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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

  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.

    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

  4. 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.

  5. 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.

  6. Coherent and incoherent dipole-dipole interactions between atoms

    NASA Astrophysics Data System (ADS)

    Robicheaux, Francis

    2016-05-01

    Results will be presented on the collective interaction between atoms due to the electric dipole-dipole coupling between states of different parity on two different atoms. A canonical example of this effect is when the electronic state of one atom has S-character and the state of another atom has P-character. The energy difference between the two states plays an important role in the interaction since the change in energy determines the wave number of a photon that would cause a transition between the states. If the atoms are much closer than the wave length of this photon, then the dipole-dipole interaction is in the near field and has a 1 /r3 dependence on atomic separation. If the atoms are farther apart than the wave length, then the interaction is in the far field and has a 1 / r dependence. When many atoms interact, collective effects can dominate the system with the character of the collective effect depending on whether the atomic separation leads to near field or far field coupling. As an example of the case where the atoms are in the far field, the line broadening of transitions and strong deviations from the Beer-Lambert law in a diffuse gas will be presented. As an example of near field collective behavior, the radiative properties of a Rydberg gas will be presented. Based upon work supported by the National Science Foundation under Grant No. 1404419-PHY in collaboration with R.T. Sutherland.

  7. 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

  8. 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.

  9. 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…

  10. 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.

  11. Critical properties of entanglement in the Dicke model with the dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Nie, J.; Huang, X. L.; Yi, X. X.

    2009-04-01

    In this paper, we investigate two aspects of entanglement properties of the ground state for the Dicke model with the dipole-dipole interaction between the atoms in the thermodynamic limit, and observe how they are affected by the quantum phase transition. The appearance of dipole-dipole interactions between the atoms does not change the maximum atom-field entanglement at the critical point, while it changes the maximum atom-atom entanglement at the critical point, and has an important influence on the atom-atom entanglement behavior.

  12. Cooperative Self-Assembly of Carbazole Derivatives Driven by Multiple Dipole-Dipole Interactions.

    PubMed

    Ikeda, Toshiaki; Iijima, Tatsuya; Sekiya, Ryo; Takahashi, Osamu; Haino, Takeharu

    2016-08-01

    Carbazole possessing phenylisoxazoles self-assembled in a cooperative manner in decalin. X-ray crystal structure analysis revealed that the isoxazole dipoles align in a head-to-tail fashion. DFT calculations suggested that the linear array of dipoles induced the polarization of each dipole, leading to an increase in dipole-dipole interactions. This dipole polarization resulted in cooperative assembly. PMID:27391525

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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 Tg is strongly anticorrelated with the polarity of the molecule. The larger the dielectric relaxation strength Δ ɛ (Tg) of the system, the narrower is the α -loss peak. This remarkable property is explained by the contribution from the dipole-dipole interaction potential Vd d(r )=-D r-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 Δ ɛ (Tg) in view of the relation, D ∝(μ4/k Tg)∝k Tg[Δɛ (Tg)] 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.

  16. Probing dipole-dipole interaction in a rubidium gas via double-quantum 2D spectroscopy.

    PubMed

    Gao, Feng; Cundiff, Steven T; Li, Hebin

    2016-07-01

    We have implemented double-quantum 2D spectroscopy on a rubidium vapor and shown that this technique provides sensitive and background-free detection of the dipole-dipole interaction. The 2D spectra include signals from both individual atoms and interatomic interactions, allowing quantitative studies of the interaction. A theoretical model based on the optical Bloch equations is used to reproduce the experimental spectrum and confirm the origin of double-quantum signals. PMID:27367074

  17. 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.

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  20. 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

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

    NASA Astrophysics Data System (ADS)

    Afrousheh, K.; Bohlouli-Zanjani, P.; Vagale, D.; Mugford, A.; Fedorov, M.; Martin, J. D.

    2004-11-01

    Resonant electric dipole-dipole interactions between cold Rydberg atoms were observed using microwave spectroscopy. Laser-cooled 85Rb atoms in a magneto-optical trap were optically excited to 45d5/2 Rydberg states using a pulsed laser. A microwave pulse transferred a fraction of these Rydberg atoms to the 46p3/2 state. A second microwave pulse then drove atoms in the 45d5/2 state to the 46d5/2 state, and was used as a probe of interatomic interactions. The spectral width of this two-photon probe transition was found to depend on the presence of the 46p3/2 atoms, and is due to the resonant electric dipole-dipole interaction between 45d5/2 and 46p3/2 Rydberg atoms.

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  3. Study of atomic dipole-dipole interactions via measurement of atom-pair kinetics

    NASA Astrophysics Data System (ADS)

    Thaicharoen, Nithiwadee; Gonçalves, Luís Felipe; Raithel, Georg

    2016-05-01

    We observe atom-pair kinetics due to binary dipolar forces by direct imaging of the center-of-mass positions of the individual Rydberg atoms and pair-correlation analysis. To prepare a highly dipolar quantum state, Rydberg-atom ensembles are switched from a weakly- into a strongly-interacting regime via adiabatic state transformation. The transformed atoms exhibit a large permanent electric dipole moment that is locked to the direction of an applied electric field. The resultant electric dipole-dipole forces reveal dumbbell-shaped pair correlation images that demonstrate the anisotropy of the binary dipolar force. The dipole-dipole interaction coefficient C3, derived from the time dependence of the images, agrees with the value calculated from the known permanent electric-dipole moment of the atoms. The observations also show the dynamics reminiscent of disorder-induced heating in strongly coupled particle systems.

  4. Microwave observations of the dipole-dipole interaction between cold Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Afrousheh, K.; Bohlouli, P. Z.; Vagale, D.; Fedorov, M.; Mugford, A.; Martin, J. D. D.

    2004-05-01

    Neighboring Rydberg atoms may strongly interact through electric dipole-dipole couplings. Thus, temporary excitation to Rydberg states has been proposed for implementing elements of quantum information processing using cold neutral atoms. In this work we excited Rb atoms in a MOT to the 45d_5/2 Rydberg state. A microwave pulse was then used to transfer a variable amount of 45d_5/2 atoms to the 46p_3/2 state. Atoms in the 45d and 46p states strongly interact through an always resonant dipole-dipole interaction. We probe this by introducing a second microwave pulse which drives the 45d_5/2-46d_5/2 two photon transition. The dipole-dipole interaction between 46d and 46p states is relatively weak, so the observed spectra are dominated by the 45d-46p couplings between neighboring atoms. These results are discussed in the context of dipole-blockade, as proposed by Lukin et al., Phys. Rev. Lett., 87, 37901 (2001).

  5. Master equation with quantized atomic motion including dipole-dipole interactions

    NASA Astrophysics Data System (ADS)

    Damanet, François; Braun, Daniel; Martin, John

    2016-05-01

    We derive a markovian master equation for the internal dynamics of an ensemble of two-level atoms including all effects related to the quantization of their motion. Our equation provides a unifying picture of the consequences of recoil and indistinguishability of atoms beyond the Lamb-Dicke regime on both their dissipative and conservative dynamics, and is relevant for experiments with ultracold trapped atoms. We give general expressions for the decay rates and the dipole-dipole shifts for any motional states, and we find analytical formulas for a number of relevant states (Gaussian states, Fock states and thermal states). In particular, we show that the dipole-dipole interactions and cooperative photon emission can be modulated through the external state of motion. The effects predicted should be experimentally observable with Rydberg atoms. FD would like to thank the F.R.S.-FNRS for financial support. FD is a FRIA Grant holder of the Fonds de la Recherche Scientifique-FNRS.

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

    NASA Astrophysics Data System (ADS)

    Yu, Yue; Luo, Zhuxi; Wang, Ziqiang

    2014-07-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    Bashkirov, Eugene K.; Litvinova, Darya V.

    2015-03-01

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

  9. 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.

  10. Induced dipole-dipole interactions in light diffusion from point dipoles

    NASA Astrophysics Data System (ADS)

    Cherroret, Nicolas; Delande, Dominique; van Tiggelen, Bart A.

    2016-07-01

    We develop a perturbative treatment of induced dipole-dipole interactions in the diffusive transport of electromagnetic waves through disordered atomic clouds. The approach is exact at order 2 in the atomic density and accounts for the vector character of light. It is applied to the calculations of the electromagnetic energy stored in the atomic cloud, which modifies the energy transport velocity, and of the light scattering and transport mean free paths. Results are compared to those obtained from a purely scalar model for light.

  11. Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field

    NASA Astrophysics Data System (ADS)

    Afrousheh, Kourosh; Bohlouli-Zanjani, Parisa; Carter, Jeffery; Mugford, Ashton; Martin, James D. D.

    2006-05-01

    Laser cooled Rb atoms were optically excited to 46d5/2 Rydberg states. A microwave pulse transferred a fraction of the atoms to the 47p3/2 Rydberg state. The resonant electric dipole-dipole interactions between atoms in these two states were probed using the linewidth of the two-photon microwave transitions 46d5/2 -- 47d5/2. The presence of a weak magnetic field (roughly 1 G) reduced the observed line broadening, indicating that the interaction is suppressed by the field. The field removes some of the energy degeneracies responsible foe the resonant interaction, and this is the basis for a quantitative model of the resulting suppression. A technique for the calibration of magnetic field strengths using the 34s1/2 -- 34p1/2 one-photon transition is also presented.

  12. Resonant electric dipole-dipole interactions between cold Rydberg atoms in a magnetic field

    NASA Astrophysics Data System (ADS)

    Afrousheh, K.; Bohlouli-Zanjani, P.; Carter, J. D.; Mugford, A.; Martin, J. D. D.

    2006-06-01

    Laser-cooled Rb85 atoms were optically excited to 46d5/2 Rydberg states. A microwave pulse transferred a fraction of the atoms to the 47p3/2 Rydberg state. The resonant electric dipole-dipole interactions between atoms in these two states were probed using the linewidth of the two-photon microwave transition 46d5/2-47d5/2 . The presence of a weak magnetic field ≈0.5G reduced the observed line broadening, indicating that the interaction is suppressed by the field. The field removes some of the energy degeneracies responsible for the resonant interaction, and this is the basis for a quantitative model of the resulting suppression. A technique for the calibration of magnetic field strengths using the 34s1/2-34p1/2 one-photon transition is also presented.

  13. 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.

