecular vibrational modes are highly sensitive to the stacking geometry of the crystal and can, in certain cases, significantly accelerate SF. This result may help in understanding the fast SF experimentally observed in a broad range of molecular crystals and offers a new direction for the engineering of efficient SF sensitizers. PMID:26261948

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

    PubMed Central

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

    2015-01-01

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

  13. Roles of intramolecular and intermolecular interactions in functional regulation of the Hsp70 J-protein co-chaperone Sis1.

    PubMed

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

    2015-04-10

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

  14. 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.

  15. Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an ab initio, SAPT and QTAIM study.

    PubMed

    Esrafili, Mehdi D

    2012-05-01

    We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene-BX(3) complexes, where X = H, OH, NH(2), CH(3), CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B-C(carbene) interaction due to the short B-C(carbene) distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH(2) > OH > CH(3) > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with nabla(2)ρ(BCP) >0, the B-C(carbene) bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ(BCP)) and H(BCP) <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B-C(carbene) bond is a polar covalent bond. PMID:21877151

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

    NASA Astrophysics Data System (ADS)

    Cody, Vivian; Murray-Rust, Peter

    1984-02-01

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

  17. Structural variability and new intermolecular interactions of Z-DNA in crystals of d(pCpGpCpGpCpG).

    PubMed Central

    Malinina, L; Tereshko, V; Ivanova, E; Subirana, J A; Zarytova, V; Nekrasov, Y

    1998-01-01

    We have determined the single crystal x-ray structure of the synthetic DNA hexamer d(pCpGpCpGpCpG) in two different crystal forms. The hexamer pCGCGCG has the Z-DNA conformation and in both cases the asymmetric unit contains more than one Z-DNA duplex. Crystals belong to the space group C222(1) with a = 69.73, b = 52.63, and c = 26.21 A, and to the space group P2(1) with a = 49.87, b = 41.26, c = 21.91 A, and gamma = 97.12 degrees. Both crystals show new crystal packing modes. The molecules also show striking new features when compared with previously determined Z-DNA structures: 1) the bases in one duplex have a large inclination with respect to the helical axis, which alters the overall shape of the molecule. 2) Some cytosine nitrogens interact by hydrogen bonding with phosphates in neighbor molecules. Similar base-phosphate interactions had been previously detected in some B-DNA crystals. 3) Basepair stacking between the ends of neighbor molecules is variable and no helical continuity is maintained between contiguous hexamer duplexes. PMID:9591674

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

    NASA Astrophysics Data System (ADS)

    Spiess, Hans Wolfgang

    2011-12-01

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

  19. Spin and orbital exchange interactions from Dynamical Mean Field Theory

    NASA Astrophysics Data System (ADS)

    Secchi, A.; Lichtenstein, A. I.; Katsnelson, M. I.

    2016-02-01

    We derive a set of equations expressing the parameters of the magnetic interactions characterizing a strongly correlated electronic system in terms of single-electron Green's functions and self-energies. This allows to establish a mapping between the initial electronic system and a spin model including up to quadratic interactions between the effective spins, with a general interaction (exchange) tensor that accounts for anisotropic exchange, Dzyaloshinskii-Moriya interaction and other symmetric terms such as dipole-dipole interaction. We present the formulas in a format that can be used for computations via Dynamical Mean Field Theory algorithms.

  20. 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…

  1. 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

  2. Intermolecular artifacts in probe microscope images of C60 assemblies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  3. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

    PubMed

    Gresh, Nohad; Sponer, Judit E; Devereux, Mike; Gkionis, Konstantinos; de Courcy, Benoit; Piquemal, Jean-Philip; Sponer, Jiri

    2015-07-30

    Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds of nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of noncanonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on 14 stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for the results of high-level quantum chemistry (QC) on the total interaction energies, and the individual energy contributions and their nonisotropic behaviors. Good agreements are found at both uncorrelated HF and correlated DFT and CCSD(T) levels. Resorting in SIBFA to distributed QC multipoles and to an explicit representation of the lone pairs is essential to respectively account for the anisotropies of the Coulomb and of the exchange-repulsion QC contributions. PMID:26119247

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

  5. Energy exchange in systems of particles with nonreciprocal interaction

    NASA Astrophysics Data System (ADS)

    Vaulina, O. S.; Lisina, I. I.; Lisin, E. A.

    2015-10-01

    A model is proposed to describe the sources of additional kinetic energy and its redistribution in systems of particles with a nonreciprocal interaction. The proposed model is shown to explain the qualitative specific features of the dust particle dynamics in the sheath region of an RF discharge. Prominence is given to the systems of particles with a quasi-dipole-dipole interaction, which is similar to the interaction induced by the ion focusing effects that occur in experiments on a laboratory dusty plasma, and with the shadow interaction caused by thermophoretic forces and Le Sage's forces.

  6. 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.

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

    PubMed

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

    2009-10-22

    When heated above room temperature, some crystalline polymorphs of the 1,3-bis(hydroxyalkylamino)-4,6-dinitrobenzenes (BDBn, n = 2-5), bis(hydroxyalkyl) analogues of the intramolecular charge-transfer molecule 1,3-diamino-4,6-dinitrobenzene, exhibit "dual" thermochromism: gradual color change from yellow to orange at lower temperatures, and sharp color change from orange to red at higher temperatures. These two thermochromic changes are related to different solid-state processes. When allowed to cool to room temperature, the yellow color of the thermochromic molecules with different alkyl length (n) is recovered with unexpectedly different kinetics, the order of the respective rate constants ranging from 10(-7)-10(-6) s(-1) for BDB2 to about 0.1 s(-1) in the case of BDB3. The thermochromic mechanism and the reasons behind the different kinetics were clarified on the basis of detailed crystallographic characterization, kinetic thermoanalysis, and spectroscopic study of eight crystalline forms (seven polymorphs and one solvate). It was found that the polymorphism is due to the possibility of "locking" and "unlocking" of the alkyl arms by formation of a strong intramolecular hydrogen bond between the hydroxyl groups at their hydroxyl termini. The locking of BDB2, with shortest alkyl arms, is reversible and it can be controlled thermally; either of the two conformations can be obtained in the solid state by proper thermal treatment. By use of high temperature in situ single crystal X-ray diffraction analysis of BDB3, direct evidence was obtained that the gradual thermochromic change is related to increased distance and weakened pi-pi interactions between the stacked benzene rings: the lattice expands preferably in the stacking direction, causing enhanced oscillator strength and red shift of the absorption edge of the intramolecular charge transfer transition. The second, sharp thermochromic change had been assigned previously to solid-solid phase transition triggered by intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular pi-pi interactions and thermal intramolecular proton transfer to aromatic nitro group. PMID:19780605

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

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

    When heated above room temperature, some crystalline polymorphs of the 1,3-bis(hydroxyalkylamino)-4,6-dinitrobenzenes (BDBn, n = 2-5), bis(hydroxyalkyl) analogues of the intramolecular charge-transfer molecule 1,3-diamino-4,6-dinitrobenzene, exhibit "dual" thermochromism: gradual color change from yellow to orange at lower temperatures, and sharp color change from orange to red at higher temperatures. These two thermochromic changes are related to different solid-state processes. When allowed to cool to room temperature, the yellow color of the thermochromic molecules with different alkyl length (n) is recovered with unexpectedly different kinetics, the order of the respective rate constants ranging from 10-7-10-6 s-1 for BDB2 to about 0.1 s-1 in the case of BDB3. The thermochromic mechanism and the reasons behind the different kinetics were clarified on the basis of detailed crystallographic characterization, kinetic thermoanalysis, and spectroscopic study of eight crystalline forms (seven polymorphs and one solvate). It was found that the polymorphism is due to the possibility of "locking" and "unlocking" of the alkyl arms by formation of a strong intramolecular hydrogen bond between the hydroxyl groups at their hydroxyl termini. The locking of BDB2, with shortest alkyl arms, is reversible and it can be controlled thermally; either of the two conformations can be obtained in the solid state by proper thermal treatment. By use of high temperature in situ single crystal X-ray diffraction analysis of BDB3, direct evidence was obtained that the gradual thermochromic change is related to increased distance and weakened π-π interactions between the stacked benzene rings: the lattice expands preferably in the stacking direction, causing enhanced oscillator strength and red shift of the absorption edge of the intramolecular charge transfer transition. The second, sharp thermochromic change had been assigned previously to solid-solid phase transition triggered by intramolecular proton transfer of one amino proton to the nitro group, whereupon an aci-nitro form is thermally populated. Contrary to the numerous examples of solid thermochromic molecules based on either pericyclic reactions or keto-enol tautomerism, this system appears to be the first organic thermochromic family where the thermochromic change appears as an effect of intermolecular π-π interactions and thermal intramolecular proton transfer to aromatic nitro group.

  9. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

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

    2010-09-07

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

  10. Quantum dynamics with strongly interacting Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Qian, Jing; Zhou, Lu; Zhao, Xingdong; Zhang, Weiping; East China Normal University Collaboration; Henan Normal University Collaboration

    2014-03-01

    Rydberg atoms with high principal quantum number have exaggerated atomic properties, including strong dipole-dipole interactions, long radiative lifetimes and so on. These properties can provide intriguing routes to study attractive quantum many-body dynamics. In this talk, we present three research works with strongly interacting Rydberg atoms. We study quantum non-equilibrium phases of Rydberg atoms in cubic and triangular optical lattices and find exotic quantum phases such as uniform phase, antiferromagnetic phase, and oscillatory phase. In some parameter areas, bi-stability phase can be observable. Except that, in a triangle lattice, we also identify dynamical chaos effect in the strong-interaction limit. Besides, depending on the strong dipole-dipole interactions between Rydberg states, Rydberg blockade effect appears. In a more recent work, we find the effective two-atom-blockade spherical model can reveal anisotropic deformation and shrunken properties when the real number of atoms increases from two to three in few-tom systems. These results will all be discussed in the talk. We acknowledge support from NSFC No. 11104076 and the Specialized Research Fund for the Doctoral Program of Higher Education No.20110076120004.

  11. Pattern formation in systems with competing interactions

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Lebowitz, Joel L.; Lieb, Elliott H.

    2009-01-01

    There is a growing interest, inspired by advances in technology, in the low temperature physics of thin films. These quasi-2D systems show a wide range of ordering effects including formation of striped states, reorientation transitions, bubble formation in strong magnetic fields, etc. The origins of these phenomena are, in many cases, traced to competition between short ranged exchange ferromagnetic interactions, favoring a homogeneous ordered state, and the long ranged dipole-dipole interaction, which opposes such ordering on the scale of the whole sample. The present theoretical understanding of these phenomena is based on a combination of variational methods and a variety of approximations, e.g., mean-field and spin-wave theory. The comparison between the predictions of these approximate methods and the results of MonteCarlo simulations are often difficult because of the slow relaxation dynamics associated with the long-range nature of the dipole-dipole interactions. In this note we will review recent work where we prove existence of periodic structures in some lattice and continuum model systems with competing interactions. The continuum models have also been used to describe micromagnets, diblock polymers, etc.

  12. Intermolecular domain docking in the hairpin ribozyme

    PubMed Central

    Sumita, Minako; White, Neil A.; Julien, Kristine R.; Hoogstraten, Charles G.

    2013-01-01

    The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodynamics and kinetics of the docking process using constructs in which loop A and loop B reside on separate molecules. Using a novel CD difference assay to isolate the effects of metal ions linked to domain docking, we find the intermolecular docking process to be driven by sub-millimolar concentrations of the exchange-inert Co(NH3)63+. RNA self-cleavage requires binding of lower-affinity ions with greater apparent cooperativity than the docking process itself, implying that, even in the absence of direct coordination to RNA, metal ions play a catalytic role in hairpin ribozyme function beyond simply driving loop-loop docking. Surface plasmon resonance assays reveal remarkably slow molecular association, given the relatively tight loop-loop interaction. This observation is consistent with a “double conformational capture” model in which only collisions between loop A and loop B molecules that are simultaneously in minor, docking-competent conformations are productive for binding. PMID:23324606

  13. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

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

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

    NASA Astrophysics Data System (ADS)

    Lee, Alex; Kim, Minjung; Chelikowsky, James

    2015-03-01

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

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  17. 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.

  18. 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.

  19. The role of directed van der Waals bonded interactions in the determination of the structures of molecular arsenate solids

    NASA Astrophysics Data System (ADS)

    Gibbs, G. V.; Wallace, A. F.; Cox, D. F.; Dove, P. M.; Downs, R. T.; Ross, N. L.; Rosso, K. M.

