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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 dipole-dipole and van der Waals (vdWs) forces at l/s interface. It is believed that the results are of significance to the fields of solvent induced polymorphism assembly and surface science. PMID:25554245

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

    NASA Astrophysics Data System (ADS)

    Shimada, Rintaro; Hamaguchi, Hiro-o.

    2014-05-01

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

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

    SciTech Connect

    Shimada, Rintaro; Hamaguchi, Hiro-o

    2014-05-28

    We quantitatively interpret the recently discovered intriguing phenomenon related to resonance Hyper-Raman (HR) scattering. In resonance HR spectra of all-trans-?-carotene (?-carotene) in solution, vibrations of proximate solvent molecules are observed concomitantly with the solute ?-carotene HR bands. It has been shown that these solvent bands are subject to marked intensity enhancements by more than 5 orders of magnitude under the presence of ?-carotene. We have called this phenomenon the molecular-near field effect. Resonance HR spectra of ?-carotene in benzene, deuterated benzene, cyclohexane, and deuterated cyclohexane have been measured precisely for a quantitative analysis of this effect. The assignments of the observed peaks are made by referring to the infrared, Raman, and HR spectra of neat solvents. It has been revealed that infrared active and some Raman active vibrations are active in the HR molecular near-field effect. The observed spectra in the form of difference spectra (between benzene/deuterated benzene and cyclohexane/deuterated cyclohexane) are quantitatively analyzed on the basis of the extended vibronic theory of resonance HR scattering. The theory incorporates the coupling of excited electronic states of ?-carotene with the vibrations of a proximate solvent molecule through solutesolvent dipoledipole and dipolequadrupole interactions. It is shown that the infrared active modes arise from the dipoledipole interaction, whereas Raman active modes from the dipolequadrupole 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.

  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. 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

  7. 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.

  8. 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

  9. 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 ? -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 ? ? (Tg) of the system, the narrower is the ? -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 ? and ? ? (Tg) in view of the relation, D ?(?4/k Tg)?k Tg[?? (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.

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

    NASA Astrophysics Data System (ADS)

    Khan, Salman; Jan, Munsif

    2015-09-01

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

  12. Geometrical simplification of the dipole-dipole interaction formula

    NASA Astrophysics Data System (ADS)

    Kocbach, Ladislav; Lubbad, Suhail

    2010-07-01

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

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

    NASA Astrophysics Data System (ADS)

    El-Ganainy, Ramy; John, Sajeev

    2013-08-01

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

  14. 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…

  15. 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

  16. 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

  17. Experimental investigations of the resonant dipole-dipole interaction between cold Rydberg atoms

    NASA Astrophysics Data System (ADS)

    Browaeys, Antoine

    2015-05-01

    This talk will present our on-going effort to control the dipole-dipole interaction between cold Rydberg atoms. In our experiment, we trap individual atoms in two-dimensional arrays of optical tweezers separated by few micrometers and excite them to Rydberg states using lasers. The arrays are produced by a spatial light modulator, which shapes the dipole trap beam. We can create almost arbitrary geometries of the arrays. We have measured the van der Waals interaction between two individual atoms, and show efficient Rydberg blockade in arrays of three atoms. We have also demonstrated the control of the interaction between atoms with microwave and DC electric fields. We observe in particular the coherent energy exchange between two atoms resulting from their dipole-dipole interaction. This control of the interaction will find applications in quantum state engineering, quantum information and quantum simulation.

  18. 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.

  19. Spectroscopic observation of resonant electric dipole-dipole interactions between cold Rydberg atoms.

    PubMed

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

    2004-12-01

    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 45d(5/2) Rydberg states using a pulsed laser. A microwave pulse transferred a fraction of these Rydberg atoms to the 46p(3/2) state. A second microwave pulse then drove atoms in the 45d(5/2) state to the 46d(5/2) 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 46p(3/2) atoms, and is due to the resonant electric dipole-dipole interaction between 45d(5/2) and 46p(3/2) Rydberg atoms. PMID:15601153

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

    NASA Astrophysics Data System (ADS)

    Mu, Yan; Gao, Yi Qin

    2007-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  2. Ultracold fermi gases with resonant dipole-dipole interaction.