  14. Quantum defect theory for the van der Waals plus dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Wang, Gao-Ren; Xie, Ting; Huang, Yin; Zhang, Wei; Cong, Shu-Lin

    2012-12-01

    We investigate the scattering dynamics governed by the long-range van der Waals plus dipole-dipole interaction potential, -C6/R6-C3/R3, which describes the long-range interaction between two polar molecules in an electric field. In the spirit of quantum defect theory, a set of parameters which are nearly constants in the threshold regime is defined to characterize the scattering process. Using appropriate boundary conditions for the scattering wave functions and relevant parameters, we explore the quantum reflection by and quantum tunneling through the long-range potential. As a sample application, the reactive collision rates of 40K87Rb + 40K87Rb are calculated.

  15. 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

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

    NASA Astrophysics Data System (ADS)

    Bigelow, Jacob L.; Hollingsworth, Jacob; Paul, Jacob T.; Peleg, Matan; Sanford, Veronica L.; Carroll, Thomas J.; Noel, Michael W.

    2016-05-01

    The dipole-dipole interaction between two Rydberg atoms depends on the relative orientation of the atoms and on the change in the magnetic quantum number. We simulate the effect of this anisotropy on the energy transport in an amorphous many atom system of ultracold Rydberg atoms subject to a homogeneous applied electric field. We consider two experimentally feasible geometries and find that the effects should be measurable in current generation imaging experiments. We also examine evidence for Anderson localization. This work was supported by the National Science Foundation under Grants No. 1205895 and No. 1205897 and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation Grant Number OCI-1053575.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  19. 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.

  20. 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.

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

    SciTech Connect

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

    2007-09-13

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

  2. Interstrand dipole-dipole interactions can stabilize the collagen triple helix.

    PubMed

    Shoulders, Matthew D; Raines, Ronald T

    2011-07-01

    The amino acid sequence of collagen is composed of GlyXaaYaa repeats. A prevailing paradigm maintains that stable collagen triple helices form when (2S)-proline (Pro) or Pro derivatives that prefer the C(γ)-endo ring pucker are in the Xaa position and Pro derivatives that prefer the C(γ)-exo ring pucker are in the Yaa position. Anomalously, an amino acid sequence in an invertebrate collagen has (2S,4R)-4-hydroxyproline (Hyp), a C(γ)-exo-puckered Pro derivative, in the Xaa position. In certain contexts, triple helices with Hyp in the Xaa position are now known to be hyperstable. Most intriguingly, the sequence (GlyHypHyp)(n) forms a more stable triple helix than does the sequence (GlyProHyp)(n). Competing theories exist for the physicochemical basis of the hyperstability of (GlyHypHyp)(n) triple helices. By synthesizing and analyzing triple helices with different C(γ)-exo-puckered proline derivatives in the Xaa and Yaa positions, we conclude that interstrand dipole-dipole interactions are the primary determinant of their additional stability. These findings provide a new framework for understanding collagen stability. PMID:21482820

  3. Effects of dipole-dipole interaction on the single-photon transport in a hybrid atom-optomechanical system coupling to a single-mode waveguide

    NASA Astrophysics Data System (ADS)

    Zhang, Yu-Qing; Zhu, Zhong-Hua; Peng, Zhao-Hui; Jiang, Chun-Lei; Tan, Lei

    2016-07-01

    We theoretically investigate the single-photon transport in a hybrid atom-optomechanical system embedded with two dipole-coupled two-level atoms, interacting with a single-mode optical waveguide. The transmission amplitudes for the single-photon propagation in such a hybrid system are obtained via a real-space approach. It is shown that the dipole-dipole interaction can significantly change the amplitudes and symmetries of the single-photon spectra. Interestingly, we find that the dipole-dipole interaction plays a similar role as does the positive atom-cavity detuning. In addition, the influence from the atomic dissipation can be weakened by increasing the dipole-dipole interaction.

  4. Long-range dipole-dipole interaction and anomalous Förster energy transfer across a hyperbolic metamaterial

    NASA Astrophysics Data System (ADS)

    Biehs, S.-A.; Menon, Vinod M.; Agarwal, G. S.

    2016-06-01

    We study radiative energy transfer between a donor-acceptor pair across a hyperbolic metamaterial slab. We show that similar to a perfect lens a hyperbolic lens allows for giant energy transfer rates. For a realistic realization of a hyperbolic multilayer metamaterial we find an enhancement of up to three orders of magnitude with respect to the transfer rates across a plasmonic silver film of the same size especially for frequencies which coincide with the epsilon-near zero and the epsilon-near pole frequencies. Furthermore, we compare exact results based on the S -matrix method with results obtained from effective medium theory. Our finding of very large dipole-dipole interaction at distances of the order of a wavelength has important consequences for producing radiative heat transfer, quantum entanglement, etc.

  5. Vertical Liquid Crystal Orientation on Amorphous Tantalum Pentoxide Surfaces Depending on Anisotropic Dipole-Dipole Interaction via Ion Beam Irradiation

    NASA Astrophysics Data System (ADS)

    Lee, Jong-Jin; Kim, Hyung-Jun; Kang, Young-Gu; Kim, Young-Hwan; Park, Hong-Gyu; Kim, Byoung-Yong; Seo, Dae-Shik

    2011-03-01

    We achieved vertically aligned (VA) liquid crystals (LCs) on amorphous tantalum pentoxide (Ta2O5) alignment films deposited by radio frequency (rf) magnetron sputtering using ion beam (IB) irradiation. By analyzing measurements by X-ray photoelectron spectroscopy (XPS), we confirmed the bond breaking, as detected from the O 1s spectra, which caused an isotropic dipole-dipole interaction between the LC molecules and the Ta2O5 alignment film to uniformly align the vertical LC molecular orientation as a function of IB energy density. Moreover, by examining the electro-optical (EO) characteristics of the Ta2O5 surfaces compared with those of the polyimide (PI) alignment layer, we confirmed that Ta2O5 has a low threshold voltage and a low power consumption when used as an LC alignment layer.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    Gligorić, Goran; Maluckov, Aleksandra; Hadžievski, Ljupčo; Malomed, Boris A.

    2008-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-07-01

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

  9. 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

  10. An exact analytical solution for the evolution of a dipole-dipole interacting system under spherical diffusion in magnetic resonance experiments.

    PubMed

    Sturniolo, Simone; Pieruccini, Marco

    2012-10-01

    A model system consisting of an isotropic ensemble of spin pairs, where dipole-dipole interaction is assumed to be effective only within each pair, is considered. The ideal segment connecting the spins in a couple has a fixed length but is free to rotate following a diffusion dynamics. This allows the free induction decay (FID) to be derived non-perturbatively by solving the appropriate Dyson equation associated to the problem. Motional narrowing can be described analytically in terms of only two parameters, i.e. the coupling constant of the interaction hamiltonian, b, and the orientational diffusion coefficient D. Salient features of the transverse correlation function thus obtained are discussed, and a comparison with numerical simulations performed with the software SPINEVOLUTION is presented. Interpreting b and D as effective parameters describing multiple interactions of a single spin with its neighbors in a real system, the analysis of published experimental data on poly(ethyl acrylate) has been carried out. It is found that for temperatures higher than and not too close to the glass transition, the results are the same as those found within the Anderson-Weiss approach by assuming a single time exponential decay of the average dipole-dipole interaction. On the other hand, as D tends to zero, FID oscillations characteristic of a rigid lattice show up. PMID:22975242

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

    PubMed

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

    2014-08-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-02-01

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

  13. 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

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

    NASA Astrophysics Data System (ADS)

    Ren, Jinjun; Eckert, Hellmut

    2015-11-01

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

  15. 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

  16. 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.

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

    PubMed Central

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

    1990-01-01

    We report electron paramagnetic resonance (EPR) experiments in frozen solutions of unreduced and reduced photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides R-26 in which Fe2+ has been chemically replaced by the isotope 65Cu2+. Samples in which the primary quinone acceptor QA is unreduced (Cu2+QA:RCs) give a powder EPR spectrum typical for Cu2+ having axial symmetry, corresponding to a d(x2 - y2) ground state orbital, with g values g parallel = 2.314 +/- 0.001 and g perpendicular = 2.060 +/- 0.003. The spectrum shows a hyperfine structure for the nuclear spin of copper (65I = 3/2) with A parallel = (-167 +/- 1) x 10(-4) cm-1 and /A perpendicular/ = (16 +/- 2) x 10(-4) cm-1, and hyperfine couplings with three nitrogen ligands. This has been verified in samples containing the naturally occurring 14N isotope (l = 1), and in samples where the nitrogen ligands to copper were replaced by the isotope 15N (l = 1/2). We introduce a model for the electronic structure at the position of the metal ion which reflects the recently determined three-dimensional structure of the RCs of Rb. sphaeroides (Allen, J. P., G. Feher, T. O. Yeates, H. Komiya, and D. C. Rees. 1987. Proc. Natl. Acad. Sci. USA. 84:5730: Allen, J. P., G. Feher, T. O. Yeates, H. Komiya, and D. C. Rees. 1988. Proc. Natl. Acad. Sci. USA, 85:8487) as well as our EPR results. In this model the copper ion is octahedrally coordinated to three nitrogens from histidine residues and to one carboxylate oxygen from a glutamic acid, forming a distorted square in the plane of the d(x2 = y2) ground state orbital. It is also bound to a nitrogen of another histidine and to the other carboxylate oxygen of the same glutamic acid residue, in a direction approximately normal to this plane. The EPR spectrum changes drastically when the quinone acceptor QA is chemically reduced (Cu2+QA-:RCs); the change is due to the exchange and dipole-dipole interactions between the Cu2+ and QA- spins. A model spin Hamiltonian

  18. Theoretical study of intermolecular interactions in nanoporous networks on boron doped silicon surface

    NASA Astrophysics Data System (ADS)

    Boukari, Khaoula; Duverger, Eric; Hanf, Marie-Christine; Stephan, Régis; Sonnet, Philippe

    2014-11-01

    Supramolecular networks on a doped boron silicon surface under ultra high vacuum (UHV) have been recently obtained (Makoudi et al., 2013). The used molecule contains different end-groups, bearing either bromine, iodine or hydrogen atoms denoted 1,3,5-tri(4‧-bromophenyl)benzene (TBB), 1,3,5-tri(4-iodophenyl)benzene (TIB) and 1,3,5-triphenyl-benzene (THB). To explain the formation of the nanoporous structures, interactions of the type aryl-X⋯H hydrogen bonds (X being a halogen atom) have been proposed. In order to obtain a complete insight of the stabilizing interaction in these networks adsorbed on the Si(1 1 1)√3x√3R30°-boron surface, we present a full density-functional-theory study taking the van der Waals interactions into account. We investigated the energetic and structural properties of three different nanoporous networks constituted by TBB, TIB and THB molecules. The electronic studies allow us to identify hydrogen bond and dipole-dipole intermolecular interactions in the supramolecular halogen networks, whereas only dipole-dipole interactions are present in the 1,3,5-triphenyl-benzene nanoporous network.