    2008-12-01

    On the basis of his famous electrostatic theorem, Feynman (1939) showed that it is not the fluctuating dipole- dipole interactions among neighboring molecules that lead to van der Waals forces, but rather it is the net attraction of the nuclei for the distorted electron density, ED, accumulated between the nuclei of bonded atoms that accounts for the van der Waals R-7 forces. Bader and his coworkers (1990) have since concluded that the distortions in the internuclear region arise by dint of the formation of local maxima and minima of the Laplacian distribution, L(r) = ▽2ρ(r), with the formation of van der Waals bond paths associated with the maxima and minima. The maxima are ascribed to Lewis base domains where the ED is locally charge concentrated, CC, whereas the minima are ascribed to Lewis acid domains where the ED is locally charge depleted, CD. For the As2O3 molecular crystals arsenolite, claudetite I and claudetite II, AsO2 and the As- metalloid, arsenolamprite, the ED of the constituent molecules were found to adopt a configuration where the Lewis acid and base domains of molecules are aligned and connected by As-O, O-O and As-As van der Waals intermolecular bond paths. Despite the relative weakness of the van der Waals bonded interactions relative to the intramolecular As-O bonded interactions, the interactions are concluded to serve as mainstays for the individual molecules in each of the molecular solids. Intermolecular As-O bond paths between the bonded atoms connect Lewis base CC and Lewis acid CD domains whereas the O-O and As-As paths connect Lewis base-pair CC-CC domains and Lewis acid pair CD-CD domains, respectively, give rise to sets of directed van der Waals bond paths. The alignment of the bond paths, like any other bond path, results in the periodic structures adopted by the molecules in the arsenates. The cubic structure adopted by arsenolite polymorph can be understood in terms of sets of As-O and O-O directed bond paths that radiate from the tetrahedral faces of its constituent molecules, serving as face-to-face Fischer key-lock mainstays in forming a periodic tetrahedral array of molecules. The arrangements of the As atoms in the claudetite polymorphs of As2O3 and those in the As metalloid arsenolamprite are similar. The arrangement of the molecules in the thiosulfides realgar, AsS, alancranite, AsS, α-dimorphite, As4S3 and uzonite, As4S5 can also be understood in terms of the Lewis domains and the van der Waals bond paths that radiate from the faces of the constituient molecules. Like the two clausetite polymorphs, arsenolamprite is a molecular solid bound by relatively weak intermolecular van der Waals bonded interactions. The bond critical point and local energy density properties of the intermolecular As-As interactions in arsenolamprite are comparable with those in claudetite I. As such, the structure of claudetite I can be viewed in large part as a stuffed derivative of the arsenolamprite structure with O atoms between pairs of As atoms comprising the layers of the structure.

  20. Intermolecular Vibrations of Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, Michael Roy Casselman

    Hydrophobic amino acids interact with their chemical environment through a combination of electrostatic, hydrogen bonding, dipole, induced dipole, and dispersion forces. These interactions all have their own characteristic energy scale and distance dependence. The low-frequency (0.1-5 THz, 5-150 cm-1) vibrational modes of amino acids in the solid state are a direct indicator of the interactions between the molecules, which include interactions between an amino acid functional group and its surroundings. This information is central to understanding the dynamics and morphology of proteins. The alpha-carbon is a chiral center for all of the hydrophobic amino acids, meaning that they exist in two forms, traditionally referred to as L- and D-enantiomers. This nomenclature indicates which direction the molecule rotates plane-polarized visible light (levorotory and dextrorotory). Chiral a-amino acids in proteins are exclusively the L-variety In the solid state, the crystal lattice of the pure L-enantiomer is the mirror image of the D-enantiomer crystal lattice. These solids are energetically identical. Enantiomers also have identical spectroscopic properties except when the measurement is polarization sensitive. A mixture of equal amounts D- and L-amino acid enantiomers can crystallize into a racemic (DL-) structure that is different from that of the pure enantiomers. Whether a solution of both enantiomers will crystallize into a racemic form or spontaneously resolve into a mixture of separate D- and L-crystals largely depends on the interactions between molecules available in the various possible configurations. This is an active area of research. Low-frequency vibrations with intermolecular character are very sensitive to changes in lattice geometry, and consequently the vibrational spectra of racemic crystals are usually quite distinct from the spectra of the crystals of the corresponding pure enantiomers in the far-infrared (far-IR). THz time-domain spectroscopy (THz-TDS) was used to measure the absorption spectra of low-frequency vibrational modes for a variety of hydrophobic amino acids in the solid (polycrystalline) state. The THz-TDS technique uses ultrafast (<50 fs) pulses of light from a visible/near-IR laser to generate single-cycle pulses of THz (far-IR) light. Pulses from the ultrafast laser are also used to coherently gate a THz detector, allowing phase-sensitive measurements of the THz electric field. In some cases, Raman scattering spectra of some of the polycrystalline hydrophobic amino acid samples were measured as well, in this case using an Ar+ laser and a triple monochromator to detect signals at the low Raman-shift values corresponding to the far-IR. THz-TDS was used to measure the low-frequency vibrational absorption spectra of pure L- and pure D-valine crystals as well as the racemic cocrystal, DL-valine. As expected, the Land D-valine THz-TDS absorption spectra are identical to one another (they are enantiomorphous crystals) but very different from the spectrum of DL-valine. In the process of these experiments, it was discovered that it was possible to prepare two distinct polymorphs (different crystalline arrangements) of DL-valine by varying the conditions under which stock material was recrystallized. Once crystallized in a particular form, both polymorphs remained (meta)stable at all temperatures investigated (from 80 K to room temperature), i.e., no phase transformation was observed. The THz-TDS and Raman spectra of the two polymorphs of DL-valine were measured. In addition, THz-TDS and Raman spectra of DL-leucine were measured; this substance has a crystal structure closely analagous to one of the DL-valine polymorphs. The temperature-dependence of the THz-TDS spectrum of each material was also measured. At lower temperatures, it is generally expected that intermolecular vibration frequencies increase (blueshift) due to a shrinking unit cell (effectively squeezing the oscillator potential into a smaller space). While most peaks were indeed observed to blueshift as the sample was cooled, the temperature dependence of the peak position and intensity varied significantly for different modes: while some peaks were hardly affected by the decreasing temperature, others sharpened and/or blueshifted appreciably. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals dispersion interactions between the molecules are not accounted for in standard density functional theory (DFT). However, recent advances in theory have made it possible to incorporate these non-local electron correlation forces within the framework of DFT. In addition to carrying out these calculations, methods for comparing results from different theoretical models were devised and evaluated. Perhaps most significantly, a new approach was developed to allow for concise description and easy comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements.

  1. Electron-mediated nuclear-spin interactions between distant nitrogen-vacancy centers.

    PubMed

    Bermudez, A; Jelezko, F; Plenio, M B; Retzker, A

    2011-10-01

    We propose a scheme enabling controlled quantum coherent interactions between separated nitrogen-vacancy centers in diamond in the presence of strong magnetic fluctuations. The proposed scheme couples nuclear qubits employing the magnetic dipole-dipole interaction between the electron spins and, crucially, benefits from the suppression of the effect of environmental magnetic field fluctuations thanks to a strong microwave driving. This scheme provides a basic building block for a full-scale quantum-information processor or quantum simulator based on solid-state technology. PMID:22107276

  2. Electron-Mediated Nuclear-Spin Interactions between Distant Nitrogen-Vacancy Centers

    NASA Astrophysics Data System (ADS)

    Bermudez, A.; Jelezko, F.; Plenio, M. B.; Retzker, A.

    2011-10-01

    We propose a scheme enabling controlled quantum coherent interactions between separated nitrogen-vacancy centers in diamond in the presence of strong magnetic fluctuations. The proposed scheme couples nuclear qubits employing the magnetic dipole-dipole interaction between the electron spins and, crucially, benefits from the suppression of the effect of environmental magnetic field fluctuations thanks to a strong microwave driving. This scheme provides a basic building block for a full-scale quantum-information processor or quantum simulator based on solid-state technology.

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

    NASA Astrophysics Data System (ADS)

    Zhang, Peng; Jie, Jianwen

    2014-12-01

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

  4. Visualizing the orientational dependence of an intermolecular potential

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  5. Visualizing the orientational dependence of an intermolecular potential

    PubMed Central

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

    2016-01-01

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

  6. Electrostatic protein-protein interactions: Comparison of point-dipole and finite-length dipole potentials of mean force

    SciTech Connect

    Coen, C.J.; Newman, J.; Blanch, H.W.; Prausnitz, J.M.

    1996-01-15

    Based on summation of Coulombic interactions, a model is developed for finite-length dipole potentials of mean force in a salt-free dielectric continuum. Point-dipole and finite-length dipole potentials of mean force are compared for protein-protein interactions using parameters for bovine {alpha}-chymotrypsin. The two approximations made in the commonly used analytical point-dipole potentials of mean force are not valid at distances near contact. Relative to the finite-length dipole model, the high-temperature approximation overpredicts, and the point-dipole approximation underpredicts charge-dipole and dipole-dipole attractions.

  7. An improved intermolecular potential for sulfur hexafluoride

    SciTech Connect

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

    1991-01-15

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

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

    SciTech Connect

    Astrakharchik, G. E.; Boronat, J.; Casulleras, J.; Kurbakov, I. L.; Lozovik, Yu. E.

    2007-06-15

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

  9. Thermodynamic curvature for attractive and repulsive intermolecular forces.

    PubMed

    May, Helge-Otmar; Mausbach, Peter; Ruppeiner, George

    2013-09-01

    The thermodynamic curvature scalar R for the Lennard-Jones system is evaluated in phase space, including vapor, liquid, and solid state. We paid special attention to the investigation of R along vapor-liquid, liquid-solid, and vapor-solid equilibria. Because R is a measure of interaction strength, we traced out the line R=0 dividing the phase space into regions with effectively attractive (R<0) or repulsive (R>0) interactions. Furthermore, we analyzed the dependence of R on the strength of attraction applying a perturbation ansatz proposed by Weeks-Chandler-Anderson. Our results show clearly a transition from R>0 (for poorly repulsive interaction) to R<0 when loading attraction in the intermolecular potential. PMID:24125229

  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; Arıcan, 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. Intermolecular dimerization with pillared layered clay templates.

    SciTech Connect

    Wiederrecht, G. P.; Sandi, G.; Carrado, K. A.; Seifert, S.; Chemistry

    2001-11-19

    Solutions of pyrene in the presence of a pillared, layered montmorillonite clay produce hybrid organic-inorganic materials with substantial molecular loading in the gallery regions between the clay layers. The results are in sharp contrast to other aromatics, such as benzene, naphthalene, or perylene, which show minimal incorporation of the molecules into the gallery regions of the clay. We present evidence that the unusual affinity for pyrene to form intermolecular dimers is the reason for the high loading. Pyrene monomers are easily introduced to the layers. Through steric hindrance, subsequent intermolecular dimer formation is allowed, and they are captured by the pillared, layered structure. CW and time-resolved emission spectra strongly indicate the presence of face-to-face intermolecular dimers (excimers) within the clay galleries. The combination of the ease of high molecular loading into an inorganic, high aspect ratio template and the collective optical properties of the organic layer may be useful as a new means to create hybrid structures.

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

    PubMed

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

    2009-10-14

    Electrical interactions between molecular vibrations can be non-linear and thereby produce intermolecular coupling even in the absence of a chemical bond. We use this fact to detect the formation of an intermolecular complex using electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) and also to determine the distance and angle between the two molecular species. PMID:19774270

  13. Motile Microbots from Dynamically Interacting and Self-Reconfiguring Assemblies of Metallo-Dielectric Janus Microcubes

    NASA Astrophysics Data System (ADS)

    Han, Koohee; Shields, C. Wyatt, IV; Bharti, Bhuvnesh; Lopez, Gabriel P.; Velev, Orlin D.

    A new class of dynamically and reversibly reconfigurable active matter made by magnetic assembly and actuation of metallo-dielectric microcubes will be presented. We describe how magnetically responsive Janus microcubes can be assembled hierarchically into dynamically reconfiguring microclusters. Ferromagnetic cobalt patches of the cubes act as assembly directors. The residual magnetic polarization of the metal-coated facets leads to directional dipole-dipole and field-dipole interactions and reconfiguration of the neighboring cubic particles, which is directed by the conformational restrictions. Dynamic reconfiguration of assembled clusters can be achieved by on-demand switching between the dipole-field interaction and the residual dipole-dipole interaction when the field is turned on and off. We show how pre-assembled Janus microcube clusters can be directionally motile in non-Newtonian fluids by applying asymmetric magnetic fields. The modulation of the viscosity of non-Newtonian fluids upon varying the shear rate allowed demonstrating directional motion, resulting from time-asymmetric stroke patterns (e.g., rapid opening and slow closing). These motile clusters can serve as early prototypes of self-propelling microswimmers capable of in-situ assembly. NSF Grant #DMR-1121107.

  14. Measurement of untruncated nuclear spin interactions via zero- to ultralow-field nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Blanchard, J. W.; Sjolander, T. F.; King, J. P.; Ledbetter, M. P.; Levine, E. H.; Bajaj, V. S.; Budker, D.; Pines, A.