    PubMed

    Shi, T; Zou, S-H; Hu, H; Sun, C-P; Yi, S

    2013-01-25

    The superfluid phases in resonant dipolar Fermi gases are investigated by the standard mean-field theory. In contrast to the crossover from Bose-Einstein condensation (BEC) to Bardeen-Cooper-Schrieffer superfluid in Fermi gases with isotropic interactions, resonant dipolar interaction leads to two completely different BEC phases of the tight-binding Fermi molecules on both sides of the resonance, which are characterized by two order parameters with distinct internal symmetries. We point out that, near the resonances, the two competitive phases can coexist, and an emergent relative phase between the two order parameters spontaneously breaks time-reversal symmetry, which could be observed in momentum resolved rf spectroscopy. PMID:25166174

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

    SciTech Connect

    Ditzhuijzen, C. S. E. van; Noordam, L. D.; Heuvell, H. B. van Linden van den; Koenderink, A. F.; Hernandez, J. V.; Robicheaux, F.

    2008-06-20

    We have observed resonant energy transfer between cold Rydberg atoms in spatially separated cylinders. Resonant dipole-dipole coupling excites the 49s atoms in one cylinder to the 49p state while the 41d atoms in the second cylinder are transferred down to the 42p state. We have measured the production of the 49p state as a function of separation of the cylinders (0-80 {mu}m) and the interaction time (0-25 {mu}s). In addition, we measured the width of the electric field resonances. A full many-body quantum calculation reproduces the main features of the experiments.

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

    SciTech Connect

    Baudin, Emmanuel

    2014-08-07

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

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

    NASA Astrophysics Data System (ADS)

    Baudin, Emmanuel

    2014-08-01

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

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

    PubMed

    Baudin, Emmanuel

    2014-08-01

    New composite rf pulses are proposed during which the average dipole-dipole interactions within a spin ensemble are controlled, while a global rotation is achieved. The method used to tailor the pulses is based on the average Hamiltonian theory and relies on the geometrical properties of the spin-spin dipolar interaction. I describe several such composite pulses and analyze quantitatively the improvement brought on the control of the NMR dynamics. Numerical simulations show that the magic sandwich pulse sequence, during which the average dipolar field is effectively reversed, is plagued by defects originating from the finite initial and final ?/2 rf pulses. A numerical test based on a classical description of nuclear magnetic resonance is used to check that, when these pulses are replaced by magic composite pulses, the efficiency of the magic sandwich is improved. PMID:25106579

  7. 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

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

    NASA Astrophysics Data System (ADS)

    Andreev, Pavel

    2015-05-01

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

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

    PubMed Central

    Wohlert, Jakob; Edholm, Olle

    2004-01-01

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

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

    SciTech Connect

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

    2006-06-15

    Laser-cooled {sup 85}Rb atoms were optically excited to 46d{sub 5/2} Rydberg states. A microwave pulse transferred a fraction of the atoms to the 47p{sub 3/2} 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 46d{sub 5/2}-47d{sub 5/2}. The presence of a weak magnetic field {approx_equal}0.5 G 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 34s{sub 1/2}-34p{sub 1/2} one-photon transition is also presented.

  11. Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions

    ERIC Educational Resources Information Center

    Yoder, Claude H.

    1977-01-01

    Discusses how electrostatic interactions can be taught quantitatively through Coulomb's Law at a variety of points in a chemistry curriculum. Each type of interaction is shown at both the intramolecular and the inter-"molecular" levels. (MR)

  12. 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 Avils, 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.

  13. 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.

  14. 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.

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

    NASA Astrophysics Data System (ADS)

    Olson, Abraham; Chen, Yong P.

    2010-03-01

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

  16. Oscillations of echo amplitude in glasses in a magnetic field induced by nuclear dipole-dipole interaction

    NASA Astrophysics Data System (ADS)

    Shumilin, A. V.; Parshin, D. A.

    2009-08-01

    The influence of a magnetic field on the dipole echo amplitude in glasses (at temperatures of about 10 mK) induced by the dipole-dipole interaction of nuclear spins has been theoretically studied. It has been shown that a change in the mutual position of nuclear spins at tunneling and the Zeeman energy E H of their interaction with the external magnetic field lead to a nonmonotonic magnetic-field dependence of the dipole echo amplitude. The approximation that the nuclear dipole-dipole interaction energy E d is much smaller than the Zeeman energy has been found to be valid in the experimentally important cases. It has been shown that the dipole echo amplitude in this approximation may be described by a simple universal analytic function independent of the microscopic structure of the two-level systems. An excellent agreement of the theory with the experimental data has been obtained without fitting parameters (except for the unknown echo amplitude).

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

    NASA Astrophysics Data System (ADS)

    Ota, Satoshi; Yamada, Tsutomu; Takemura, Yasushi

    2015-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  20. 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.