  19. 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…

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Kent-Dobias, Jaron; Bernoff, Andrew J.

    2015-03-01

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

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

    PubMed

    Kent-Dobias, Jaron; Bernoff, Andrew J

    2015-03-01

    We study pattern formation in planar fluid systems driven by intermolecular cohesion (which manifests as a line tension) and dipole-dipole repulsion, which are observed in physical systems including ferrofluids in Hele-Shaw cells and Langmuir layers. When the dipolar repulsion is sufficiently strong, domains undergo forked branching reminiscent of viscous fingering. A known difficulty with these models is that the energy associated with dipole-dipole interactions is singular at small distances. Following previous work, we demonstrate how to ameliorate this singularity and show that in the macroscopic limit only the scale of the microscopic details relative to the macroscopic extent of a system is relevant and develop an expression for the system energy that depends only on a generalized line tension Λ that in turn depends logarithmically on that scale. We conduct numerical studies that use energy minimization to find equilibrium states. Following the subcritical bifurcations from the circle, we find a few highly symmetric stable shapes, but nothing that resembles the observed diversity of experimental and dynamically simulated domains. The application of a weak random background to the energy landscape stabilizes a wide range of domain morphologies recovering the diversity observed experimentally. With this technique, we generate a large sample of qualitatively realistic shapes and use them to create an empirical model for extracting Λ with high accuracy using only a shape's perimeter and morphology. PMID:25871184

  3. 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.

  4. 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

  5. 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

  6. Estimation of intermolecular interactions in polymer networks

    SciTech Connect

    Subrananian, P.R.; Galiatsatos, V.

    1993-12-31

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

  7. Dipole-dipole-induced giant Goos-Hänchen shift in a photonic crystal doped with quantum dot nanostructures

    NASA Astrophysics Data System (ADS)

    Panahi, M.; Solookinejad, G.; Ahmadi Sangachin, E.; Hossein Asadpour, Seyyed

    2016-07-01

    The impact of the dipole-dipole interaction on the Goo-Hänchen (GH) shifts in reflected and transmitted lights is investigated. A weak probe beam is incident on a cavity containing the donor and acceptor quantum dots embedded in a nonlinear photonic crystal. We deduced that the GH shifts can be easily adjusted via controlling the corresponding parameters of the system in the presence or absence of dipole-dipole interaction. Our proposed model may be useful to developing the all-optical devices based on photonic materials doped with nanoparticles.

  8. 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.

  9. Experimental static dipole-dipole polarizabilities of molecules

    NASA Astrophysics Data System (ADS)

    Hohm, U.

    2013-12-01

    A compilation of the static mean dipole-dipole polarizability α is given for 174 molecules. All data are evaluated from gas phase measurements. For some molecules like H2, N2, and O2 very precise experimental data exist with an uncertainty of better than 0.1%. In general however, the experimental error is much higher. There are also molecules like HI, CH2Cl2 or CH2Br2 for which the available data do not even overlap within their error bars. The present tabulations should be used if highly accurate experimental values are needed.

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

    PubMed

    Haslmayr, Johannes; Renger, Thomas

    2013-07-28

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

  11. 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…

  12. 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

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  16. 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.

  17. Direct observation of intermolecular interactions mediated by hydrogen bonding

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    Covalent bonds arise from the overlap of the electronic clouds in the internucleus region, which is a pure quantum effect and cannot be obtained in any classical way. If the intermolecular interaction is of covalent character, the result from direct applications of classical simulation methods to the molecular system would be questionable. Here, we analyze the special intermolecular interaction between two NO molecules based on quantum chemical calculation. This weak intermolecular interaction, which is of covalent character, is responsible for the formation of the NO dimer, (NO)2, in its most stable conformation, a cis conformation. The natural bond orbital (NBO) analysis gives an intuitive illustration of the formation of the dimer bonding and antibonding orbitals concomitant with the breaking of the π bonds with bond order 0.5 of the monomers. The dimer bonding is counteracted by partially filling the antibonding dimer orbital and the repulsion between those fully or nearly fully occupied nonbonding dimer orbitals that make the dimer binding rather weak. The direct molecular mechanics (MM) calculation with the UFF force fields predicts a trans conformation as the most stable state, which contradicts the result of quantum mechanics (QM). The lesson from the investigation of this special system is that for the case where intermolecular interaction is of covalent character, a specific modification of the force fields of the molecular simulation method is necessary. Project supported by the National Natural Science Foundation of China (Grant Nos. 90403007 and 10975044), the Key Subject Construction Project of Hebei Provincial Universities, China, the Research Project of Hebei Education Department, China (Grant Nos. Z2012067 and Z2011133), the National Natural Science Foundation of China (Grant No. 11147103), and the Open Project Program of State Key Laboratory of Theoretical Physics, Institute of Theoretical Physics, Chinese Academy of Sciences, China (Grant No. Y5

  20. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

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

    2015-08-14

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

  1. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGESBeta

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

    2015-08-14

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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

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

    PubMed

    Lynch, Michael; Hagner, Kyle

    2015-01-01

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

  10. 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

  11. 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…

  12. 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

  13. 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.

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

    PubMed

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-23

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

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

    NASA Astrophysics Data System (ADS)

    Yamane, Hiroyuki; Kosugi, Nobuhiro

    2013-08-01

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

  16. 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.

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

    SciTech Connect

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

    1993-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-07-01

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

  19. 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)....

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

    NASA Astrophysics Data System (ADS)

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

    2002-05-01

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

  1. 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.

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

    SciTech Connect

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

    2006-01-15

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

  3. 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

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

    PubMed Central

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

    2013-01-01

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

  5. 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

  6. 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

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

    SciTech Connect

    Harbola, Upendra; Mukamel, Shaul

    2004-11-01

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

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

    PubMed

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

    2016-07-13

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

  9. 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.

  10. Intermolecular interaction as the origin of red shifts in absorption spectra of zinc-phthalocyanine from first-principles.

    PubMed

    Yanagisawa, Susumu; Yasuda, Taiga; Inagaki, Kouji; Morikawa, Yoshitada; Manseki, Kazuhiro; Yanagida, Shozo

    2013-11-01

    We investigate electronic origins of a redshift in absorption spectra of a dimerized zinc phthalocyanine molecule (ZnPc) by means of hybrid density functional theoretical calculations. In terms of the molecular orbital (MO) picture, the dimerization splits energy levels of frontier MOs such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the constituent molecules. Consequently, the absorption wavelength seems to become longer than the monomer as the overlap between the monomers becomes larger. However, for a ZnPc dimer configuration with its cofacially stacked monomer arrangement, the calculated absorption spectra within the time-dependent density functional theory indicates no redshift but blueshift in the Q-band absorption spectrum, i.e., a typical H-aggregate. The origin of the apparently contradictory result is elucidated by the conventional description of the interaction between monomer transition dipoles in molecular dimers [Kasha, M. Radiat. Res. 1963, 20, 55]. The redshift is caused by an interaction between the two head-to-tail transition dipoles of the monomers, while the side-by-side arranged transition dipoles result in a blueshift. By tuning the dipole-dipole interaction based on the electronic natures of the HOMO and the LUMO, we describe a slipped-stacked ZnPc dimer configuration in which the Q-band absorption wavelength increases by as large as 144 nm relative to the monomer Q-band. PMID:24106753

  11. Evidence for a noncovalent intermolecular interaction of opiates with thiamine.

    PubMed

    Misra, A L; Vadlamani, N L; Pontani, R B

    1977-11-01

    Opiate agonists and antagonists formed reversible molecular complexes with thiamine. The absorption maxima of these complexes were at wavelengths longer than those of the individual components and their intensities depended on the concentration and nature of the opiate component. The possible implications of such an interaction are discussed. PMID:928957

  12. 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.

  13. Probing Intermolecular Interaction through Thermal-Lens Spectroscopy

    PubMed Central

    Bhattacharyya, Indrajit; Kumar, Pardeep; Goswami, Debabrata

    2013-01-01

    Binary liquid mixtures are studied using femtosecond pump–probe thermal-lens (TL) spectroscopy. Changes in the measured TL signals as a function of relative concentration of binary mixtures show that these result from a combined effect of physical and molecular properties of the constituent binary liquids. The experimental TL values deviate from the ones calculated from phenomenological equations. These, we argue, are due to an underestimation of the influence of molecular interactions when the TL signals are calculated by using physical parameters only. PMID:21166402

  14. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    SciTech Connect

    Alocci, Davide; Bernini, Andrea; Niccolai, Neri

    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

  15. 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.

  16. Virtual photon exchange, intermolecular interactions and optical response functions

    NASA Astrophysics Data System (ADS)

    Salam, A.

    2015-11-01

    According to molecular quantum electrodynamics, coupling between material particles occurs due to an exchange of one or more virtual photons. In this work, the relationship between polarisability and hyperpolarisability tensors of atoms and molecules that feature in linear and nonlinear optical processes, and their analytically continued form in the complex frequency domain that appear in formulae describing fundamental inter-particle interactions, is studied. Examples involving a single virtual photon exchange, which are linearly proportional to electric dipole moments at each centre, include the electrostatic energy and the resonant transfer of excitation energy. The Casimir-Polder dispersion potential, and its discriminatory counterpart applicable to coupled chiral molecules, are used to illustrate response properties depending on the exchange of two virtual photons. Meanwhile, the energy shift between two hyperpolarisable species, a higher order discriminatory contribution to the dispersion potential, is employed to represent forces arising from the three virtual photon exchange. It is shown that for energy shifts that are quadratic or bilinear or cubic in the transition dipole moment, it is necessary to account for all two- and three-photon optical processes, such as absorption, emission and linear and nonlinear scattering of light in order to arrive at the correct form of the molecular response tensor.

  17. 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.

  18. 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.

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

    PubMed

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

    2016-07-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  1. Intermolecular interactions in multi-component crystals of acridinone/thioacridinone derivatives: Structural and energetics investigations

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Trzybiński, Damian; Zadykowicz, Beata

    2016-12-01

    A single crystal X-ray analysis of two multi-component crystals consisting of an acridinone/thioacridinone moiety and a solvent moiety - water and ammonia (1 and 2), respectively, was carried out to determine the crystal structures of obtained crystals. A theoretical approach was undertaken - using the DFT method, lattice energies calculations and Hirshfeld surfaces (HS) - to qualitatively and quantitatively assess the intermolecular interactions within the crystal. HS analysis was showed that the H⋯H, C⋯H/H⋯C and C⋯C contacts for both structures (altogether 81.6% of total Hirshfeld surface area for 1 and 79.3% for 2) and the O⋯H/H⋯O (14.3%) for 1 and the S⋯H/H⋯S (15.2%) contacts for 2 were the characteristic intermolecular contacts in the related crystal structures. Using a computational methods were confirmed that the main contribution to the stabilization of the crystal lattice of compound 1 comes from the Coulombic interactions, whereas in compound 2 electrostatic and van der Waals appear to have similar contribution to the crystal lattice energy. Theoretical calculations of the investigated compounds have also allowed to determine the energy of a single specific intermolecular interaction.