    2015-12-01

    Zero- to ultralow-field nuclear magnetic resonance (ZULF NMR) provides a new regime for the measurement of nuclear spin-spin interactions free from the effects of large magnetic fields, such as truncation of terms that do not commute with the Zeeman Hamiltonian. One such interaction, the magnetic dipole-dipole coupling, is a valuable source of spatial information in NMR, though many terms are unobservable in high-field NMR, and the coupling averages to zero under isotropic molecular tumbling. Under partial alignment, this information is retained in the form of so-called residual dipolar couplings. We report zero- to ultralow-field NMR measurements of residual dipolar couplings in acetonitrile-2-13C aligned in stretched polyvinyl acetate gels. This permits the investigation of dipolar couplings as a perturbation on the indirect spin-spin J coupling in the absence of an applied magnetic field. As a consequence of working at zero magnetic field, we observe terms of the dipole-dipole coupling Hamiltonian that are invisible in conventional high-field NMR. This technique expands the capabilities of zero- to ultralow-field NMR and has potential applications in precision measurement of subtle physical interactions, chemical analysis, and characterization of local mesoscale structure in materials.

  15. Intermolecular forces and energies between ligands and receptors.

    PubMed

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

    1994-10-14

    The recognition mechanisms and dissociation pathways of the avidin-biotin complex and of actin monomers in actin filaments were investigated. The unbinding forces of discrete complexes of avidin or streptavidin with biotin analogs are proportional to the enthalpy change of the complex formation but independent of changes in the free energy. This result indicates that the unbinding process is adiabatic and that entropic changes occur after unbinding. On the basis of the measured forces and binding energies, an effective rupture length of 9.5 +/- 1 angstroms was calculated for all biotin-avidin pairs and approximately 1 to 3 angstroms for the actin monomer-monomer interaction. A model for the correlation among binding forces, intermolecular potential, and molecular function is proposed. PMID:7939660

  16. 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.

  17. Multi-layer coarse-graining polarization model for treating electrostatic interactions of solvated α-conotoxin peptides

    NASA Astrophysics Data System (ADS)

    Jiang, Nan; Ma, Jing

    2012-04-01

    A multi-layer coarse-graining (CG) model is presented for treating the electrostatic interactions of solvated α-conotoxin peptides. According to the sensitivity to the electrostatic environment, a hybrid set of electrostatic parameters, such as secondary-structure- and residue-based dipoles, and atom-centered partial charges, are adopted. For the polarization "inert" secondary-structures and residues, the fragment dipole moments are distributed within narrow ranges with the magnitude close to zero. The coarse-graining fragment dipoles are parameterized from a large training set (10 000 configurations) to reproduce the electrostatic features of molecular fragments. In contrast, the electrostatically "sensitive" atoms exhibit large fluctuations of charges with the varied environments. The environment-dependent variable charges are updated in each energetic calculation. The electrostatic interaction of the whole chemical system is hence partitioned into several sub-terms coming from the fragment dipole-dipole, (fragment) dipole-(atom) charge, and atom charge-charge interactions. A large number of test calculations on the relative energies of cyclo-peptide conformers have demonstrated that the multi-layer CG electrostatic model presents better performance than the non-polarized force fields, in comparison with the density-functional theory and the fully polarized force field model. The selection of CG fragment centers, mass or geometric center, has little influence on the fragment-based dipole-dipole interactions. The multi-layer partition of electrostatic polarization is expected to be applied to many biologically interesting and complicated phenomena.

  18. Multipole expansion in plasmas: Effective interaction potentials between compound particles

    NASA Astrophysics Data System (ADS)

    Ramazanov, T. S.; Moldabekov, Zh. A.; Gabdullin, M. T.

    2016-05-01

    In this paper, the multipole expansion method is used to determine effective interaction potentials between particles in both classical dusty plasma and dense quantum plasma. In particular, formulas for interactions of dipole-dipole and charge-dipole pairs in a classical nondegenerate plasma as well as in degenerate quantum and semiclassical plasmas were derived. The potentials describe interactions between atoms, atoms and charged particles, dust particles in the complex plasma, atoms and electrons in the degenerate plasma, and metals. Correctness of the results obtained from the multipole expansion is confirmed by their agreement with the results based on other methods of statistical physics and dielectric response function. It is shown that the method of multipole expansion can be used to derive effective interaction potentials of compound particles, if the effect of the medium on the potential of individual particles comprising compound particles is known.

  19. Maximizing Singlet Fission by Intermolecular Packing.

    PubMed

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

    2014-10-01

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

  20. Importance of Intermolecular Hydrogen Bonding for the Stereochemical Control of Allene-Enone (3+2) Annulations Catalyzed by a Bifunctional, Amino Acid Derived Phosphine Catalyst.

    PubMed

    Holland, Mareike C; Gilmour, Ryan; Houk, K N

    2016-02-01

    The origin of stereoselectivity in the (3+2) annulation of allenes and enones catalyzed by an amino acid derived phosphine catalyst has been investigated by the use of dispersion-corrected density functional theory. An intermolecular hydrogen bond between the intermediate zwitterion and the enone was found to be the key interaction in the two enantiomeric transition states. Additional stabilization is provided by intermolecular hydrogen-bonding interactions between acidic positions on the catalyst backbone and the substrate. Enantioselectivity occurs because the intermolecular hydrogen bond in the transition state leading to the minor enantiomer is only possible at the expense of reactant distortion. PMID:26732907

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

    SciTech Connect

    Muenter, J.S.

    1992-01-01

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

  2. 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

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

    PubMed

    Balraj, Chellamuthu; Elango, Kuppanagounder P

    2012-02-01

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

  4. Structure, vibrational spectra and DFT characterization of the intra- and inter-molecular interactions in 2-hydroxy-5-methylpyridine-3-carboxylic acid--normal modes of the eight-membered HB ring.

    PubMed

    Godlewska, P; Jańczak, J; Kucharska, E; Hanuza, J; Lorenc, J; Michalski, J; Dymińska, L; Węgliński, Z

    2014-01-01

    Fourier transform IR and Raman spectra, XRD studies and DFT quantum chemical calculations have been used to characterize the structural and vibrational properties of 2-hydroxy-5-methylpyridine-3-carboxylic acid. In the unit-cell of this compound two molecules related by the inversion center interact via OH⋯N hydrogen bonds. The double hydrogen bridge system is spaced parallel to the (102) crystallographic plane forming eight-membered arrangement characteristic for pyridine derivatives. The six-membered ring is the second characteristic unit formed via the intramolecular OH⋯O hydrogen bond. The geometry optimization of the monomer and dimer have been performed applying the Gaussian03 program package. All calculations were performed in the B3LYP/6-31G(d,p) basis set using the XRD data as input parameters. The relation between the molecular and crystal structures has been discussed in terms of the hydrogen bonds formed in the unit cell. The vibrations of the dimer have been discussed in terms of the resonance inside the system built of five rings coupled via hydrogen bonds. PMID:24184924

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

    SciTech Connect

    Fournier, Joseph A.; Wolke, Conrad T.; Johnson, Christopher J.; Johnson, Mark A. E-mail: mccoy@chemistry.ohio-state.edu; McCoy, Anne B. E-mail: mccoy@chemistry.ohio-state.edu

    2015-02-14

    We clarify the role of the critical imidazolium C{sub (2)}H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF{sub 4}] ionic liquid by analyzing the vibrational spectra of the bare EMIM{sup +} ion as well as that of the cationic [EMIM]{sub 2}[BF{sub 4}]{sup +} (EMIM{sup +} = 1-ethyl-3-methylimidazolium, C{sub 6}H{sub 11}N{sub 2}{sup +}) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D{sub 2} molecules formed in a 10 K ion trap. The C{sub (2)}H behavior is isolated by following the evolution of key vibrational features when the C{sub (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{sup +} 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{sup +} ⋅ ⋅ ⋅ BF{sub 4}{sup −} ⋅ ⋅ ⋅ EMIM{sup +} ternary complex, the C{sub (2)}H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM{sup +} 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{sub (2)}H is replaced by a methyl group are consistent with BF{sub 4}{sup −} attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    PubMed

    Salam, A

    2013-12-28

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

  9. 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.

  10. Unravelling the effect of interparticle interactions and surface spin canting in ?-Fe2O3@SiO2 superparamagnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Pereira, Andr M.; Pereira, Clara; Silva, Ana S.; Schmool, David S.; Freire, Cristina; Grenche, Jean-Marc; Arajo, Joo P.

    2011-06-01

    The present study investigates the magnetic properties of spherical monodispersed maghemite (?-Fe2O3) nanoparticles coated with multiple silica (SiO2) layers of different thicknesses, forming core-shell multifunctional nanomaterials. This study was performed using a combination of local probe techniques (Mssbauer spectrometry) and magnetization measurements. At room temperature, both techniques confirm the superparamagnetic state of the samples, even after being coated with the SiO2 shells. The zero-field-cooling-field-cooling magnetization curves of the silica-coated ?-Fe2O3 nanomaterials with different shell thicknesses allow the evaluation of the intensity of the interparticle dipole-dipole interactions. We estimate the interparticle energy within the framework of dipolar interaction models and relate it with the hyperfine parameters. We further observe that this dipole-dipole interaction increases the superparamagnetic energy barrier, which largely depends on the interparticle distance. Finally, we consider the effect of spin canting at the surface ("dead layer") of uncoated ?-Fe2O3 nanoparticles manifested by a layer of 0.5(1) nm.

  11. Evaporation of spherical particles with various models of the intermolecular-collision potential

    SciTech Connect

    Ivchenko, I.N.

    1985-07-01

    The quasisteady evaporation of drops of dibutyl sebacate in gases with arbitrary Knudsen numbers is investigated for various models of the intermolecular-interaction potential. Theoretical and experimental results are compared. The analysis shows that the theory of the evaporation of spherical drops developed here is in good agreement with experimental data; the difference between theory and experiment is almost an order of magnitude less.

  12. 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.

  13. 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.

  14. Fluorescence photoactivation by intermolecular proton transfer.

    PubMed

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

    2012-10-11

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

  15. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    NASA Astrophysics Data System (ADS)

    Gruodis, A.; Galikova, N.; Šarka, K.; Saulė, R.; Batiuškaitė, D.; Saulis, G.

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

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

    PubMed

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

    2008-08-27

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

  17. 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.

  18. 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.

  19. 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 ρ 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 + x4π 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.

  20. 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.

  1. Carbon dioxide-methanol intermolecular complexes in interstellar grain mantles

    NASA Astrophysics Data System (ADS)

    Dartois, E.; Demyk, K.; d'Hendecourt, L.; Ehrenfreund, P.

    1999-11-01

    We present new laboratory data to interpret the Infrared Space Observatory (ISO) spectra of protostellar objects, and particularly RAFGL7009S. Our experimental results show that solid methanol and carbon dioxide exhibit specific intermolecular interactions. We propose the formation of a Lewis acid-base complex between carbon dioxide and methanol molecules to explain specific substructure of the 15.2 mu m CO_2 bending mode observed in different objects. The various CO_2 bending mode patterns observed in many lines of sight can be interpreted as a combination of both this complex formation and the temperature evolution of the ices. The temperature induced segregation of ice mantles containing CO_2 can be monitored by the 13CO_2 stretching mode shift toward the pure CO_2 ice position. The large width observed for this mode towards interstellar sources partly results from the different temperatures sampled along the line of sight. Given the amount of methanol involved in RAFGL7009S, on the basis of ground based observations, we derive that about half of the so called ``6.85 mu m'' band and a quarter of the 4.9 mu m bands can be accounted for by the deformation modes and 2nu_8 transitions of CH_3OH. Based on observations with ISO, an ESA project with instruments funded by ESA Member States (especially the PI countries: France, Germany, the Netherlands and the United Kingdom) and with the participation of ISAS and NASA

  2. 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)

  3. Frontier orbital symmetry control of intermolecular electron transfer

    NASA Astrophysics Data System (ADS)

    Stevens, B.

    1990-11-01

    Research continued on the study of intermolecular electron transfer. The following topics are discussed: 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.

  4. 1H NMR Relaxation Investigation of Inhibitors Interacting with Torpedo californica Acetylcholinesterase

    NASA Astrophysics Data System (ADS)

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

    2000-05-01

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

  5. Van der Waals interactions among alkali Rydberg atoms with excitonic states

    NASA Astrophysics Data System (ADS)

    Zoubi, Hashem

    2015-09-01

    We investigate the influence of the appearance of excitonic states on van der Waals interactions among two Rydberg atoms. The atoms are assumed to be in different Rydberg states, e.g., in the | {ns}> and | {np}> states. The resonant dipole-dipole interactions yield symmetric and antisymmetric excitons, with energy splitting that give rise to new resonances as the atoms approach each other. Only away from these resonances can the van der Waals coefficients, C6sp, be defined. We calculate the C6 coefficients for alkali atoms and present the results for lithium by applying perturbation theory. At short interatomic distances of several μ {{m}}, we show that the widely used simple model of two-level systems for excitons in Rydberg atoms breaks down, and the correct representation implies multi-level atoms. Even though, at larger distances one can keep the two-level systems but in including van der Waals interactions among the atoms .

  6. 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.