  2. 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.

  3. Intermolecular Interactions and Cooperative Effects from Electronic Structure Calculations: An Effective Means for Developing Interaction Potentials for Condensed Phase Simulations

    SciTech Connect

    Xantheas, Sotiris S.

    2004-05-01

    The modeling of the macroscopic properties of homogeneous and inhomogeneous systems via atomistic simulations such as molecular dynamics (MD) or Monte Carlo (MC) techniques is based on the accurate description of the relevant solvent-solute and solvent-solvent intermolecular interactions. The total energy (U) of an n-body molecular system can be formally written as [1,2,3

  4. 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.

  5. 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.

  6. Intermolecular interactions in photodamaged DNA from density functional theory symmetry-adapted perturbation theory.

    PubMed

    Sadeghian, Keyarash; Bocola, Marco; Schütz, Martin

    2011-05-01

    The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry-adapted perturbation theory (DFT-SAPT) and compared to the original (or repaired) case with pyrimidines (TpT) instead of CPD. The CPD aggregation is on average destabilized by about 6 kcal mol(-1) relative to that involving TpT. The effect of destabilization is asymmetric, that is, it involves a single H-bonding (Watson-Crick (WC) type) base-pair interaction. PMID:21452189

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

    PubMed

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

    2015-10-01

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

  8. 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.

  9. 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

  10. 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

  11. Structure and intermolecular interactions of glipizide from laboratory X-ray powder diffraction.

    PubMed

    Burley, Jonathan C

    2005-12-01

    The crystal structure of glipizide, used as a major treatment of type-2 diabetes, has been determined ab initio using variable-temperature laboratory X-ray powder diffraction combined with a direct-space Monte Carlo/simulated annealing methodology. The strengths of the intermolecular interactions (van der Waals, pi-pi stacking, hydrogen bonding and steric interlock) were quantitatively estimated using the thermal expansion data, which were collected in the same set of experiments as those used to determine the structure. PMID:16306678

  12. Intermolecular Interactions between Eosin Y and Caffeine Using (1)H-NMR Spectroscopy.

    PubMed

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

    2013-12-31

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

  13. Application of Dipole-dipole, Induced Polarization, and CSAMT Electrical Methods to Detect Evidence of an Underground Nuclear Explosion

    NASA Astrophysics Data System (ADS)

    Sweeney, J. J.; Felske, D.

    2013-12-01

    There is little experience with application of electrical methods that can be applied during the continuation period of an on-site inspection (OSI), one of the verification methods of the Comprehensive Nuclear-Test-Ban Treaty (CTBT). In order add to such experience, we conducted controlled source audiomagnetotelluric (CSAMT), dipole-dipole resistivity, and induced polarization electrical measurements along three survey lines over and near to ground zero of an historic nuclear explosion. The presentation will provide details and results of the surveys, an assessment of application of the method toward the purposes of an OSI, and an assessment of the manpower and time requirements for data collection and processing that will impact OSI inspection team operations. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

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

    DOE PAGESBeta

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

    2015-02-19

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

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

    SciTech Connect

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

    2015-02-19

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

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

    SciTech Connect

    Christensen, Anders S. E-mail: cui@chem.wisc.edu; Cui, Qiang E-mail: cui@chem.wisc.edu; Elstner, Marcus

    2015-08-28

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

  17. Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.

    PubMed

    Zhang, Zhiyong; Sanbonmatsu, Karissa Y; Voth, Gregory A

    2011-10-26

    The ribosome is a very large complex that consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, intermolecular interactions in the Escherichia coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins and to capture functional motions in the ribosome, and then the CG sites are connected by harmonic springs, and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, and they are in good agreement with various experimental data. Nearly all the bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has minimal CG interactions with the rest of the subunit; however, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the intermolecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models. PMID:21910449

  18. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed

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

    2015-10-01

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

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

    SciTech Connect

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

    2015-10-07

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

  2. 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

  3. 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.

  4. 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

  5. Structural changes and intermolecular interactions of filled ice Ic structure for hydrogen hydrate under high pressure

    NASA Astrophysics Data System (ADS)

    Machida, S.; Hirai, H.; Kawamura, T.; Yamamoto, Y.; Yagi, T.

    2010-03-01

    High-pressure experiments of hydrogen hydrate were performed using a diamond anvil cell under conditions of 0.1-44.2 GPa and at room temperature. Also, high pressure Raman studies of solid hydrogen were performed in the pressure range of 0.1-43.7 GPa. X-ray diffractometry (XRD) for hydrogen hydrate revealed that a known high-pressure structure, filled ice Ic structure, of hydrogen hydrate transformed to a new high-pressure structure at approximately 35-40 GPa. A comparison of the Raman spectroscopy of a vibron for hydrogen molecules between hydrogen hydrate and solid hydrogen revealed that the extraction of hydrogen molecules from hydrogen hydrate occurred above 20 GPa. Also, the Raman spectra of a roton revealed that the rotation of hydrogen molecules in hydrogen hydrate was suppressed at around 20 GPa and that the rotation recovered under higher pressure. These results indicated that remarkable intermolecular interactions in hydrogen hydrate between neighboring hydrogen molecules and between guest hydrogen molecules and host water molecules might occur. These intermolecular interactions could produce the stability of hydrogen hydrate.

  6. Effect of the electronic structure of quinoline and its derivatives on the capacity for intermolecular interactions

    SciTech Connect

    Privalova, N.Yu.; Sokolova, I.V.

    1985-05-01

    Calculations of the ground and excited states of quinoline and its 20H-, 70H-, 7NH2-, 7N(CH3)2-, and 7N(C2H5)2- substituted derivatives were undertaken by the INDO method, and the effect of intramolecular proton transfer (IPT) on their electronic structure was studied. The proton-accepting capacity of the compounds for intermolecular interactions was estimated by the molecular electrostatic potential method. It was shown that the proton-accepting capacity with respect to intermolecular interactions increases during the tautomeric transformation of the enolic form of 2-OH-quinoline to its keto form. The change in the basicity of the two forms of the molecules is affected by the orbital nature, and the multiplicity of the state is also important for the keto form. Substitution by electron-donating groups leads to increase in the proton-accepting capacity of both forms of the compounds in the S0, S/sub */, and T/sub */ states.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Manifestation of structure and intermolecular interactions of biologically active brassinosteroids in infrared spectra

    NASA Astrophysics Data System (ADS)

    Borisevich, N. A.; Skornyakov, I. V.; Khripach, V. A.; Tolstorozhev, G. B.; Zhabinskii, V. N.

    2007-09-01

    We have analyzed the IR spectra obtained for steroidal phytohormones 24-epibrassinolide, 24-epicastasterone, 28-homobrassinolide, and 28-homocastasterone. The characteristic frequencies of the stretching vibrations of the hydrocarbon groups CH3, CH2, and CH and also the C=O groups in the spectra of brassinolides are higher than in the spectra of castasterones, which makes it possible to identify them from the IR spectra. Study of the spectra of these brassinosteroids in different media (pressed samples in KBr, films, solutions in CHCl3 and CDCl3) allowed us to establish the presence of intermolecular interactions in which C=O and OH groups, OH-OH groups participate, and also the possible formation of intramolecular hydrogen bonds between the OH groups of the molecules.

  12. 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.

  13. Predicted occupancies in gas hydrates on Titan and Mars: sensitivity on treatment of intermolecular interactions.

    NASA Astrophysics Data System (ADS)

    Thomas, Caroline; Picaud, Sylvain; Ballenegger, Vincent; Mousis, Olivier

    2010-05-01

    We investigate here the sensitivity of gas hydrate occupancies predicted on the basis of van der Waals-Platteeuw theory, as a function of the treatment of the intermolecular guest-water interaction potential. First, we determine the minimum number of water molecules that have to be taken into account in the calculations of this interaction potential. We show that analytical correction terms that account for the interactions with the water molecules beyond the cutoff distance (typically chosen to take into account at least 4 water layers around the guest molecule) must be introduced to improve significantly the convergence rate, and hence the efficiency of the computation of the Langmuir constants. Then we use different recent guest-water interaction potential models to calculate the cage occupancies in pure methane or carbon dioxide clathrates. We show that the corresponding predicted cage occupancies can vary significantly depending on the model, although all the results are within the uncertainties of the available experimental data. That sensitivity becomes especially strong in the case of multiple guest clathrates, and, for instance, the results obtained for guest clathrate hydrates potentially formed on the surface of Mars can vary by more than two orders of magnitude depending on the model. These results underline the strong need for experimental data on pure and multiple guest clathrate hydrates, in particular in the temperature and pressure range that are relevant in extreme environment conditions, to discriminate among the theoretical models.

  14. 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

  15. Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals.

    PubMed

    Iwura, Takafumi; Fukuda, Jun; Yamazaki, Katsuyoshi; Kanamaru, Shuji; Arisaka, Fumio

    2014-01-01

    Intermolecular interactions and conformation in dimer species of Palivizumab, a monoclonal antibody (IgG1), were investigated to elucidate the physical and chemical properties of the dimerized antibody. Palivizumab solution contains ∼1% dimer and 99% monomer. The dimer species was isolated by size-exclusion chromatography and analysed by a number of methods including analytical ultracentrifugation-sedimantetion velocity (AUC-SV). AUC-SV in the presence of sodium dodecyl sulphate indicated that approximately half of the dimer fraction was non-covalently associated, whereas the other half was dimerized by covalent bond. Disulphide bond and dityrosine formation were likely to be involved in the covalent dimerization. Limited proteolysis of the isolated dimer by Lys-C and mass spectrometry for the resultant products indicated that the dimer species were formed by Fab-Fc or Fab-Fab interactions, whereas Fc-Fc interactions were not found. It is thus likely that the dimerization occurs mainly via the Fab region. With regard to the conformation of the dimer species, the secondary and tertiary structures were shown to be almost identical to those of the monomer. Furthermore, the thermal stability turned out also to be very similar between the dimer and monomer. PMID:24155259

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  20. 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

  1. 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

  2. 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

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

    SciTech Connect

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

    2015-10-15

    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. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.

  4. 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.

  5. 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)+ṡX- (X = Cl-, 1; Br-, 2), [(C7H9FN)2ṡ(18-crown-6)2]2+ṡ(MCl4)2- (M = Mn, 3; Co, 5; Zn, 7; Cd, 8), [(C7H9FN)ṡ(18-crown-6)]+ṡ(FeCl4)- (4) and [(C7H9FN)ṡ(18-crown-6)]+ṡ1/2(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, π) 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.

  6. Sensitivity of predicted gas hydrate occupancies on treatment of intermolecular interactions

    NASA Astrophysics Data System (ADS)

    Thomas, Caroline; Picaud, Sylvain; Ballenegger, Vincent; Mousis, Olivier

    2010-03-01

    The sensitivity of gas hydrate occupancies predicted on the basis of van der Waals-Platteeuw theory is investigated, as a function of the intermolecular guest-water interaction potential model, and of the number of water molecules taken into account. Simple analytical correction terms that account for the interactions with the water molecules beyond the cutoff distance are introduced, and shown to improve significantly the convergence rate, and hence the efficiency of the computation of the Langmuir constants. The predicted cage occupancies in pure methane and pure carbon dioxide clathrates, calculated using different recent guest-water pair potentials models derived from ab initio calculations, can vary significantly depending on the model. That sensitivity becomes especially strong in the case of multiple guest clathrates. It is shown that the abundances of coenclathrated molecules in multiple guest clathrate hydrates potentially formed on the surface of Mars can vary by more than two orders of magnitude depending on the model. These results underline the strong need for experimental data on pure and multiple guest clathrate hydrates, in particular in the temperature and pressure range that are relevant in extreme environment conditions, to discriminate among the theoretical models.

  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. Ab initio intermolecular potential energy surfaces of He-CS2, Ne-CS2 and Ar-CS2 complexes

    NASA Astrophysics Data System (ADS)

    Farrokhpour, H.; Tozihi, M.

    2013-03-01

    The potential energy surfaces of the He-CS2, Ne-CS2 and Ar-CS2 van der Waals complexes were calculated for the first time at the CCSD(T) level of theory using the aug-cc-pVDZ basis set augmented with a set of midbond functions (3s3p2d1f1g). It was found that the calculated interaction potential, using the applied basis set, readily converges to the complete basis set limit. For a broad range of intermolecular separations and configurations, the interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error (BSSE). In addition, symmetry-adapted perturbation theory (SAPT) calculations were performed with the same basis set in order to determine the character of the interaction energy of the most stable configuration of each complex at different intermolecular separations in order to make a comparison with the CCSD(T) results. The CCSD(T) calculated potential energy surface of each complex was fitted to an analytic expression to obtain the values of the isotropic dipole-dipole ( ? ) and dipole-quadruple ( ? ) dispersion coefficients of each complex. Finally, the interaction second virial coefficients (B12) were obtained using the calculated potential energy surface and used together with the experimental second virial coefficients of pure gases (CS2, Ar, Ne and He) to obtain the second virial coefficient of mixtures of CS2 with rare gas at different temperatures and mole fractions.

  9. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-10-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

  10. Possible intermolecular interaction between quinolones and biphenylacetic acid inhibits gamma-aminobutyric acid receptor sites.

    PubMed Central

    Akahane, K; Kimura, Y; Tsutomi, Y; Hayakawa, I

    1994-01-01

    The combination of some new quinolone antibacterial agents with 4-biphenylacetic acid (BPAA), a metabolite of fenbufen, is known to specifically induce functional blockade of the gamma-aminobutyric acid (GABA) receptors. The mechanisms of these drug interactions were further examined. Scatchard analysis of [3H]muscimol binding to rat brain plasma membranes in the presence of enoxacin and BPAA revealed that a significant decrease in the number of muscimol binding sites was produced without affecting the affinity of binding to the receptors. In the presence of norfloxacin, BPAA inhibited muscimol binding the most potently of the six BPAA-related compounds tested. Fenbufen and 9,10-dihydro-gamma-oxo-2-phenanthrenebutyric acid also inhibited the binding, and 4-biphenylcarboxylic acid and methyl 4-biphenylacetate inhibited it slightly, but 3-benzoylpropionic acid exhibited no competitive inhibition. Accordingly, hybrid molecules of norfloxacin and BPAA were synthesized for stereochemical analysis of these drug interactions. A hybrid with a -CONH(CH2)3- chain between norfloxacin and BPAA (flexible structure) inhibited muscimol binding, and intracisternal injection of this hybrid caused clonic convulsions in mice more potently than the combination of norfloxacin and BPAA did. In contrast, a hybrid linked by -CONH- (stretched structure) showed almost no such inhibitory effect. 1H NMR analysis indicated the presence of intramolecular attraction at the quinoline ring of the hybrid exhibiting the antagonistic activity. These results suggest the possibility that quinolones and BPAA interact with the GABA receptor at nearby sites and that the binding affinity of quinolones to the GABA receptors is largely enhanced by the intermolecular interaction with BPAA. PMID:7840564

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

    PubMed

    Lao, Ka Un; Herbert, John M

    2016-06-14

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

  12. Conformational analysis and intramolecular/intermolecular interactions of N,N‧-dibenzylideneethylenediamine derivatives

    NASA Astrophysics Data System (ADS)

    Dabbagh, Hossein A.; Zamani, Mehdi; Farrokhpour, Hossein; Hossein Habibi, Mohammad; Barati, Kazem

    2010-11-01

    The molecular structures, conformational stability and molecular energy profile of three derivatives of RC 6H 4CHNCH 2CH 2NCHC 6H 4R including N, N'-dibenzylideneethylenediamine ( 1, R = H), N, N'-bis(4-trifluoromethoxybenzylidene)ethylenediamine ( 2, R = OCF 3), and N, N'-bis(4-dimethylaminobenzylidene)ethylenediamine ( 3, R = N(CH 3) 2) were obtained at B3LYP/6-31++G ** and HF/6-31++G ** levels of theory and compared with X-ray single crystal structures. The conformation of 1 and 2 is anti, while that of 3 is gauche in solid state (X-ray geometry). Based on calculations, there are seven energy minima in potential energy curves. A gauche conformer of 1, 2 and 3 has the lowest energy minimum (in the calculations modeling gas phase conditions) among all the other conformers. This is in contrast to X-ray findings (solid phase) for 1 and 2 but complements the X-ray finding for 3. These results were analyzed by natural bond orbital (NBO) and molecular orbital (MO) to determine the role of intra- and/or intermolecular interactions in the crystal structures.

  13. Kirromycin-induced modifications facilitate the separation of EF-Tu species and reveal intermolecular interactions.

    PubMed

    Anborgh, P H; Swart, G W; Parmeggiani, A

    1991-11-01

    A simplified method for the separation of a kirromycin-sensitive tufB-encoded elongation factor Tu (EF-TuBs) from a kirromycin-resistant tufA product (EF-TuAr) was obtained by exploiting the specific increase of negative [corrected] charges induced by the antibiotic, resulting in a retarded elution of kirromycin-bound EF-TuBs on ionic chromatography. The kirromycin-free EF-TuBs is active in poly(Phe) synthesis and shows similar properties to EF-TuAsBs. As expected for these two distinct species, the dissociation of the EF-TuArBs.GTP complex in the presence of kirromycin shows a biphasic curve; in contrast, a monophasic GTP dissociation rate was found for a combination of two mutated EF-Tu species, EF-TuArBo, revealing the existence of intermolecular interactions. These observations prove for the first time the existence of cooperative phenomena between EF-Tu species in vitro, as suggested earlier by in vivo experiments. PMID:1959611

  14. Intermolecular interactions and solvent diffusion in ordered nanostructures formed by self-assembly of block copolymers

    NASA Astrophysics Data System (ADS)

    Gu, Zhiyong

    Hydrogels formed by Poloxamer poly(ethylene oxide)-poly(propylene oxide) (PEO-PPO) block copolymers find various pharmaceutical and biomedical applications. A variety of ordered structures can be exhibited by Poloxamer block copolymers in selective solvents such as water, for example, micellar cubic phase, hexagonal phase, lamellar phase, etc. We are interested in the thermodynamic and transport properties of water in such hydrogels that have an ordered (lyotropic liquid crystalline) structure. We have investigated the time evolution of water loss from Poloxamer gel films under a driving force of known water vapor pressure in the air in contact with the film. The experimental data on the drying process have been fitted to the diffusion equation for water in the film, under a boundary condition that includes the water concentration in the gel at infinite time; the water diffusion coefficient and other parameters have thus been obtained. The water chemical potential and osmotic pressure in the gel have been obtained from osmotic stress measurements. The osmotic pressure (force), together with data on the corresponding lyotropic liquid crystal spacing (distance) that we obtained from Small Angle X-Ray Scattering (SAXS) measurements, have been analyzed to provide information on the prevailing intermolecular (inter-assembly) forces in the gel. The forces in the gel reveal interactions that occur at two levels, that of the PEO coil and that of the PEO segment.

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

    SciTech Connect

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

    2009-10-28

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

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

    SciTech Connect

    Horn, Paul R. E-mail: mhg@cchem.berkeley.edu; Head-Gordon, Martin E-mail: mhg@cchem.berkeley.edu

    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{sup +}, water–Mg{sup 2+}, water–F{sup −}, and water–Cl{sup −} 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.

  17. 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

  18. Aggregation and other intermolecular interactions of biological buffers observed by capillary electrophoresis and UV photometry.