  7. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water

    NASA Astrophysics Data System (ADS)

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-01

    Full classical molecular dynamics (MD) simulations of two-dimensional (2D) infrared-Raman and 2D Raman spectroscopies of liquid water were carried out to elucidate a mode-mode coupling mechanism using a polarizable water model for intermolecular and intramolecular vibrational spectroscopy (POLI2VS). This model is capable of describing both infrared and Raman spectra. Second-order response functions, which consist of one molecular polarizability and two molecular dipole moments for 2D IR-Raman and three molecular polarizabilities for 2D Raman spectroscopies, were calculated using an equilibrium-non-equilibrium hybrid MD approach. The obtained signals were analyzed using a multi-mode Brownian oscillator (BO) model with nonlinear system-bath interactions representing the intramolecular OH stretching, intramolecular HOH bending, hydrogen bonded (HB)-intermolecular librational motion and HB-intermolecular vibrational (translational) motion of liquid water. This model was applied through use of hierarchal Fokker-Planck equations. The qualitative features of the peak profiles in the 2D spectra obtained from the MD simulations are accurately reproduced with the BO model. This indicates that this model captures the essential features of the intermolecular and intramolecular motion. We elucidate the mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling, the nonlinearities of the polarizability and dipole moment, and the vibrational dephasing processes of liquid water even in the case that the 2D spectral peaks obtained from the MD simulation overlap or are unclear. The mode coupling peaks caused by electrical anharmonic coupling (EAHC) and mechanical anharmonic coupling (MAHC) are observed in all of the 2D spectra. We find that the strength of the MAHC between the OH-stretching and HB-intermolecular vibrational modes is comparable to that between the OH-stretching and HOH bending modes. Moreover, we find that this OH-stretching and HB-intermolecular vibrational coupling should be observed as off-diagonal cross peaks in the 2D spectra.

  8. Simulating two-dimensional infrared-Raman and Raman spectroscopies for intermolecular and intramolecular modes of liquid water.

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

    Full classical molecular dynamics (MD) simulations of two-dimensional (2D) infrared-Raman and 2D Raman spectroscopies of liquid water were carried out to elucidate a mode-mode coupling mechanism using a polarizable water model for intermolecular and intramolecular vibrational spectroscopy (POLI2VS). This model is capable of describing both infrared and Raman spectra. Second-order response functions, which consist of one molecular polarizability and two molecular dipole moments for 2D IR-Raman and three molecular polarizabilities for 2D Raman spectroscopies, were calculated using an equilibrium-non-equilibrium hybrid MD approach. The obtained signals were analyzed using a multi-mode Brownian oscillator (BO) model with nonlinear system-bath interactions representing the intramolecular OH stretching, intramolecular HOH bending, hydrogen bonded (HB)-intermolecular librational motion and HB-intermolecular vibrational (translational) motion of liquid water. This model was applied through use of hierarchal Fokker-Planck equations. The qualitative features of the peak profiles in the 2D spectra obtained from the MD simulations are accurately reproduced with the BO model. This indicates that this model captures the essential features of the intermolecular and intramolecular motion. We elucidate the mechanisms governing the 2D signal profiles involving anharmonic mode-mode coupling, the nonlinearities of the polarizability and dipole moment, and the vibrational dephasing processes of liquid water even in the case that the 2D spectral peaks obtained from the MD simulation overlap or are unclear. The mode coupling peaks caused by electrical anharmonic coupling (EAHC) and mechanical anharmonic coupling (MAHC) are observed in all of the 2D spectra. We find that the strength of the MAHC between the OH-stretching and HB-intermolecular vibrational modes is comparable to that between the OH-stretching and HOH bending modes. Moreover, we find that this OH-stretching and HB-intermolecular vibrational coupling should be observed as off-diagonal cross peaks in the 2D spectra. PMID:26896979

  9. 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.

  10. Comparing Contact and Dipolar Interactions in a Bose-Einstein Condensate

    NASA Astrophysics Data System (ADS)

    Griesmaier, Axel; Stuhler, Jürgen; Koch, Tobias; Fattori, Marco; Pfau, Tilman; Giovanazzi, Stefano

    2006-12-01

    We have measured the relative strength ɛdd of the magnetic dipole-dipole interaction compared with the contact interaction in a dipolar chromium Bose-Einstein condensate. We analyze the asymptotic velocities of expansion of the condensate with different orientations of the atomic magnetic moments. By comparing the experimental results with numerical solutions of the hydrodynamic equations for dipolar condensates, we obtain ɛdd=0.159±0.034. We use this result to determine the s-wave scattering length a=(5.08±1.06×10-9)m=(96±20)a0 of Cr52. This is fully consistent with our previous measurements on the basis of Feshbach resonances and therefore confirms the validity of the theoretical approach used to describe the dipolar Bose-Einstein condensate.

  11. Cooperative excitation and many-body interactions in a cold Rydberg gas.

    PubMed

    Viteau, Matthieu; Huillery, Paul; Bason, Mark G; Malossi, Nicola; Ciampini, Donatella; Morsch, Oliver; Arimondo, Ennio; Comparat, Daniel; Pillet, Pierre

    2012-08-01

    The dipole blockade of Rydberg excitations is a hallmark of the strong interactions between atoms in these high-lying quantum states [M. Saffman, T. G. Walker, and K. Mølmer, Rev. Mod. Phys. 82, 2313 (2010); D. Comparat and P. Pillet, J. Opt. Soc. Am. B 27, A208 (2010)]. One of the consequences of the dipole blockade is the suppression of fluctuations in the counting statistics of Rydberg excitations, of which some evidence has been found in previous experiments. Here we present experimental results on the dynamics and the counting statistics of Rydberg excitations of ultracold rubidium atoms both on and off resonance, which exhibit sub- and super-Poissonian counting statistics, respectively. We compare our results with numerical simulations using a novel theoretical model based on Dicke states of Rydberg atoms including dipole-dipole interactions, finding good agreement between experiment and theory. PMID:23006168

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

    PubMed

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

    2013-12-13

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

  13. Role of long-range intermolecular forces in the formation of inorganic nanoparticle clusters.

    PubMed

    Gibbs, G V; Crawford, T D; Wallace, A F; Cox, D F; Parrish, R M; Hohenstein, E G; Sherrill, C D

    2011-11-17

    An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite. PMID:21939256

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  15. Irreversible adiabatic decoherence of dipole-interacting nuclear-spin pairs coupled with a phonon bath

    NASA Astrophysics Data System (ADS)

    Domínguez, F. D.; González, C. E.; Segnorile, H. H.; Zamar, R. C.

    2016-02-01

    We study the quantum adiabatic decoherence of a multispin array, coupled with an environment of harmonic phonons, in the framework of the theory of open quantum systems. We follow the basic formal guidelines of the well-known spin-boson model, since in this framework it is possible to derive the time dependence of the reduced density matrix in the adiabatic time scale, without resorting to coarse-graining procedures. However, instead of considering a set of uncoupled spins interacting individually with the boson field, the observed system in our model is a network of weakly interacting spin pairs; the bath corresponds to lattice phonons, and the system-environment interaction is generated by the variation of the dipole-dipole energy due to correlated shifts of the spin positions, produced by the phonons. We discuss the conditions that the model must meet in order to fit within the adiabatic regime. By identifying the coupling of the dipole-dipole spin interaction with the low-frequency acoustic modes as the source of decoherence, we calculate the decoherence function of the reduced spin density matrix in closed way, and estimate the decoherence rate of a typical element of the reduced density matrix in one- and three-dimensional models of the spin array. Using realistic values for the various parameters of the model we conclude that the dipole-phonon mechanism can be particularly efficient to degrade multispin coherences, when the number of active spins involved in a given coherence is high. The model provides insight into the microscopic irreversible spin dynamics involved in the buildup of quasiequilibrium states and in the coherence leakage during refocusing experiments in nuclear magnetic resonance of crystalline solids.

  16. Chemical Exchange Saturation Transfer by Intermolecular Double Quantum Coherence

    PubMed Central

    Ling, Wen; Eliav, Uzi; Navon, Gil; Jerschow, Alexej

    2008-01-01

    A number of contrast enhancement effects based on the use of intermolecular multiple-quantum coherences, or distant dipolar field effects are known. This phenomenon is based on the dependence on the m-th power of the initial magnetization (where m is the coherence order used). In this article we describe the contrast enhancement based on chemical exchange saturation transfer and NOE, which is achieved by the use of intermolecular double-quantum coherences (iDQC). The method was validated using clinically relevant systems based on glycosaminoglycans and a sample of cartilage tissue, showing that the CEST contrast, as well as, NOE are enhanced by iDQC. PMID:18571444

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

    NASA Astrophysics Data System (ADS)

    Heßelmann, Andreas; Korona, Tatiana

    2014-09-01

    Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.

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

    PubMed

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

    2014-12-01

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

  19. 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

  20. 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…

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

    PubMed

    Collins, Karl D; Glorius, Frank

    2015-03-17

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

  2. From chaos to selective ordering of vortex cores in interacting mesomagnets.

    PubMed

    Jain, S; Novosad, V; Fradin, F Y; Pearson, J E; Tiberkevich, V; Slavin, A N; Bader, S D

    2012-01-01

    A spin vortex consists of an in-plane curling magnetization and a small core region (~10 nm) with out-of-plane magnetization. An oscillating field or current induce gyrotropic precession of the spin vortex. Dipole-dipole and exchange coupling between the interacting vortices may lead to excitation of collective modes whose frequencies depend on the core polarities. Here we demonstrate an effective method for controlling the relative core polarities in a model system of overlapping Ni(80)Fe(20) dots. This is achieved by driving the system to a chaotic regime of continuous core reversals and subsequently relaxing the cores to steady-state motion. It is shown that any particular core polarity combination (and therefore the spectral response of the entire system) can be deterministically preselected by tuning the excitation frequency or external magnetic field. We anticipate that this work would benefit the future development of magnonic crystals, spin-torque oscillators, magnetic storage and logic elements. PMID:23271662

  3. Revealing the signature of dipolar interactions in dynamic spectra of polydisperse magnetic nanoparticles.

    PubMed

    Ivanov, Alexey O; Zverev, Vladimir S; Kantorovich, Sofia S

    2016-04-13

    We investigate, via a modified mean field approach, the dynamic magnetic response of a polydisperse dipolar suspension to a weak, linearly polarised, AC field. We introduce an additional term into the Fokker-Planck equation, which takes into account dipole-dipole interaction in the form of the first order perturbation, and allows for particle polydispersity. The analytical expressions, obtained for the real and imaginary dynamic susceptibilities, predict three measurable effects: the increase of the real part low-frequency plateaux; the enhanced growth of the imaginary part in the low-frequency range; and the shift of the imaginary part maximum. Our theoretical predictions find an experimental confirmation and explain the changes in the spectrum. PMID:26890415

  4. Organophotocatalysis: Insights into the Mechanistic Aspects of Thiourea-Mediated Intermolecular [2+2] Photocycloadditions.

    PubMed

    Vallavoju, Nandini; Selvakumar, Sermadurai; Pemberton, Barry C; Jockusch, Steffen; Sibi, Mukund P; Sivaguru, Jayaraman

    2016-04-25

    Mechanistic investigations of the intermolecular [2+2] photocycloaddition of coumarin with tetramethylethylene mediated by thiourea catalysts reveal that the reaction is enabled by a combination of minimized aggregation, enhanced intersystem crossing, and altered excited-state lifetime(s). These results clarify how the excited-state reactivity can be manipulated through catalyst-substrate interactions and reveal a third mechanistic pathway for thiourea-mediated organo-photocatalysis. PMID:27005562

  5. 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

  6. The effect of intermolecular hydrogen bonding on the planarity of amides.

    PubMed

    Platts, James A; Maarof, Hasmerya; Harris, Kenneth D M; Lim, Gin Keat; Willock, David J

    2012-09-14

    Ab initio and density functional theory (DFT) calculations on some model systems are presented to assess the extent to which intermolecular hydrogen bonding can affect the planarity of amide groups. Formamide and urea are examined as archetypes of planar and non-planar amides, respectively. DFT optimisations suggest that appropriately disposed hydrogen-bond donor or acceptor molecules can induce non-planarity in formamide, with OCNH dihedral angles deviating by up to ca. 20° from planarity. Ab initio energy calculations demonstrate that the energy required to deform an amide molecule from the preferred geometry of the isolated molecule is more than compensated by the stabilisation due to hydrogen bonding. Similarly, the NH(2) group in urea can be made effectively planar by the presence of appropriately positioned hydrogen-bond acceptors, whereas hydrogen-bond donors increase the non-planarity of the NH(2) group. Small clusters (a dimer, two trimers and a pentamer) extracted from the crystal structure of urea indicate that the crystal field acts to force planarity of the urea molecule; however, the interaction with nearest neighbours alone is insufficient to induce the molecule to become completely planar, and longer-range effects are required. Finally, the potential for intermolecular hydrogen bonding to induce non-planarity in a model of a peptide is explored. Inter alia, the insights obtained in the present work on the extent to which the geometry of amide groups may be deformed under the influence of intermolecular hydrogen bonding provide structural guidelines that can assist the interpretation of the geometries of such groups in structure determination from powder X-ray diffraction data. PMID:22847473

  7. 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.