    PubMed

    Vespalec, R; Vlcková, M; Horáková, H

    2004-10-01

    Electrophoretic and photometric experiments strongly indicate that monovalent anions, which arise by deprotonation of the nitrogen atom in zwitterionic Good's buffers 3-(cyclohexylamino)-2-hydroxy-1-propanesulfonic acid (CAPSO) and 3-morpholinopropanesulfonic acid (MOPS), spontaneously aggregate. Cationic migration of sanguinarine (SA) and chelerythrine (CHE) in highly alkaline 1,3-bis[tris(hydroxymethyl)methylamino]propane (Bis-Tris-propane), in which the concentration of cations of both alkaloids is negligible, may be explained by the existence of an aggregate, which contains uncharged sanguinarine or chelerythrine and one monovalent cation of Bis-Tris-propane at least. Tendency of tris(hydroxymethyl)aminomethane (Tris), bis (2-hydroxyethyl)iminotris(hydroxymethyl)methane (Bis-Tris) and Bis-Tris-propane cations to ion pairing with synthetic cluster borane anions and with fused silica markedly rises up with the size and charge of these cations. The drop in mobility of cluster borane compounds sometimes exceeds 50% of their mobility found at identical pH and ionic strength in buffers with sodium cation. The electroosmosis drop approached 70% if background electrolyte contained Bis-Tris-propane cations instead of sodium cations. Nitrate, taken as a model inorganic ion, and four randomly chosen organic anions interacted markedly less with Tris, Bis-Tris and Bis-Tris-propane cations than cluster borane anions. 2-(N-morpholino)ethanesulfonic (MES) acid anions present in background electrolyte affect the ion pairing of Tris, Bis-Tris and Bis-Tris-propane cations with anionic analytes and, in this way influence also mobilites of these anionic analytes. Limited hydrophilicity at least one of interacting species appears to be the most probable cause of observed intermolecular interactions of biological buffers. PMID:15532558

  19. Dynamics of intermolecular interactions in CCl4via the isotope effect by femtosecond time-resolved spectroscopy.

    PubMed

    Konarska, Jadwiga; Gadomski, Wojciech; Ratajska-Gadomska, Bożena; Polok, Kamil; Pudłowski, Grzegorz; Kardaś, Tomasz M

    2016-06-21

    We report our study on the ultrafast dynamics of intermolecular interactions in liquid CCl4. A transient transmission time domain signal, obtained in the 40 ps delay range, exhibits beating at the difference frequency of the totally symmetric stretching vibrations of the tetrachloride isotopologues. We show that the spectra obtained as the windowed Fourier transform of different parts of the time domain signal in the range of this totally symmetric vibration, split due to the isotope effect, carry the information about the dynamics of the coherently excited, coupled molecules. We use a simple theoretical model in order to prove that the intermolecular interaction influences the relative amplitudes of the isotopologue peaks in the spectrum. Moreover, we demonstrate that the pump induced coherence in the system leads to additional strengthening of the interaction, which can be observed in the spectra obtained from the experimental time domain signal. PMID:27244535

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-01-01

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

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

    PubMed

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

    2011-11-17

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

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

    PubMed

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

    2010-03-01

    Recently, the vacuum-phase molecular polarizability tensor of various molecules has been accurately modeled (Truchon et al., J Chem Theory Comput 2008, 4, 1480) with an intramolecular 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 mechanical (QM) molecular polarizability tensors, we extend the application of the "electronic polarization from internal continuu" (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 QM abinitio electrostatic potential (ESP). 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 ESP 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-pi 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 adjusting the vacuum-phase parameters. PMID:19598266

  4. 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.

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

    SciTech Connect

    Azar, Richard Julian Head-Gordon, Martin

    2015-05-28

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

  6. 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 versions of the newly introduced [S. S. Xantheas and J. C. Werhahn, J. Chem. Phys.141, 064117 (2014)] generalized forms of some popular potential energy functions (PEFs) describing intermolecular interactions – Mie, Lennard-Jones, Morse, and Buckingham exponential-6 – have been used to fit the ab initio relaxed approach paths and fixed approach paths for the halide-water, X-(H2O), X = F, Cl, Br, I, and alkali metal-water, M+(H2O), M = Li, Na, K, Rb, Cs, interactions. The generalized forms of those PEFs have an additional parameter with respect to the original forms and produce fits to the ab initio data that are between one and two orders of magnitude better in the χ2 than the original PEFs. They were found to describe both the long-range, minimum and repulsive wall of the respective potential energy surfaces quite accurately. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gBe-6) potentials were found to best fit the ab initio data for these two classes of ion-water interactions. Finally, the fitted values of the parameter of the (eM) and (gBe-6) PEFs that control the repulsive wall of the potential correlate remarkably well with the ionic radii of the halide and alkali metal ions.

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

    PubMed

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

    2015-07-15

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

  8. 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

  9. 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

  10. 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.

  11. 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...

  12. Benchmark Calculations of Three-Body Intermolecular Interactions and the Performance of Low-Cost Electronic Structure Methods.

    PubMed

    Řezáč, Jan; Huang, Yuanhang; Hobza, Pavel; Beran, Gregory J O

    2015-07-14

    Many-body noncovalent interactions are increasingly important in large and/or condensed-phase systems, but the current understanding of how well various models predict these interactions is limited. Here, benchmark complete-basis set coupled cluster singles, doubles, and perturbative triples (CCSD(T)) calculations have been performed to generate a new test set for three-body intermolecular interactions. This "3B-69" benchmark set includes three-body interaction energies for 69 total trimer structures, consisting of three structures from each of 23 different molecular crystals. By including structures that exhibit a variety of intermolecular interactions and packing arrangements, this set provides a stringent test for the ability of electronic structure methods to describe the correct physics involved in the interactions. Both MP2.5 (the average of second- and third-order Møller-Plesset perturbation theory) and spin-component-scaled CCSD for noncovalent interactions (SCS-MI-CCSD) perform well. MP2 handles the polarization aspects reasonably well, but it omits three-body dispersion. In contrast, many widely used density functionals corrected with three-body D3 dispersion correction perform comparatively poorly. The primary difficulty stems from the treatment of exchange and polarization in the functionals rather than from the dispersion correction, though the three-body dispersion may also be moderately underestimated by the D3 correction. PMID:26575743

  13. 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.

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

    PubMed

    Hanni, Matti; Lantto, Perttu; Ilias, Miroslav; Jensen, Hans Jorgen Aagaard; Vaara, Juha

    2007-10-28

    Relativistic effects on the (129)Xe nuclear magnetic resonance shielding and (131)Xe nuclear quadrupole coupling (NQC) tensors are examined in the weakly bound Xe(2) system at different levels of theory including the relativistic four-component Dirac-Hartree-Fock (DHF) method. The intermolecular interaction-induced binary chemical shift delta, the anisotropy of the shielding tensor Deltasigma, and the NQC constant along the internuclear axis chi( parallel) 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 Moller-Plesset many-body perturbation (DMP2) theory is used to examine the cross coupling between correlation and relativity on NQC. The same is investigated for delta and Deltasigma by BPPT with a density functional theory model. A semiquantitative agreement between the BPPT and DHF binary property curves is obtained for delta and Deltasigma in Xe(2). 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 chi( parallel), 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 (129)Xe 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

  15. 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.

  16. Intermolecular interactions in rifabutin-2-hydroxypropyl-β-cyclodextrin-water solutions, according to solubility data

    NASA Astrophysics Data System (ADS)

    Anshakova, A. V.; Vinogradov, E. V.; Sedush, N. G.; Kurtikyan, T. S.; Zhokhov, S. S.; Polshakov, V. I.; Ermolenko, Yu. V.; Konyukhov, V. Yu.; Maksimenko, O. O.; Gelperin, S. E.

    2016-05-01

    The formulations of rifabutin (RB) and 2-hydroxypropyl-β-cyclodextrin (HP-β-CD), obtained using different preparation techniques, are studied by means of differential scanning calorimetry and molecular spectroscopy (FTIR, NMR, Raman scattering, and photon correlation light scattering). It is established that molecules of RB do not form inclusion complexes with the molecules of HP-β-CD, and an increase in the solubility of RB determined earlier is caused by the formation of weak intermolecular associates.

  17. 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

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

    PubMed

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

    2014-07-28

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

  19. 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).

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

    PubMed

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

    2015-01-28

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

  1. Intermolecular interactions in mixtures of ethyl formate with methanol, ethanol, and 1-propanol on density, viscosity, and ultrasonic data

    NASA Astrophysics Data System (ADS)

    Elangovan, S.; Mullainathan, S.

    2014-12-01

    Density (ρ), viscosity (η), and ultrasonic velocity ( U) have been measured for binary mixtures of ethyl formate with methanol, ethanol, and 1-propanol at 303 K. From the experimental data, adiabatic compressibility (β), acoustic impedance ( Z), viscous relaxation time (τ), free length ( L f), free volume ( V f), internal pressure (πi), and Gibbs free energy (Δ G) have been deduced. It is shown that strength of intermolecular interactions between ethyl formate with selected 1-alcohols were in the order of methanol < ethanol < 1-propanol.

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

    PubMed

    Derikvand, Zohreh; Zabardasti, Abedien; Azadbakht, Azadeh

    2015-11-01

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

  3. Lack of evidence for intermolecular epistatic interactions between adiponectin and resistin gene polymorphisms in Malaysian male subjects

    PubMed Central

    Lau, Cia-Hin; Muniandy, Sekaran

    2012-01-01

    Epistasis (gene-gene interaction) is a ubiquitous component of the genetic architecture of complex traits such as susceptibility to common human diseases. Given the strong negative correlation between circulating adiponectin and resistin levels, the potential intermolecular epistatic interactions between ADIPOQ (SNP+45T > G, SNP+276G > T, SNP+639T > C and SNP+1212A > G) and RETN (SNP-420C > G and SNP+299G > A) gene polymorphisms in the genetic risk underlying type 2 diabetes (T2DM) and metabolic syndrome (MS) were assessed. The potential mutual influence of the ADIPOQ and RETN genes on their adipokine levels was also examined. The rare homozygous genotype (risk alleles) of SNP-420C > G at the RETN locus tended to be co-inherited together with the common homozygous genotypes (protective alleles) of SNP+639T > C and SNP+1212A > G at the ADIPOQ locus. Despite the close structural relationship between the ADIPOQ and RETN genes, there was no evidence of an intermolecular epistatic interaction between these genes. There was also no reciprocal effect of the ADIPOQ and RETN genes on their adipokine levels, i.e., ADIPOQ did not affect resistin levels nor did RETN affect adiponectin levels. The possible influence of the ADIPOQ gene on RETN expression warrants further investigation. PMID:22481872

  4. Key Inter-molecular Interactions in the E. Coli 70S Ribosome Revealed by Coarse-Grained Analysis

    PubMed Central

    Zhang, Zhiyong; Sanbonmatsu, Karissa Y.; Voth, Gregory A.

    2011-01-01

    The ribosome is a very large complex, which consists of many RNA and protein molecules and plays a central role in protein biosynthesis in all organisms. Extensive interactions between different molecules are critical to ribosomal functional dynamics. In this work, inter-molecular interactions in the E. coli 70S ribosome are investigated by coarse-grained (CG) analysis. CG models are defined to preserve dynamic domains in RNAs and proteins, and capture functional motions in the ribosome, then the CG sites are connected by harmonic springs and spring constants are obtained by matching the computed fluctuations to those of an all-atom molecular dynamics (MD) simulation. Those spring constants indicate how strong the interactions are between the ribosomal components, which are in good agreement with various experimental data. Nearly all of bridges between the small and large ribosomal subunits are indicated by CG interactions with large spring constants. The head of the small subunit is very mobile because it has the minimal CG interactions with the rest of the subunit; However, a large number of small subunit proteins bind to maintain the internal structure of the head. The results show a clear connection between the inter-molecular interactions and the structural and functional properties of the ribosome because of the reduced complexity in domain-based CG models. The present approach also provides a useful strategy to map interactions between molecules within large biomolecular complexes since it is not straightforward to investigate these by either atomistic MD simulations or residue-based elastic network models. PMID:21910449

  5. 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

  6. 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.