  8. Effect of spatial confinement on magnetic hyperthermia via dipolar interactions in Fe₃O₄ 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

  9. An intermolecular heterobimetallic system for photocatalytic water reduction.

    PubMed

    Hansen, Sven; Klahn, Marcus; Beweries, Torsten; Rosenthal, Uwe

    2012-04-01

    Teamwork: A new intermolecular heterobimetallic system for photocatalytic water reduction, consisting of a photosensitizer of the type [Ru(bpy)(2)(L)](PF(6))(2) (L=bidentate ligand), a dichloro palladium complex PdCl(2)(L) serving as the water reduction catalyst, and triethyl amine as electron donor, is presented. Variations of the ligand as well as of the palladium source results in a significant improvement of the performance of the catalyst system. PMID:22422641

  10. 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 μ 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 μ eV

  11. 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 μeV 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 μeV

  12. 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.

  13. Small Molecule Activation by Intermolecular Zr(IV)-Phosphine Frustrated Lewis Pairs.

    PubMed

    Metters, Owen J; Forrest, Sebastian J K; Sparkes, Hazel A; Manners, Ian; Wass, Duncan F

    2016-02-17

    We report intermolecular transition metal frustrated Lewis pairs (FLPs) based on zirconocene aryloxide and phosphine moieties that exhibit a broad range of small molecule activation chemistry that has previously been the preserve of only intramolecular pairs. Reactions with D2, CO2, THF, and PhCCH are reported. By contrast with previous intramolecular examples, these systems allow facile access to a variety of steric and electronic characteristics at the Lewis acidic and Lewis basic components, with the three-step syntheses of 10 new intermolecular transition metal FLPs being reported. Systematic variation to the phosphine Lewis base is used to unravel steric considerations, with the surprising conclusion that phosphines with relatively small Tolman steric parameters not only give highly reactive FLPs but are often seen to have the highest selectivity for the desired product. DOSY NMR spectroscopic studies on these systems reveal for the first time the nature of the Lewis acid/Lewis base interactions in transition metal FLPs of this type. PMID:26788963

  14. Intermolecular complexation and phase separation in aqueous solutions of oppositely charged biopolymers.

    PubMed

    Singh, S Santinath; Siddhanta, A K; Meena, Ramavatar; Prasad, Kamalesh; Bandyopadhyay, S; Bohidar, H B

    2007-07-01

    Turbidity measurements performed at 450nm were used to follow the process of complex formation, and phase separation in gelatin-agar aqueous solutions. Acid (Type-A) and alkali (Type-B) processed gelatin (polyampholyte) and agar (anionic polyelectrolyte) solutions, both having concentration of 0.1% (w/v) were mixed in various proportions, and the mixture was titrated (with 0.01 M HCl or NaOH) to initiate associative complexation that led to coacervation. The titration profiles clearly established observable transitions in terms of the solution pH corresponding to the first occurrence of turbidity (pH(C), formation of soluble complexes), and a point of turbidity maximum (pH(phi), formation of insoluble complexes). Decreasing the pH beyond pH(phi) drove the system towards precipitation. The values of pH(C) and pH(phi) characterized the initiation of the formation of intermolecular charge neutralized soluble aggregates, and the subsequent formation of microscopic coacervate droplets. These aggregates were characterized by dynamic light scattering. It was found that Type-A and -B gelatin samples formed soluble intermolecular complexes (and coacervates) with agar molecules through electrostatic and patch-binding interactions, respectively. PMID:17367849

  15. 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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  17. Intermolecular stabilization of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) compressed to 20 GPa.

    PubMed

    Chellappa, Raja S; Dattelbaum, Dana M; Coe, Joshua D; Velisavljevic, Nenad; Stevens, Lewis L; Liu, Zhenxian

    2014-08-01

    The room temperature stability of 3,3'-diamino-4,4'-azoxyfurazan (DAAF) has been investigated using synchrotron far-infrared, mid-infrared, Raman spectroscopy, and synchrotron X-ray diffraction (XRD) up to 20 GPa. The as-loaded DAAF samples exhibited subtle pressure-induced ordering phenomena (associated with positional disorder of the azoxy "O" atom) resulting in doubling of the a-axis, to form a superlattice similar to the low-temperature polymorph. Neither high pressure synchrotron XRD, nor high pressure infrared or Raman spectroscopies indicated the presence of structural phase transitions up to 20 GPa. Compression was accommodated in the unit cell by a reduction of the c-axis between the planar DAAF layers, distortion of the β-angle of the monoclinic lattice, and an increase in intermolecular hydrogen bonding. Changes in the ring and -NH2 deformation modes and increased intermolecular hydrogen bonding interactions with compression suggest molecular reorganizations and electronic transitions at ∼ 5 GPa and ∼ 10 GPa that are accompanied by a shifting of the absorption band edge into the visible. A fourth-order Birch-Murnaghan fit to the room temperature isotherm afforded an estimate of the zero-pressure isothermal bulk modulus, K0 = 12.4 ± 0.6 GPa and its pressure derivative K0' = 7.7 ± 0.3. PMID:25011055

  18. 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

  19. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions.

    PubMed

    Haubenreisser, Stefan; Wste, Thorsten H; Martnez, Claudio; Ishihara, Kazuaki; Muiz, Kilian

    2016-01-01

    Molecular structures of the most prominent chiral non-racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen-bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

  20. Intermolecular Peptide Cross-Linking by Using Diaminodicarboxylic Acids.

    PubMed

    Kamalov, Meder; Kaur, Harveen; Brimble, Margaret A

    2016-03-01

    Synthetic methods aimed at preparing peptides cross-linked by diaminodiacids remain an important chemical challenge. These cross-links are known to play a crucial role on the activity, structural stability, and folding of the host peptides and proteins. Recent developments in the syntheses of such systems have led to intriguing advances in the understanding of intermolecular side-chain cross-linking and the role that these structural motifs play in the biochemistry of proteins. Herein we provide an overview of the existing synthetic methodology that has been developed to effect protein cross-linking using diaminodiacids. PMID:26749083

  1. Structurally Defined Molecular Hypervalent Iodine Catalysts for Intermolecular Enantioselective Reactions

    PubMed Central

    Haubenreisser, Stefan; Wöste, Thorsten H.; Martínez, Claudio; Ishihara, Kazuaki

    2015-01-01

    Abstract Molecular structures of the most prominent chiral non‐racemic hypervalent iodine(III) reagents to date have been elucidated for the first time. The formation of a chirally induced supramolecular scaffold based on a selective hydrogen‐bonding arrangement provides an explanation for the consistently high asymmetric induction with these reagents. As an exploratory example, their scope as chiral catalysts was extended to the enantioselective dioxygenation of alkenes. A series of terminal styrenes are converted into the corresponding vicinal diacetoxylation products under mild conditions and provide the proof of principle for a truly intermolecular asymmetric alkene oxidation under iodine(I/III) catalysis. PMID:26596513

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

    NASA Astrophysics Data System (ADS)

    Li, Jun; Guo, Hua

    2015-12-01

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

  3. 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.

  4. 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

  5. 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

  6. Intra- and intermolecular reaction selectivities of γ-substituted adamantanylidenes.

    PubMed

    Knoll, Wolfgang; Kaneno, Daisuke; Bobek, Michael M; Brecker, Lothar; Rosenberg, Murray G; Tomoda, Shuji; Brinker, Udo H

    2012-02-01

    A study of adamantanylidenes having a γ-substituent (R) was undertaken to gauge how inductive and steric effects of remotely positioned functional groups influence intra- and intermolecular product selectivity. 3H-Diazirines were thermolyzed or photolyzed to generate the corresponding carbenes. On rapid heating, the resulting carbenes isomerized to 2,4-didehydroadamantanes by intramolecular 1,3-CH insertions. When R was an electron donor (R(D)) mostly asymmetric 1-substituted derivatives were produced but when it was an electron acceptor (R(A)) the symmetric 7-substituted ones were formed. When solutions were exposed to UV-A light, intermolecular adducts from the carbenes and solvent predominated with lesser amounts of intramolecular product being formed. Valence isomerization of 3H-diazirines also afforded diazo compounds. In methanol, protonation of diazo compounds to give the corresponding 2-adamantyl cations exceeds their coupling. This diversion was controlled with fumaronitrile by trapping the diazo compounds. The adducts possessed mostly anti configurations with R = R(D) and syn arrangements with R = R(A). The connection between as- and anti-product formation and that of s- and syn-products was deemed to be the consequence of a rapid equilibrium between two distinct carbene conformations. This was qualified and quantified using ab initio calculations and NBO analyses. PMID:22168480

  7. Nonlinear dynamics of globular proteins

    SciTech Connect

    Lomdahl, P.S.

    1983-01-01

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

  8. Interpretation of dipole-dipole electrical resistivity survey, Colado geothermal area, Pershing County, Nevada

    NASA Astrophysics Data System (ADS)

    Mackelprang, C. E.

    1980-09-01

    An electrical resistivity survey in the Colado geothermal area, Pershing County, Nevada has defined areas of low resistivity on each of five lines surveyed. Some of these areas appear to be fault controlled. Thermal fluids encountered in several drill holes support the assumption that the hot fluids may be associated with areas of low resistivity. The evidence of faulting as interpreted from modeling of the observed resistivity data is therefore particularly significant since these structures may be the conduits for the thermal fluids. Sub-alluvial fault zones are interpreted to occur between stations 0-5 NW on Line D and on Line A between stations 4 NW and 4 SE. Fault zones are also interpreted on Line C near stations 1 NW, 1 SE, and 3 SE, and on Line E between stations 2-4 NW and near 1 SE. No faulting is evident under the alluvial cover on the southwest end of Line B. A deep conductive zone is noted within the mountain range on two resistivity lines. There is no definite indication that thermal fluids are associated with this resistivity feature.

  9. Photoinduced intermolecular cross-linking of gas phase triacylglycerol lipid ions.

    PubMed

    Nie, Shuai; Pham, Huong T; Blanksby, Stephen J; Reid, Gavin E

    2015-01-01

    Complex mixtures of plant derived triglycerol (TG) lipids are commonly used as feedstock components for the production of industrial polymers. However, there remains a need for the development of analytical strategies to investigate the intrinsic intermolecular cross-linking reactivity of individual TG molecules within these mixtures as a function of their structures and physicochemical properties, and for the characterization of the resultant products. Here, to address this need, we describe a novel multistage tandem mass spectrometry based method for intermolecular cross-linking and subsequent structural characterization of TG lipid ions in the gas phase. Cross-linking reactions were initiated using 266 nm ultraviolet photodissociation tandem mass spectrometry (UVPD-MS/MS) of saturated or unsaturated TG dimers introduced via electrospray ionization into a linear ion trap mass spectrometer as noncovalent complexes with protonated 3,4-, 2,4- or 3,5- diiodoaniline (diIA). UVPD resulted in the initial formation of an anilinyl biradical via the sequential loss of two iodine radicals, which underwent further reaction to yield multiple cross-linked TG products along with competing noncross-linking processes. These chemistries are proposed to occur via sequential combinations of hydrogen abstraction (H-abstraction), radical addition and radical recombination. Multistage collision induced dissociation tandem mass spectrometry (CID-MS(n)) was used to obtain evidence for the structures and mechanisms of formation for these products, as a function of both the TG lipid and diIA ion structures. The efficiency of the UVPD reaction was shown to be dependent on the number of unsaturation sites present within the TG lipids. However, when unsaturation sites were present, formation of the cross-linked and noncross-linked product ions via H-abstraction and radical addition mechanisms was found to be competitive. Finally, the identity of the anilinyl biradical (e.g., 3,4- versus 2,4-substituted) was found to significantly affect the distribution of these two types of product ions. Importantly, owing to the observed propensity for cross-linking to occur via H-abstraction-initiated processes, this novel gas-phase cross-linking reaction provides a convenient method to link two molecules covalently without the requirement of any specific functional group, and therefore could be applied to examine the gas-phase intermolecular interactions and cross-linking of a wide range of biomolecular classes. PMID:26307708

  10. Dissecting Anion Effects in Gold(I)-Catalyzed Intermolecular Cycloadditions

    PubMed Central

    Homs, Anna; Obradors, Carla; Lebœuf, David; Echavarren, Antonio M

    2014-01-01

    From a series of gold complexes of the type [t-BuXPhosAu(MeCN)]X (X=anion), the best results in intermolecular gold(I)-catalyzed reactions are obtained with the complex with the bulky and soft anion BAr4F− [BAr4F−=3,5-bis(trifluoromethyl)phenylborate] improving the original protocols by 10–30% yield. A kinetic study on the [2+2] cycloaddition reaction of alkynes with alkenes is consistent with an scenario in which the rate-determining step is the ligand exchange to generate the (η2-phenylacetylene)gold(I) complex. We have studied in detail the subtle differences that can be attributed to the anion in this formation, which result in a substantial decrease in the formation of unproductive σ,π-(alkyne)digold(I) complexes by destabilizing the conjugated acid formed. PMID:26190958

  11. Iron-catalyzed intermolecular [2π+2π] cycloaddition.

    PubMed

    Russell, Sarah K; Lobkovsky, Emil; Chirik, Paul J

    2011-06-15

    The bis(imino)pyridine iron dinitrogen compounds, ((iPr)PDI)Fe(N(2))(2) and [((Me)PDI)Fe(N(2))](2)(μ(2)-N(2)) ((R)PDI = 2,6-(2,6-R(2)-C(6)H(3)N═CMe)(2)C(5)H(3)N; R = (i)Pr, Me), promote the catalytic intermolecular [2π + 2π] cycloaddition of ethylene and butadiene to form vinylcyclobutane. Stoichiometric experiments resulted in isolation of a catalytically competent iron metallocycle intermediate, which was shown to undergo diene-induced C-C reductive elimination. Deuterium labeling experiments establish competitive cyclometalation of the bis(imino)pyridine aryl substituents during catalytic turnover. PMID:21598972

  12. 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

  13. 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

  14. Intermolecular vibrations and fast relaxations in supercooled ionic liquids

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.