  7. 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

  8. Intermolecular interactions in methyl formate-ethanol mixtures at 303-313 K according to ultrasonic data

    NASA Astrophysics Data System (ADS)

    Elangovan, S.; Mullainathan, S.

    2014-04-01

    Density (ρ), viscosity (η), and ultrasonic velocity ( U) have been measured for a binary mixture composed of methyl formate and ethanol at 303, 308, and 313 K. The adiabatic compressibility (β), acoustic impedance (Z), free length ( L f ), free volume ( V f ), internal pressure (π i ), viscous relaxation time (τ), and Gibbs free energy (Δ G) were calculated from the experimental data. The excess values of these parameters (β E , Z E , L {/f E }, V {/f E }, π {/i E }, τ E , and Δ G E ) have also been calculated using the determined parameters and interpreted in terms of molecular interactions. The deviations in the sign and values of these excess parameters from the ideal mixing reveal the nature of intermolecular interactions between components of the mixture.

  9. 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

  10. 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.

  11. 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

  12. 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

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

    SciTech Connect

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

    1988-10-26

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

  14. 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

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

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

    SciTech Connect

    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{sup 6}) methods like MP2.5 or even spin-component-scaled coupled cluster models for 3-body intermolecular interactions with only O(N{sup 5}) computational cost.

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  19. [Intermolecular Interactions between Cytisine and Bovine Serum Albumin A Synchronous Fluorescence Spectroscopic Analysis and Molecular Docking Research].

    PubMed

    Wu, Yu-hang; Han, Zhong-bao; Ma, Jia-ze; He, Yan; Liu, Li-yan; Xin, Shi-gang; Yu, Zhan

    2016-03-01

    Cytisine (Cy) is one of the alkaloids that exist naturally in the plant genera Laburnum of the family Fabaceae. With strong bioactivities, Cy is commercialized for smoking cessation for years. In this work, the study of intermolecular interactions between Cy and bovine serum albumin (BSA) was performed by applying fluorescence spectroscopic methods under simulated physiological conditions. The mechanism of fluorescence quenching of BSA by Cy was also studied. Parameters such as bathing temperature, time and solution pH were investigated to optimize the fluorescence quenching. The binding type, binding ratio and binding constant between BSA and Cy were calculated by using the Stem-Volmer equation. Experimental results indicated that Cy can quench the fluorescent emission of BSA statically by forming a 1 : 1 type non-covalent complex and the binding constant is 5.6 x 10(3) L x mol(-1). Synchronous fluorescence spectral research shows Cy may affect the fluorescence emission of Trp residues of BSA. Furthermore, molecular docking is utilized to model the complex and probe the plausible quenching mechanism. It can be noted that the hydrogen bindings and hydrophobic interactions between Cy and BSA change the micro-environment of Trp213, which leads to the fluorescence quenching of BSA. PMID:27400521

  20. 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.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  3. 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.

  4. 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

  5. The effects of intermolecular interactions on the physical properties of organogels in edible oils.

    PubMed

    Lupi, Francesca R; Greco, Valeria; Baldino, Noemi; de Cindio, Bruno; Fischer, Peter; Gabriele, Domenico

    2016-12-01

    The microstructure of organogels based on monoglycerides of fatty acids (MAGs) and policosanol and on different edible oils was investigated by using different techniques (calorimetry, nuclear magnetic resonance, infrared spectroscopy, rheology, polarized light microscopy) towards a better understanding and control of the oil gelation phenomena. Dynamic moduli were related via a fractal model to microstructural information such as solid content and fractal dimension. Infrared spectroscopy evidenced that network structure in MAGs gel is mainly due to hydrogen bonding, whereas in policosanol system is mainly given by van der Waals interactions. Because of the different relative contribution of molecular interactions, the investigated organogelators exhibit a distinguished macroscopic behavior. MAGs are sensitive to the utilized oil and structuration occurs quickly, even though at a temperature lower than policosanol. Policosanol organogels exhibit a behavior independent of the used oil and a slower gelation rate, as a result of the weaker van der Waals interactions. Nevertheless, at lower concentration a stronger final gel is obtained, probably due to of the large number of interactions arising among the long alkyl chains of the fatty alcohols. Obtained results evidenced that policosanol is very effective in gelation of different oils and seems promising for potential commercial uses. PMID:27552424

  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. 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.

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

    PubMed Central

    2015-01-01

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

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

    PubMed

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

    2014-12-14

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

  10. Studies on intermolecular interaction on binary mixtures of methyl orange-water system: excess molar functions of ultrasonic parameters at different concentrations and at different temperatures.

    PubMed

    Thanuja, B; Kanagam, Charles; Sreedevi, S

    2011-11-01

    Density (ρ), viscosity (η) and ultrasonic velocity (u) of binary mixtures of methyl orange and water were measured at different concentrations and at different temperatures; several useful parameters such as excess volume, excess velocity, and excess adiabatic compressibility have been calculated. These parameters are used to explain the nature of intermolecular interactions taking place in the binary mixture. The above study is helpful in understanding the dye/solvent interaction at different concentration and temperatures. PMID:21596612

  11. 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

  12. Estimation of the mutual orientation and intermolecular interaction of C12Ex from molecular dynamics simulations.

    PubMed

    Velinova, Maria; Tsoneva, Yana; Ivanova, Anela; Tadjer, Alia

    2012-04-26

    Nonionic surfactants, such as poly(ethylene glycol) alkyl ethers (abbreviated as CyEx) show a rich phase behavior in aqueous solution, i.e., they form micellar, lamellar, cubic, and so forth phases depending on experimental parameters such as the hydrophobic and hydrophilic chain lengths, temperature, or concentration. The aim of the present study is to determine the nature of the preaggregates, which are inferred to exist before the actual self-assembly process in aqueous solution, and to assess the aptitude to their formation. The target molecules are C12E3, C12E4 and C12E5, surfactants of moderate water solubility. Coarse-grained and all-atom molecular dynamics simulations (NPT/293 K) of two molecules of each species with explicit water in periodic boundary conditions are carried out to estimate the mutual orientation and the interaction between the surfactants in their dimers. The force fields are MARTINI and Amber99, the latter with self-derived parameters for the ether groups. The change in the orientation and distance between the molecules in the dimers are discussed based on different structural parameters. In addition, the interaction between the surfactants is evaluated from quantum chemistry calculations in terms of binding energy for the average structures from the cluster analysis. The solvent-solute interaction is quantified by the mean number of hydrogen bonds formed between them. On the basis of combined analysis, a series of different structures for subsequent study of the possible self-assembly patterns of C12E3, C12E4, and C12E5 is outlined. PMID:22448734

  13. 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.

  14. 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.

  15. Intermolecular Interactions and Protein Dynamics by Solid‐State NMR Spectroscopy

    PubMed Central

    Lamley, Jonathan M.; Öster, Carl; Stevens, Rebecca A.

    2015-01-01

    Abstract Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site‐specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small‐amplitude overall anisotropic motion sampling the interaction interface in the complex. PMID:27478273

  16. Intermolecular Interactions and Protein Dynamics by Solid‐State NMR Spectroscopy

    PubMed Central

    Lamley, Jonathan M.; Öster, Carl; Stevens, Rebecca A.

    2015-01-01

    Abstract Understanding the dynamics of interacting proteins is a crucial step toward describing many biophysical processes. Here we investigate the backbone dynamics for protein GB1 in two different assemblies: crystalline GB1 and the precipitated GB1–antibody complex with a molecular weight of more than 300 kDa. We perform these measurements on samples containing as little as eight nanomoles of GB1. From measurements of site‐specific 15N relaxation rates including relaxation dispersion we obtain snapshots of dynamics spanning nine orders of magnitude in terms of the time scale. A comparison of measurements for GB1 in either environment reveals that while many of the dynamic features of the protein are conserved between them (in particular for the fast picosecond–nanosecond motions), much greater differences occur for slow motions with motions in the >500 ns range being more prevalent in the complex. The data suggest that GB1 can potentially undergo a small‐amplitude overall anisotropic motion sampling the interaction interface in the complex. PMID:26537742

  17. Ferromagnetic intermolecular interactions in a series of organic mixed crystals of galvinoxyl radical and its precursory closed shell compound

    NASA Astrophysics Data System (ADS)

    Awaga, Kunio; Sugano, Tadashi; Kinoshita, Minoru

    1986-08-01

    The magnetic properties of the 4:1, 6:1, 9:1, and 19:1 mixed crystals of galvinoxyl (4-[[3,5-bis(1,1-dimethylethyl)-4-oxo-2,5-cyclohexadien-1-ylidene]methyl]-2,6 -bis(1,1-dimethylethyl) phenoxy) radical and its precursory closed shell compound, hydrogalvinoxyl, have been studied. From the measurements of the temperature dependence of the magnetic susceptibility, it is found that the ferromagnetic intermolecular interactions, which are lost below about 85 K in pure galvinoxyl because of the phase transition, are maintained down to 2 K in these mixed crystals, and that the number of galvinoxyl radicals keeping the ferromagnetically coupled structure at low temperature increases as the concentration of hydrogalvinoxyl increases. The magnetic behavior of the mixed crystals at low temperature depends on the thermal history of the sample and is well interpreted by assuming the presence of a glassy state into which the high-temperature, ferromagnetically coupled phase is quenched. The magnetization curves show the spin multiplicity to be almost in proportion to the radical concentration in the mixed crystal and may be qualitatively understood by assuming that the mixed crystal is an assembly of one-dimensional chain segments partitioned by hydrogalvinoxyl within which the galvinoxyl radicals are coupled ferromagnetically.