    2011-06-01

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

  15. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1, Q2, Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1, v2, v3) = (0, 0, 0), (0, 0, 1), (1, 0, 0), (0, 1, 0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm-1, and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm-1 for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings.

  16. Hyperfine interactions in two-dimensional HgTe topological insulators

    NASA Astrophysics Data System (ADS)

    Lunde, Anders Mathias; Platero, Gloria

    2013-09-01

    We study the hyperfine interaction between the nuclear spins and the electrons in a HgTe quantum well, which is the prime experimentally realized example of a two-dimensional topological insulator. The hyperfine interaction is a naturally present, internal source of broken time-reversal symmetry from the point of view of the electrons. The HgTe quantum well is described by the so-called Bernevig-Hughes-Zhang (BHZ) model. The basis states of the BHZ model are combinations of both S- and P-like symmetry states, which means that three kinds of hyperfine interactions play a role: (i) the Fermi contact interaction, (ii) the dipole-dipole-like coupling, and (iii) the electron-orbital to nuclear-spin coupling. We provide benchmark results for the forms and magnitudes of these hyperfine interactions within the BHZ model, which give a good starting point for evaluating hyperfine interactions in any HgTe nanostructure. We apply our results to the helical edge states of a HgTe two-dimensional topological insulator and show how their total hyperfine interaction becomes anisotropic and dependent on the orientation of the sample edge within the plane. Moreover, for the helical edge states, the hyperfine interaction due to the P-like states can dominate over the S-like contribution in certain circumstances.

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

    PubMed

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

    2007-01-01

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

  18. 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.

  19. Dispersive light-matter interaction in programmable optical tweezers

    NASA Astrophysics Data System (ADS)

    Sawyer, Bianca J.; Horvath, Milena S. J.; Deb, Amita B.; Kjørgaard, Niels

    2015-08-01

    We have developed a robust interrogation system using frequency modulation spectroscopy to measure the quantum state-dependent phase shift incurred on an off-resonant optical probe when transmitted by an atomic medium. Recently, our focus has been on extending this technique for the detection of Feshbach resonances in 87Rb atoms. Feshbach resonance is a mechanism which allows the atomic interaction strength to be precisely tuned via an external magnetic field. To access a Feshbach resonance atoms must be independently prepared in certain internal states, during which we utilize programmable optical tweezers to perform precise spatial micro-manipulation of the ensemble in laser "test-tubes." We use our dispersive probing system to identify the resonant magnetic field value in a sample with a dense "ball" geometry. An important design consideration for such a probing scheme is the three-dimensional mode-matching at the interface between light and the atomic sample when coupled by the dispersive interaction. We discuss challenges which dealing with this new geometry compared to the previously used prolate geometry, and consider the possibility of dipole-dipole interactions in our sample leading to cooperative light scattering processes.

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

    PubMed Central

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

    2014-01-01

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

  1. 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.

  2. Rh-Catalyzed Intermolecular Reactions of α-Alkyl-α-Diazo Carbonyl Compounds with Selectivity over β-Hydride Migration.

    PubMed

    DeAngelis, Andrew; Panish, Robert; Fox, Joseph M

    2016-01-19

    Rh-carbenes derived from α-diazocarbonyl compounds have found broad utility across a remarkable range of reactivity, including cyclopropanation, cyclopropenation, C-H insertions, heteroatom-hydrogen insertions, and ylide forming reactions. However, in contrast to α-aryl or α-vinyl-α-diazocarbonyl compounds, the utility of α-alkyl-α-diazocarbonyl compounds had been moderated by the propensity of such compounds to undergo intramolecular β-hydride migration to give alkene products. Especially challenging had been intermolecular reactions involving α-alkyl-α-diazocarbonyl compounds. This Account discusses the historical context and prior limitations of Rh-catalyzed reactions involving α-alkyl-α-diazocarbonyl compounds. Early studies demonstrated that ligand and temperature effects could influence chemoselectivity over β-hydride migration. However, effects were modest and conflicting conclusions had been drawn about the influence of sterically demanding ligands on β-hydride migration. More recent advances have led to a more detailed understanding of the reaction conditions that can promote intermolecular reactivity in preference to β-hydride migration. In particular, the use of bulky carboxylate ligands and low reaction temperatures have been key to enabling intermolecular cyclopropenation, cyclopropanation, carbonyl ylide formation/dipolar cycloaddition, indole C-H functionalization, and intramolecular bicyclobutanation with high chemoselectivity over β-hydride migration. Cyclic α-diazocarbonyl compounds have been shown to be particularly resilient toward β-hydride migration and are the first class of compounds that can engage in intermolecular reactivity in the presence of tertiary β-hydrogens. DFT calculations were used to propose that for cyclic α-diazocarbonyl compounds, ring constraints relieve steric interaction for intermolecular reactions and thereby accelerate the rate of intermolecular reactivity relative to intramolecular β-hydride migration. Enantioselective reactions of α-alkyl-α-diazocarbonyl compounds have been developed using bimetallic N-imido-tert-leucinate-derived complexes. The most effective complexes were found by computation and X-ray crystallography to adopt a "chiral crown" conformation in which all of the imido groups are presented on one face of the paddlewheel complex in a chiral arrangement. Insight from computational studies guided the design and synthesis of a mixed ligand paddlewheel complex, Rh2(S-PTTL)3TPA, the structure of which bears similarity to the chiral crown complex Rh2(S-PTTL)4. Rh2(S-PTTL)3TPA engages substrate classes (aliphatic alkynes, silylacetylenes, α-olefins) that are especially challenging in intermolecular reactions of α-alkyl-α-diazoesters and catalyzes enantioselective cyclopropanation, cyclopropenation, and indole C-H functionalization with yields and enantioselectivities that are comparable or superior to Rh2(S-PTTL)4. The work detailed in this Account describes progress toward enabling a more general utility for α-alkyl-α-diazo compounds in Rh-catalyzed carbene reactions. Further studies on ligand design and synthesis will continue to broaden the scope of their selective reactions. PMID:26689221

  3. Strong orbital interaction in a weak CH-π hydrogen bonding system.

    PubMed

    Li, Jianfu; Zhang, Rui-Qin

    2016-01-01

    For the first time, the intermolecular orbital interaction between benzene and methane in the benzene-methane complex, a representative of weak interaction system, has been studied by us using ab initio calculations based on different methods and basis sets. Our results demonstrate obvious intermolecular orbital interaction between benzene and methane involving orbital overlaps including both occupied and unoccupied orbitals. Similar to interatomic orbital interaction, the intermolecular interaction of orbitals forms "bonding" and "antibonding" orbitals. In the interaction between occupied orbitals, the total energy of the complex increases because of the occupation of the antibonding orbital. The existence of the CH-π hydrogen bond between benzene and methane causes a decrease in rest energy level, leading to at least -1.51 kcal/mol intermolecular interaction energy. Our finding extends the concept of orbital interaction from the intramolecular to the intermolecular regime and gives a reliable explanation of the deep orbital reformation in the benzene-methane complex. PMID:26927609

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

  6. Evidence for a strong intermolecular bond in the phenolṡN2 cation

    NASA Astrophysics Data System (ADS)

    Haines, S. R.; Geppert, W. D.; Chapman, D. M.; Watkins, M. J.; Dessent, C. E. H.; Cockett, M. C. R.; Müller-Dethlefs, K.

    1998-12-01

    The phenolṡN2 complex cation has been studied with a combination of two-color resonant zero kinetic energy (ZEKE) and mass analyzed threshold ionization (MATI) spectroscopies to probe the interaction of a polar cation with a quadrupolar solvent molecule. Extended vibrational progressions are observed in three modes which are assigned as the in-plane bend (35 cm-1), the stretch (117 cm-1), and in-plane wag (130 cm-1) intermolecular vibrations, and are consistent with a structure where the N2 forms a directional bond to the phenol OH group in the plane of the aromatic ring. Ab initio calculations at the UMP2/6-31G*, UHF/cc-pVDZ, and UMP2/cc-pVDZ levels of theory support this assignment. The spectra also provide a value for the adiabatic ionization energy (67 423 cm-1±4.5 cm-1) and an estimate of the dissociation energy of the cluster (1650±20 cm-1) which illustrate that the quadrupolar nitrogen molecule binds considerably more strongly to the phenol cation than a rare gas atom. These results constitute the first report of an aromaticṡN2 complex where the interaction can be described in terms of weak hydrogen bonding, rather than in terms of a van der Waals bond to the π-system of the benzene ring.

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

    SciTech Connect

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-12-15

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

  8. 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.

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

    PubMed

    Tiwari, Shraeddha; Kumar, Anil

    2012-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

  11. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  13. Determination of stepsize parameters for intermolecular vibrational energy transfer

    SciTech Connect

    Tardy, D.C.

    1992-03-01

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

  14. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  15. 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.

  16. Supramolecular step in design of nonlinear optical materials: Effect of π…π 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 β. 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 π-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 β 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 βFF vs βelm (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 β 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 β 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 β. 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 β 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.

  17. The intermolecular potential of methane A neutron diffraction study on low-density CD 4

    NASA Astrophysics Data System (ADS)

    Guarini, E.; Bafile, U.; Cilloco, F.; Magli, R.; Barocchi, F.

    1997-02-01

    Neutron diffraction on low-density systems offers the possibility of a direct probing of the intermolecular forces. This method, used in the last few years for monatomic systems like rare gases, is applied here to the case of gaseous CD 4 at low densities on the 180 K isotherm. The intermolecular scattering has been analysed in order to extract C( q), i.e. the Fourier transform of the direct correlation function. The zero-density limit of C( q), which depends on the (spherical average of the) pair potential only, is compared to the same quantity obtained from effective intermolecular pair potentials found in the literature.

  18. Pattern formation and Interactions of Like-Charged Colloidal Particles at the Air/Water Interface

    NASA Astrophysics Data System (ADS)

    Ruiz-Garcia, J.; Ivlev, B. I.; Gil-Villegas, A.

    2008-03-01

    In the last decade, there have been experimental reports on the formation of colloidal mesostructures at the air/water interface. These patterns, range from the formation of transient colloidal chains and soap-froth structures that evolve to more energetically stable colloidal clusters. If the surface colloidal density is high, a crystalline-like structure can also be formed. This kind of mesostructures has been observed in particles that range in size from a few nanometers to a few microns. In the case of micron-size charged colloidal particles, the charge asymmetries on the particle's surface at the air/water interface produce the formation of dipole-dipole interaction, which should be repulsive. The formation of these mesostructures, where the equilibrium distance among particles is in the micrometer range, has been interpreted as the result of a competition between long-range repulsive and attractive interactions. Measurements of the pair interaction potential in these systems show clear evidence of micron-range attractive interactions between the colloidal particles, whose pattern formation behavior has been reproduced by computer simulations that use such micrometer range attractive interaction. However, a good theoretical understanding on the origin of the attractive component is still missing. Here, we review our main findings on these systems and we discussed them in view of recent results obtained by other groups.

  19. 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.

  20. 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)

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  2. Model for entangled states with spin-spin interaction

    SciTech Connect

    Aharonov, Yakir; Anandan, Jeeva; Suzuki, Jun; Maclay, G. Jordan

    2004-11-01

    A system consisting of two neutral spin-1/2 particles is analyzed for two magnetic field perturbations: (1) an inhomogeneous magnetic field over all space, and (2) external fields over a half space containing only one of the particles. The field is chosen to point from one particle to the other, which results in essentially a one-dimensional problem. A number of interesting features are revealed for the first case: the singlet, which has zero potential energy in the unperturbed case, remains unstable in the perturbing field. The spin-zero component of the triplet evolves into a bound state with a double well potential, with the possibility of tunneling. Superposition states can be constructed which oscillate between entangled and unentangled states. For the second case, we show that changes in the magnetic field around one particle affect measurements of the spin of the entangled particle not in the magnetic field nonlocally. By using protective measurements, we show it is possible in principle to establish a nonlocal interaction using the two particles, provided the dipole-dipole potential energy does not vanish and is comparable to the potential energy of the particle in the external field.

  3. Parallel β-sheets and polar zippers in amyloid fibrils formed by residues 10–39 of the yeast prion protein Ure2p

    PubMed Central

    Chan, Jerry C.C.; Oyler, Nathan A.; Yau, Wai-Ming; Tycko, Robert

    2005-01-01

    We report the results of solid state nuclear magnetic resonance (NMR) and atomic force microscopy measurements on amyloid fibrils formed by residues 10–39 of the yeast prion protein Ure2p (Ure2p10–39). Measurements of intermolecular 13C-13C nuclear magnetic dipole-dipole couplings indicate that Ure2p10–39 fibrils contain in-register parallel β-sheets. Measurements of intermolecular 15N-13C dipole-dipole couplings, using a new solid state NMR technique called DSQ-REDOR, are consistent with hydrogen bonds between sidechain amide groups of Gln18 residues. Such sidechain hydrogen bonding interactions have been called “polar zippers” by M.F. Perutz and have been proposed to stabilize amyloid fibrils formed by peptides with glutamine- and asparagine-rich sequences, such as Ure2p10–39. We propose that polar zipper interactions account for the in-register parallel β-sheet structure in Ure2p10–39 fibrils and that similar peptides will also exhibit parallel β-sheet structures in amyloid fibrils. We present molecular models for Ure2p10–39 fibrils that are consistent with available experimental data. Finally, we show that solid state 13C NMR chemical shifts for 13C-labeled Ure2p10–39 fibrils are insensitive to hydration level, indicating that the fibril structure is not affected by the presence or absence of bulk water. PMID:16060675

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

    PubMed

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

    2014-10-28

    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. PMID:25362343

  5. 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.

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

    PubMed

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

    2005-10-22

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

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

    PubMed

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

    2014-01-28

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

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

    SciTech Connect

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

    1994-11-15

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

  9. Real-time Monitoring of Ligand-receptor Interactions with Fluorescence Resonance Energy Transfer

    PubMed Central

    Dogra, Navneet; Reyes, Julia C.; Garg, Nishi; Kohli, Punit

    2012-01-01

    FRET is a process whereby energy is non-radiatively transferred from an excited donor molecule to a ground-state acceptor molecule through long-range dipole-dipole interactions1. In the present sensing assay, we utilize an interesting property of PDA: blue-shift in the UV-Vis electronic absorption spectrum of PDA (Figure 1) after an analyte interacts with receptors attached to PDA2,3,4,7. This shift in the PDA absorption spectrum provides changes in the spectral overlap (J) between PDA (acceptor) and rhodamine (donor) that leads to changes in the FRET efficiency. Thus, the interactions between analyte (ligand) and receptors are detected through FRET between donor fluorophores and PDA. In particular, we show the sensing of a model protein molecule streptavidin. We also demonstrate the covalent-binding of bovine serum albumin (BSA) to the liposome surface with FRET mechanism. These interactions between the bilayer liposomes and protein molecules can be sensed in real-time. The proposed method is a general method for sensing small chemical and large biochemical molecules. Since fluorescence is intrinsically more sensitive than colorimetry, the detection limit of the assay can be in sub-nanomolar range or lower8. Further, PDA can act as a universal acceptor in FRET, which means that multiple sensors can be developed with PDA (acceptor) functionalized with donors and different receptors attached on the surface of PDA liposomes. PMID:22929922

  10. 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.

  11. Optimizing Noncovalent Interactions Between Lignin and Synthetic Polymers to Develop Effective Compatibilizers

    SciTech Connect

    Henry, Nathan; Harper, David; Dadmun, Mark D

    2012-01-01

    Experiments are designed and completed to identify an effective polymeric compatibilizer for lignin polystyrene blends. Copolymers of styrene and vinylphenol are chosen as the structure of the compatibilizer as the VPh unit can readily form intermolecular hydrogen bonds with the lignin molecule. Electron microscopy, thermal analysis, and neutron refl ectivity results demonstrate that among these compatibilizers, a copolymer of styrene and VPh with 20% 30% VPh most readily forms intermolecular interactions with the lignin molecule and results in the most well-dispersed blends with lignin. This behavior is explained by invoking the competition of intra- and intermolecular hydrogen bonding and functional group accessibility in forming intermolecular interactions.

  12. Mapping of the epitope/paratope interactions of a monoclonal antibody directed against adenosine 3',5'-monophosphate.

    PubMed Central

    Nass, N; Colling, C; Cramer, M; Genieser, H G; Butt, E; Winkler, E; Jaenicke, L; Jastorff, B

    1992-01-01

    A series of systematically modified cyclic AMP (cAMP) analogues, including newly synthesized benzimidazole ribofuranosyl 3',5'-monophosphates was used to map the essential molecular interactions between cAMP and the monoclonal antibody 4/2C2 (mab 4/2C2) directed against 2'-O-succinoyl cAMP [Colling, Gilles, Nass, Moka & Jaenicke (1988) Second Messengers Phosphoproteins 12, 123-133]. Its paratope binds the purine base in syn conformation by dipole-dipole interactions and hydrophobic forces and/or stacking interactions. The ribose phosphate moiety is recognized by a combination of charge interactions and H-bonds to the exocyclic and the 5'-oxygen atoms and a hydrophobic interaction at the 2'-position. There is no regioselectivity for the exocyclic oxygen atoms. Compared with the known types of binding, mab 4/2C2 thus shows a new combination of molecular interactions which may be the basis of its strikingly specific recognition and binding of the cyclic adenylates. On this account mab 4/2C2 may become an important tool in studies on cAMP metabolism. PMID:1379038

  13. Application of saturation transfer double difference NMR to elucidate the mechanistic interactions of pesticides with humic acid.

    PubMed

    Shirzadi, Azadeh; Simpson, Myrna J; Xu, Yunping; Simpson, André J

    2008-02-15

    Elucidation of mechanistic interactions of anthropogenic chemicals is critical to understanding and eventually predicting their behavior in the environment Here, a recently developed technique, saturation transfer double difference (STDD) NMR spectroscopy is employed to determine the interactions of pesticides with humic acid (HA) at the molecular level. The degree of interaction at each NMR observable nucleus in the pesticide can be quantified in the form of an epitope map, which depicts the mechanism of the pesticide-HA interaction. Our results indicate that, at pH 7, halogen atoms (F and Cl) in water-soluble pesticides (diflufenzopyr, acifluorfen, and chlorsulfuron) play a dominant role in influencing binding to HA, whereas carboxyl groups likely play a secondary role when halogen atoms are also present in the molecule, as observed with diflufenzopyr and acifluorfen. However, when present on its own, the carboxyl group dominates in binding affinityto HA (e.g., imazapyr). Electronegativity and electron density appear to play a key role in the mechanism of binding and results suggest that polar bonds are the primary points of HA contact in the water soluble pesticides investigated. Likely interactions may include hydrogen bonding and dipole-dipole interactions. PMID:18351076

  14. 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.

  15. 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

  16. 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.

  17. Mass analyzed threshold ionization of phenolṡCO: Intermolecular binding energies of a hydrogen-bonded complex

    NASA Astrophysics Data System (ADS)

    Haines, Stephen R.; Dessent, Caroline E. H.; Müller-Dethlefs, Klaus

    1999-08-01

    [PhenolṡCO]+ was studied using a combination of two-color resonant zero kinetic energy (ZEKE) spectroscopy and mass analyzed threshold ionization (MATI) spectroscopy to investigate the interaction of the CO ligand with a hydrogen-bonding cation. Vibrational progressions were observed in three intermolecular modes, the in-plane bend (42 cm-1), stretch (130 cm-1), and in-plane wag (160 cm-1), and are consistent with a planar hydrogen-bonded structure where the CO bonds through the carbon atom to the phenol OH group. Dissociation energies for the S0, S1, and D0 states were determined as 659±20, 849±20, and 2425±10 cm-1, respectively. The cationic and neutral dissociation energies of the phenolṡCO complex are considerably stronger than those of phenolṡN2, demonstrating the extent to which the larger quadrupole of CO affects the strength of binding.

  18. 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

  19. The origins of intra- and inter-molecular vibrational couplings: A case study of H2O-Ar on full and reduced-dimensional potential energy surface.

    PubMed

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

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1,  Q2,  Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1,  v2,  v3) =  (0,  0,  0), (0,  0,  1), (1,  0,  0), (0,  1,  0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm(-1), and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. PMID:26747800

  20. Near-field spatial mapping of strongly interacting multiple plasmonic infrared antennas.

    PubMed

    Grefe, Sarah E; Leiva, Daan; Mastel, Stefan; Dhuey, Scott D; Cabrini, Stefano; Schuck, P James; Abate, Yohannes

    2013-11-21

    Near-field dipolar plasmon interactions of multiple infrared antenna structures in the strong coupling limit are studied using scattering-type scanning near-field optical microscope (s-SNOM) and theoretical finite-difference time-domain (FDTD) calculations. We monitor in real-space the evolution of plasmon dipolar mode of a stationary antenna structure as multiple resonantly matched dipolar plasmon particles are closely approaching it. Interparticle separation, length and polarization dependent studies show that the cross geometry structure favors strong interparticle charge-charge, dipole-dipole and charge-dipole Coulomb interactions in the nanometer scale gap region, which results in strong field enhancement in cross-bowties and further allows these structures to be used as polarization filters. The nanoscale local field amplitude and phase maps show that due to strong interparticle Coulomb coupling, cross-bowtie structures redistribute and highly enhance the out-of-plane (perpendicular to the plane of the sample) plasmon near-field component at the gap region relative to ordinary bowties. PMID:24097054

  1. Solitons in quasi-one-dimensional Bose-Einstein condensates with competing dipolar and local interactions

    SciTech Connect

    Cuevas, J.; Kevrekidis, P. G.; Frantzeskakis, D. J.

    2009-05-15

    We study families of one-dimensional matter-wave bright solitons supported by the competition of contact and dipole-dipole (DD) interactions of opposite signs. Soliton families are found, and their stability is investigated in the free space and in the presence of an optical lattice (OL). Free-space solitons may exist with an arbitrarily weak local attraction if the strength of the DD repulsion is fixed. In the case of the DD attraction, solitons do not exist beyond a maximum value of the local-repulsion strength. In the system which includes the OL, a stability region for subfundamental solitons is found in the second finite band gap. For the existence of gap solitons (GSs) under the attractive DD interaction, the contact repulsion must be strong enough. In the opposite case of the DD repulsion, GSs exist if the contact attraction is not too strong. Collisions between solitons in the free space are studied too. In the case of the local attraction, they merge or pass through each other at small and large velocities, respectively. In the presence of the local repulsion, slowly moving solitons bounce from each other.

  2. Helical folding of conjugated oligo(phenyleneethynylene): chain-length dependence, solvent effects, and intermolecular assembly.

    PubMed

    Zhu, Ningbo; Yan, Qifan; Luo, Zhouyang; Zhai, You; Zhao, Dahui

    2012-10-01

    As a representative folding system that features a conjugated backbone, a series of monodispersed (o-phenyleneethynylene)-alt-(p-phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side-chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain-length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light-scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self-assembling into hierarchical supramolecular structures promises application potential for the system. PMID:22829335

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

    PubMed

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

    2014-09-01

    The Casimir-Polder force is an important long-range interaction involved in adsorption and desorption of molecules in fluids. We explore Casimir-Polder interactions between methane molecules in water, and between a molecule in water near SiO(2) and hexane surfaces. Inclusion of the finite molecular size in the expression for the Casimir-Polder energy leads to estimates of the dispersion contribution to the binding energies between molecules and between one molecule and a planar surface. PMID:25314410

  4. Pd(II) -Catalyzed Intermolecular Amination of Unactivated C(sp(3) )-H Bonds.

    PubMed

    Gou, Quan; Liu, Gang; Liu, Zi-Ning; Qin, Jun

    2015-10-26

    Pd(II) -catalyzed intermolecular amination of unactivated C(sp(3) )-H bonds has been successfully developed for the first time. This method provides a new way to achieve the challenging intermolecular amination of unactivated C(sp(3) )-H bonds, producing a variety of unnatural β(2) -amino carboxylic acid analogues. This C(sp(3) )-H amination protocol is demonstrated with a broad substrate scope, good functional-group tolerance, and chemoselectivity. It is operated without use of phosphine ligand or external oxidant. PMID:26359788

  5. 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

  6. 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...

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

    NASA Astrophysics Data System (ADS)

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

    1998-03-01

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

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  10. Explosives sensing by using electron-rich supramolecular polymers: role of intermolecular hydrogen bonding in significant enhancement of sensitivity.

    PubMed

    Gole, Bappaditya; Song, Wentao; Lackinger, Markus; Mukherjee, Partha Sarathi

    2014-10-13

    We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World War II. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water. PMID:25187022

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

    SciTech Connect

    Muenter, J.S.

    1992-08-01

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

  12. 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.

  13. 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

  14. An approach to the origin of self-replicating system. I - Intermolecular interactions

    NASA Technical Reports Server (NTRS)

    Macelroy, R. D.; Coeckelenbergh, Y.; Rein, R.

    1978-01-01

    The present paper deals with the characteristics and potentialities of a recently developed computer-based molecular modeling system. Some characteristics of current coding systems are examined and are extrapolated to the apparent requirements of primitive prebiological coding systems.

  15. 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.