  18. Intermolecular interaction and the extended wormlike chain conformation of chitin in NaOH/urea aqueous solution.

    PubMed

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

    2015-04-13

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

  19. Quantifying intermolecular interactions in solid state indapamide and other popular diuretic drugs: Insights from Hirshfeld surface study

    NASA Astrophysics Data System (ADS)

    Bojarska, Joanna; Fruziński, Andrzej; Maniukiewicz, Waldemar

    2016-07-01

    Hirshfeld surfaces (HS) and two-dimensional fingerprint plots are used to analyze the intermolecular interactions in indapamide and other popular thiazide diuretic derivatives. The crystal structure of indapamide (INDP) at 100 K determined by single-crystal X-ray analysis, is also reported. The title compound crystallizes in the centrosymmetric I2/a space group with one indapamide and half water molecule (lying on the glide plane) in the asymmetric unit. An interplay of N-H⋯O hydrogen bonds connects the indapamide molecules generating chains with the graph-set motifs: C (8) and C23 (16), and together with C-H⋯O and π⋯π stacking interactions create a 3D net. The Hirshfeld surface study facilitates comparison of diverse and numerous intercontacts, such as H⋯H, O⋯H, Cl⋯H, C⋯C (π⋯π), C⋯O (π⋯lone pair), O⋯O (lone pair⋯lone pair), Cl⋯O, Cl⋯Cl, N⋯N, C⋯H (C-H⋯π) with regard to building self-assembled framework of indapamide and related thiazide derivatives retrieved from the Cambridge Structural Database. The HS analysis highlights that H⋯H, O⋯H/H⋯O and C⋯H/H⋯C contacts play an influential role contributing to about 80% of the HS areas in this class of compounds. Nevertheless, in the case of INDP the H⋯H interactions, while in hydrochlorothiazide (HCTZ) O⋯H/H⋯O are dominant amongst all intercontacts towards the HS. Notably, indapamide has the highest proportion of C⋯C contacts.

  20. Quantifying intermolecular interactions in solid state indapamide and other popular diuretic drugs: Insights from Hirshfeld surface study

    NASA Astrophysics Data System (ADS)

    Bojarska, Joanna; Fruziński, Andrzej; Maniukiewicz, Waldemar

    2016-07-01

    Hirshfeld surfaces (HS) and two-dimensional fingerprint plots are used to analyze the intermolecular interactions in indapamide and other popular thiazide diuretic derivatives. The crystal structure of indapamide (INDP) at 100 K determined by single-crystal X-ray analysis, is also reported. The title compound crystallizes in the centrosymmetric I2/a space group with one indapamide and half water molecule (lying on the glide plane) in the asymmetric unit. An interplay of N-H⋯O hydrogen bonds connects the indapamide molecules generating chains with the graph-set motifs: C (8) and C23 (16), and together with C-H⋯O and π⋯π stacking interactions create a 3D net. The Hirshfeld surface study facilitates comparison of diverse and numerous intercontacts, such as H⋯H, O⋯H, Cl⋯H, C⋯C (π⋯π), C⋯O (π⋯lone pair), O⋯O (lone pair⋯lone pair), Cl⋯O, Cl⋯Cl, N⋯N, C⋯H (C-H⋯π) with regard to building self-assembled framework of indapamide and related thiazide derivatives retrieved from the Cambridge Structural Database. The HS analysis highlights that H⋯H, O⋯H/H⋯O and C⋯H/H⋯C contacts play an influential role contributing to about 80% of the HS areas in this class of compounds. Nevertheless, in the case of INDP the H⋯H interactions, while in hydrochlorothiazide (HCTZ) O⋯H/H⋯O are dominant amongst all intercontacts towards the HS. Notably, indapamide has the highest proportion of C⋯C contacts.

  1. 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.

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

    PubMed

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

    2013-08-01

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

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

    PubMed Central

    Gingell, D; Fornes, J A

    1976-01-01

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

  4. EPR studies of intermolecular interactions and competitive binding of drugs in a drug-BSA binding model.

    PubMed

    Akdogan, Y; Emrullahoglu, M; Tatlidil, D; Ucuncu, M; Cakan-Akdogan, G

    2016-08-10

    Understanding intermolecular interactions between drugs and proteins is very important in drug delivery studies. Here, we studied different binding interactions between salicylic acid and bovine serum albumin (BSA) using electron paramagnetic resonance (EPR) spectroscopy. Salicylic acid was labeled with a stable radical (spin label) in order to monitor its mobilized (free) or immobilized (bound to BSA) states. In addition to spin labeled salicylic acid (SL-salicylic acid), its derivatives including SL-benzoic acid, SL-phenol, SL-benzene, SL-cyclohexane and SL-hexane were synthesized to reveal the effects of various drug binding interactions. EPR results of these SL-molecules showed that hydrophobic interaction is the main driving force. Whereas each of the two functional groups (-COOH and -OH) on the benzene ring has a minute but detectable effect on the drug-protein complex formation. In order to investigate the effect of electrostatic interaction on drug binding, cationic BSA (cBSA) was synthesized, altering the negative net charge of BSA to positive. The salicylic acid loading capacity of cBSA is significantly higher compared to that of BSA, indicating the importance of electrostatic interaction in drug binding. Moreover, the competitive binding properties of salicylic acid, ibuprofen and aspirin to BSA were studied. The combined EPR results of SL-salicylic acid/ibuprofen and SL-ibuprofen/salicylic acid showed that ibuprofen is able to replace up to ∼83% of bound SL-salicylic acid, and salicylic acid can replace only ∼14% of the bound SL-ibuprofen. This indicates that ∼97% of all salicylic acid and ibuprofen binding sites are shared. On the other hand, aspirin replaces only ∼23% of bound SL-salicylic acid, and salicylic acid replaces ∼50% of bound SL-aspirin, indicating that ∼73% of all salicylic acid and aspirin binding sites are shared. These results show that EPR spectroscopy in combination with the spin labeling technique is a very powerful

  5. Toward understanding the influence of intermolecular interactions and molecular orientation on the chemical enhancement of SERS.

    PubMed

    Cabalo, Jerry; Guicheteau, Jason A; Christesen, Steven

    2013-09-19

    Implementation of SERS as an analytical technique is limited because the factors that govern the enhancement of individual vibrational modes are not well understood. Although the chemical effect only accounts for up to two orders of magnitude enhancement, it can still have a significant impact on the consistency of chemical spectral signatures. We report on a combined theoretical and experimental study on the benzenethiol on silver and 4-mercaptophenol on silver systems. The primary and unique finding was that for the benzenethiol on silver system the inclusion of interaction between multiple benzenethiol analyte molecules was essential to account for the relative enhancements observed experimentally. An examination of the molecular orbitals showed sharing of electron density across the entire model of multiple benzenethiol molecules mediated by the metal atoms. The addition of multiple 4-mercaptophenol molecules to the theoretical model had little effect on the predicted spectra, and we attribute this to the fact that a much larger model is necessary to replicate the networks of hydrogen bonds. Molecular orientation was also found to affect the predicted spectra, and it was found that an upright position improved agreement between theoretical and experimental spectra. An analysis of the vibrational frequency shifts between the normal Raman spectrum of the neat compound and the SERS spectrum also suggests that both benzenethiol and 4-mercaptophenol are in an upright position. PMID:23961762

  6. Tuning intermolecular interactions in dioctyl-substituted polyfluorene via hydrostatic pressure.

    PubMed

    Paudel, K; Knoll, H; Chandrasekhar, M; Guha, S

    2010-04-01

    Polyfluorenes (PFs) represent a unique class of poly-para-phenylene-based blue-emitting polymers with intriguing structure-property relationships. Slight variations in the choice of functionalizing side chains result in dramatic differences in the inter- and intrachain structures in PFs. Dioctyl-substituted PF (PF8) is characterized by different backbone conformations that depend upon the torsion angle between the monomers. We present photoluminescence (PL) and Raman scattering studies of bulk samples and thin films of dioctyl-substituted PF (PF8) under hydrostatic pressure. The bulk sample was further thermally annealed and studied as a function of pressure. The PL energies of the as-is and thermally annealed samples both red shift but at very different rates, and the difference between their pressure coefficients elucidates the role of the backbone torsional angle. This is further corroborated by density functional theoretical calculations of a fluorene oligomer, where the energy gap is calculated as a function of both the torsion angle as well as compression. The Raman peaks harden with increasing pressures; the intraring C-C stretch frequency at 1600 cm(-1) has a pressure coefficient of 7.2 cm(-1)/GPa and exhibits asymmetric line shapes at higher pressures, characteristic of a strong electron-phonon interaction. PMID:20235499

  7. Redetermined structure, inter-molecular inter-actions and absolute configuration of royleanone.

    PubMed

    Fun, Hoong-Kun; Chantrapromma, Suchada; Salae, Abdul Wahab; Razak, Ibrahim Abdul; Karalai, Chatchanok

    2011-05-01

    The structure of the title diterpenoid, C(20)H(28)O(3), {systematic name: (4bS,8aS)-3-hy-droxy-2-isopropyl-4b,8,8-trimethyl-4b,5,6,7,8,8a,9,10-octa-hydro-phenanthrene-1,4-dione} is confirmed [Eugster et al. (1993 ▶). Private communication (refcode HACGUN). CCDC, Union Road, Cambridge] and its packing is now described. Its absolute structure was established by refinement against data collected with Cu radiation: the two stereogenic centres both have S configurations. One cyclo-hexane ring adopts a chair conformation whereas the other cyclo-hexane ring is in a half-chair conformation and the benzoquinone ring is slightly twisted. An intra-molecular O-H⋯O hydrogen bond generates an S(5) ring motif. In the crystal, mol-ecules are linked into chains along [010] by O-H⋯O hydrogen bonds and weak C-H⋯O inter-actions. The packing also features C⋯O [3.131 (3) Å] short contacts. PMID:21754362

  8. 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.

  9. 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.

  10. Facile Incorporation of Pd(PPh3)2Hal Substituents into Polymethines, Merocyanines, and Perylene Diimides as a Means of Suppressing Intermolecular Interactions.

    PubMed

    Davydenko, Iryna; Barlow, Stephen; Sharma, Rajesh; Benis, Sepehr; Simon, Janos; Allen, Taylor G; Cooper, Matthew W; Khrustalev, Victor; Jucov, Evgheni V; Castañeda, Raúl; Ordonez, Carlos; Li, Zhong'an; Chi, San-Hui; Jang, Sei-Hum; Parker, Timothy C; Timofeeva, Tatiana V; Perry, Joseph W; Jen, Alex K-Y; Hagan, David J; Van Stryland, Eric W; Marder, Seth R

    2016-08-17

    Compounds with polarizable π systems that are susceptible to attack with nucleophiles at C-Hal (Hal = Cl, Br) bonds react with Pd(PPh3)4 to yield net oxidative addition. X-ray structures show that the resulting Pd(PPh3)2Hal groups greatly reduce intermolecular π-π interactions. The Pd-functionalized dyes generally exhibit solution-like absorption spectra in films, whereas their Hal analogues exhibit features attributable to aggregation. PMID:27494823