  16. Intermolecular interactions in solutions of some amino-nitro-benzene derivatives, studied by spectral means

    NASA Astrophysics Data System (ADS)

    Dorohoi, Dana-Ortansa; Airinei, Anton; Dimitriu, Mihaela

    2009-07-01

    The spectral shifts in the visible electronic absorption spectra of three amino-nitro-benzene derivatives in different solvents were correlated with the macroscopic parameters (refractive index and electric permittivity) of the solvents. The wavenumbers in the maximum of the visible charge transfer absorption band of o-nitro-aniline, 4-amino-3-nitrophenol and 3-amino-4-nitrophenol depend linearly on the Baur-Nicol function of electric permittivity. This dependence allows to estimate the electric polarizability in the electronic excited states if the electric polarizability in the ground state of the spectrally active molecule is determined by other procedures, such as by quanto-mechanical calculations.

  17. Iodine bonding stabilizes iodomethane in MIDAS pesticide. Theoretical study of intermolecular interactions between iodomethane and chloropicrin.

    PubMed

    Glaser, Rainer; Prugger, Kaitlan

    2012-02-22

    The results are reported of a theoretical study of iodomethane (H(3)C-I, 1) and chloropicrin (Cl(3)C-NO(2), 2), of the heterodimers 3-6 formed by aggregation of 1 and 2, and of their addition products 7 and 8 and their possible fragmentation reactions to 9-18. Mixtures of iodomethane and chloropicrin are not expected to show chemistry resulting from their reactions with each other. The structures and stabilities are discussed of the iodine-bonded molecular aggregates (IBMA) 3 and 4 and of the hydrogen- and iodine-bonded molecular aggregates (IHBMA) 5 and 6. The mixed aggregates 3-5 are bound on the free enthalpy surface relative to the homodimers of 1 and 2, and the IBMA structures 3 and 4 are most stable. This result suggests that the mixture of chloropicrin and iodomethane in the pesticide Midas is a good choice to reduce the volatility of iodomethane because of thermodynamically stabilizing iodine bonding. PMID:22313191

  18. The effect of intermolecular interaction on excited states in p - DTS(FBTTH2)2

    NASA Astrophysics Data System (ADS)

    Reichenberger, Markus; Love, John A.; Rudnick, Alexander; Bagnich, Sergey; Panzer, Fabian; Stradomska, Anna; Bazan, Guillermo C.; Nguyen, Thuc-Quyen; Köhler, Anna

    2016-02-01

    Using optical spectroscopy in solution and thin film, and supported by quantum chemical calculations, we investigated the aggregation process of the donor-acceptor type molecule p - DTS(FBTTH2)2. We demonstrate that cooling a solution induces a disorder-order phase transition that proceeds in three stages analogous to the steps observed in semi-rigid conjugated polymers. By analyzing the spectra, we are able to identify the spectral signature of monomer and aggregate in absorption and emission. From this we find that in films, the fraction of aggregates is near 100% which is in contrast to films made from semi-rigid conjugated polymers.

  19. The effect of intermolecular interaction on excited states in p - DTS(FBTTH2)2.

    PubMed

    Reichenberger, Markus; Love, John A; Rudnick, Alexander; Bagnich, Sergey; Panzer, Fabian; Stradomska, Anna; Bazan, Guillermo C; Nguyen, Thuc-Quyen; Köhler, Anna

    2016-02-21

    Using optical spectroscopy in solution and thin film, and supported by quantum chemical calculations, we investigated the aggregation process of the donor-acceptor type molecule p - DTS(FBTTH2)2. We demonstrate that cooling a solution induces a disorder-order phase transition that proceeds in three stages analogous to the steps observed in semi-rigid conjugated polymers. By analyzing the spectra, we are able to identify the spectral signature of monomer and aggregate in absorption and emission. From this we find that in films, the fraction of aggregates is near 100% which is in contrast to films made from semi-rigid conjugated polymers. PMID:26896999

  20. 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...

  1. Gold(i) operational in synergistic catalysis for the intermolecular α-addition reaction of aldehydes across allenamides.

    PubMed

    Ballesteros, Alberto; Morán-Poladura, Pablo; González, Jose M

    2016-02-01

    The intermolecular reaction of allenamides with aldehydes is reported. The designed approach relies on gold(i) and organocatalysis for activating the allenamides and the aldehydes respectively. Conditions to achieve an enantioselective version of this intermolecular reaction are defined. PMID:26780935

  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. 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

  4. Palladium-catalyzed intermolecular cyclocarbonylation of 2-iodoanilines with the Michael acceptor, diethyl ethoxycarbonylbutendienoate.

    PubMed

    Okuro, Kazumi; Alper, Howard

    2012-05-01

    Palladium-catalyzed intermolecular cyclocarbonylation of 2-iodoanilines with diethyl ethoxycarbonylbutendienoate produces 2,3,3-triethoxycarbonyl-2,3-dihydro-4(1H)-quinolinone derivatives in moderate to good yields. This protocol involves Michael addition and subsequent carbonylation. PMID:22480192

  5. 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…

  6. An Analysis of Two Textbooks on the Topic of Intermolecular Forces

    ERIC Educational Resources Information Center

    Tan, Daniel Kim Chwee; Seng, Chan Kim

    2004-01-01

    This paper describes the analysis of two commonly used high school (Grades 11 and 12) chemistry textbooks in Singapore to determine if the content presented in the topic of intermolecular forces is consistent with the concepts and propositional knowledge identified by the authors as essential for the learning and understanding of the topic…

  7. 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.

  8. Stress acidulated amphoteric molecules and mechanochromism via reversible intermolecular proton transfer.

    PubMed

    Wang, Yi; Li, Minjie; Zhang, Yumo; Yang, Jin; Zhu, Shaoyin; Sheng, Lan; Wang, Xudong; Yang, Bing; Zhang, Sean Xiao-An

    2013-07-28

    Stress has been proved to acidulate amphoteric molecules and promote an intermolecular proton transfer, which results in a significant absorption and emission change. The stress acidulated amphoteric molecules open a new avenue for developing mechanochromic materials and anticipate many broad applications such as stress/pressure sensors and rewritable media. PMID:23712461

  9. Using Molecular Dynamics Simulation to Reinforce Student Understanding of Intermolecular Forces

    ERIC Educational Resources Information Center

    Burkholder, Phillip R.; Purser, Gordon H.; Cole, Renee S.

    2008-01-01

    Intermolecular forces play an important role in many aspects of chemistry ranging from inorganic to biological chemistry. These forces dictate molecular conformation, species aggregation (including self-assembly), trends in solubility and boiling points, adsorption characteristics, viscosity, phase changes, surface tension, capillary action, vapor…

  10. Copper-Catalyzed Intermolecular Hydroamination of Internal Alkynes with Anilines and Amines.

    PubMed

    Ishikawa, Tomoki; Sonehara, Taro; Minakawa, Maki; Kawatsura, Motoi

    2016-03-18

    The copper-catalyzed regioselective intermolecular hydroamination of the aryl and trifluoromethyl group or electron-withdrawing group substituted internal alkynes with amines has been accomplished. The reaction was effectively catalyzed by the ligand-free Cu(OTf)2 and afforded the intended amine derivatives in good yields after treatment of NaBH3CN. PMID:26954725

  11. 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

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

    SciTech Connect

    Stevens, B.

    1997-07-01

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

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

    PubMed

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

    2013-10-17

    The vibronic spectra of strong charge-transfer complexes are often congested or diffuse and therefore difficult to analyze. We present the spectra of the π-stacked complex perylene trans-1,2-dichloroethene, which is in the limit of weak charge transfer, the electronic excitation remaining largely confined to the perylene moiety. The complex is formed in a supersonic jet, and its S0 ↔ S1 spectra are investigated by two-color resonant two-photon ionization (2C-R2PI) and fluorescence spectroscopies. Under optimized conditions, vibrationally cold (T(vib) ≈ 9 K) and well resolved spectra are obtained. These are dominated by vibrational progressions in the “hindered-rotation” Rc intermolecular vibration with very low frequencies of 11 (S0) and 13 cm(–1) (S1). The intermolecular Tz stretch and the Ra and Rb bend vibrations are also observed. The normally symmetry-forbidden intramolecular 1a(u) “twisting” vibration of perylene also appears, showing that the π- stacking interaction deforms the perylene moiety, lowering its local symmetry from D2h to D2. We calculate the structure and vibrations of this complex using six different density functional theory (DFT) methods (CAM-B3LYP, BH&HLYP, B97-D3, ωB97X-D, M06, and M06-2X) and compare the results to those calculated by correlated wave function methods (SCS-MP2 and SCS-CC2). The structures and vibrational frequencies predicted with the CAM-B3LYP and BH&HLYP methods disagree with the other calculations and with experiment. The other four DFT and the ab initio methods all predict a π-stacked “centered” structure with nearly coplanar perylene and dichloroethene moieties and intermolecular binding energies of D(e) = −20.8 to −26.1 kJ/mol. The 000 band of the S0 → S1 transition is red-shifted by δν = −301 cm(–1) relative to that of perylene, implying that the D(e) increases by 3.6 kJ/mol or 15% upon electronic excitation. The intermolecular vibrational frequencies are assigned to the calculated Rc, Tz, Ra, and Rb vibrations by comparing to the observed/calculated frequencies and S0 ↔ S1 Franck–Condon factors. Of the three TD-DFT methods tested, the hybrid-meta-GGA functional M06-2X shows the best agreement with the experimental electronic transition energies, spectral shifts, and vibronic spectra, closely followed by the ωB97X-D functional, while the M06 functional gives inferior results. PMID:24063531

  14. Origin of spontaneous polarization, tilt, and chiral structure of smectic liquid-crystal phases composed of bent-core molecules: A molecular model

    NASA Astrophysics Data System (ADS)

    Emelyanenko, A. V.; Osipov, M. A.

    2004-08-01

    A simple molecular model is proposed for novel bent-core smectic phases that enables one to explain the origin of the experimentally observed chiral structure of the B2 phase composed of nonchiral banana-shaped molecules. It is shown that in the perfectly ordered smectic phase the distributed dispersion interaction between banana-shaped molecules stabilizes the spontaneous polarization and may be responsible for the tilt of the director. The orientation of the spontaneous polarization with respect to the tilt plane is determined by the balance between the dispersion and electrostatic dipole-dipole intermolecular interactions. In particular, sufficiently strong dipole-dipole interaction promotes the B2 phase where the polarization is normal to the tilt plane. The actual chiral structure of each smectic layer in the B2 phase appears as a result of the symmetry breaking. In the case of small molecular dipoles the nonchiral polar smectic phase is formed where the spontaneous polarization is parallel to the tilt plane. The role of the opening angle and of the axial ratio of banana-shaped molecules is also considered and a phase diagram is presented.

  15. Origin of spontaneous polarization, tilt, and chiral structure of smectic liquid-crystal phases composed of bent-core molecules: a molecular model.

    PubMed

    Emelyanenko, A V; Osipov, M A

    2004-08-01

    A simple molecular model is proposed for novel bent-core smectic phases that enables one to explain the origin of the experimentally observed chiral structure of the B2 phase composed of nonchiral banana-shaped molecules. It is shown that in the perfectly ordered smectic phase the distributed dispersion interaction between banana-shaped molecules stabilizes the spontaneous polarization and may be responsible for the tilt of the director. The orientation of the spontaneous polarization with respect to the tilt plane is determined by the balance between the dispersion and electrostatic dipole-dipole intermolecular interactions. In particular, sufficiently strong dipole-dipole interaction promotes the B2 phase where the polarization is normal to the tilt plane. The actual chiral structure of each smectic layer in the B2 phase appears as a result of the symmetry breaking. In the case of small molecular dipoles the nonchiral polar smectic phase is formed where the spontaneous polarization is parallel to the tilt plane. The role of the opening angle and of the axial ratio of banana-shaped molecules is also considered and a phase diagram is presented. PMID:15447506

  16. 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.

  17. The effect of functional groups on the SO2 adsorption on carbon surface I: A new insight into noncovalent interaction between SO2 molecule and acidic oxygen-containing groups

    NASA Astrophysics Data System (ADS)

    Liu, Xin; Sun, Fei; Qu, Zhibin; Gao, Jihui; Wu, Shaohua

    2016-04-01

    For the aim to give a new insight into the interactions between SO2 molecule and carbon surface and the effect of acidic oxygen-containing groups, density functional theory and noncovalent interaction analysis in terms of reduced density gradient were employed to investigate both the intensity and type of the interactions. The results indicate that the physisorption of SO2 molecule mainly occurs on the basal plane of pure carbon surface due to van der Waals interactions, however, when acidic oxygen-containing groups were decorated on the carbon surface, they would facilitate SO2 adsorption as a result of hydrogen bonding and dipole-dipole interactions. What's more, these groups could not affect the chemisorption of SO2 remarkably, no matter they are near the adsorption sites or not. In addition, calculation results show that the interactions between SO2 and acidic oxygen-containing groups are in physisorption nature, which challenges a long-held the viewpoint of irreversible chemisorption. Acidic oxygen-containing groups could boost the effective surface area of carbon by enhancing the physisorption on edge positions.

  18. The structure and intermolecular forces of DNA condensates

    PubMed Central

    Yoo, Jejoong; Aksimentiev, Aleksei

    2016-01-01

    Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA–DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA–DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA–DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. PMID:26883635

  19. The structure and intermolecular forces of DNA condensates.

    PubMed

    Yoo, Jejoong; Aksimentiev, Aleksei

    2016-03-18

    Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations. PMID:26883635

  20. 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