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

    NASA Astrophysics Data System (ADS)

    Saalwchter, Kay

    2014-08-01

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

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

    PubMed

    Saalwchter, Kay

    2014-08-14

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

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

    SciTech Connect

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

    2008-07-15

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

  4. Computational studies of dipole-dipole interactions among Stark manifold states

    NASA Astrophysics Data System (ADS)

    Carroll, Thomas; Mellus, Alexander; Chartrand, Alexander; Fahey, Donald; Noel, Michael

    2013-05-01

    In our experiment, we excite ultra-cold atoms in a magneto-optical trap to Rydberg states in a Stark manifold (n ~ 35). An external electric field tunes the states such that a pair of atoms can resonantly exchange energy. One atom transitions to the (n + 1) manifold and the other to the (n - 1) manifold. We present the results of a computational model of this interaction which includes as many as 6 atoms. We examine many-body effects and redistribution of initial atomic population among the densely packed manifold states. This work was supported by the National Science Foundation (grant no. 1205897) and through the Extreme Science and Engineering Discovery Environment (supported by NSF grant no. OCI-1053575).

  5. 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

  6. 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; ye, 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

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed

    Ren, Jinjun; Eckert, Hellmut

    2015-10-01

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

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

    PubMed

    Ren, Jinjun; Eckert, Hellmut

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  13. Inter and intra macro-cell model for point dipole-dipole energy calculations.

    PubMed

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

    2016-02-17

    In the field of micromagnetics, the calculation of long-range dipole-dipole interactions in non-uniformly magnetized bodies has long posed computational problems. In this paper, we present an inter and intra macro-cell point-dipole model, which can be used to speed-up the determination of dipole-dipole energies at the atomistic level. The model can be used to accurately compute the dipole-dipole energy, using macro-cells of any shape or size. PMID:26788782

  14. 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.

  15. 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

  16. 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.

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

    PubMed

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

    2014-08-14

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

  18. 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.

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

    PubMed Central

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

    2012-01-01

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

  20. Computational studies on intermolecular interactions in solvation

    NASA Astrophysics Data System (ADS)

    Song, Weiping

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    Hohm, Uwe

    1999-09-01

    Collision-induced light scattering spectra of phosphorus vapour measured at 1000 K and density 132 mol m -3 are used to deduce a Lennard-Jones type (15-6) intermolecular interaction potential U( R), the dipole-quadrupole polarizability A, and dipole-octopole polarizability E of P 4 clusters. Using a recent experimental value of the dipole-dipole polarizability ?0=14.4210 -30 m 3 at ?=514.5 nm, the experimentally recorded depolarized interaction-induced Raman spectra are best fitted with ?=4.410 -10 m, ?/ k=700 K, A=(62)10 -40 m 4, and | E|=(12717)10 -50 m 5. The analysis is hampered by the existence of the ?3- ?2 vibrational combination band at 98 cm -1.

  3. Intermolecular SulfurOxygen Interactions: Theoretical and Statistical Investigations.

    PubMed

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

    2015-10-26

    Intermolecular SO 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 SO contacts by focusing on three sulfur-containing aromatic rings. Quantum mechanics is employed to characterize the strength and directionality of the SO 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 SO 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 SO interactions and addresses their use in molecular design. PMID:26393532

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  5. Learning about Intermolecular Interactions from the Cambridge Structural Database

    ERIC Educational Resources Information Center

    Battle, Gary M.; Allen, Frank H.

    2012-01-01

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

  6. 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

  7. Transition dipole-dipole coupling between the antisymmetric stretching mode of azido ligands in K3[Co(CN)5N3].2H 2O

    NASA Astrophysics Data System (ADS)

    Piro, Oscar E.

    1985-01-01

    The nature and magnitude of intermolecular forces that couple the strongly polar N3 antisymmetric stretching vibration of the [Co(CN)5N3]3- ions in K3[CO(CN)5N3].2H 2O have been studied on the basis of previously reported results dealing with the crystal-structure determination and infrared and Raman spectra of this compound. The observed difference of 25 cm-1 between the measured wave numbers for the frequencies of the ir- and Raman-active optical fundamental vibrations associated with the N3 antisymmetric stretching mode can be interpreted in terms of a linear-chain model of [Co(CN)5N3]3- oscillators coupled through their N3 ligands via harmonic transition dipole-dipole forces operating between nearest neighbors on a chain. With this model, we obtain ||(??/?Q3)0||=263 esu/g1/2 for the dipole-moment derivative of the N3 antisymmetric stretch, a value which can be compared with the corresponding value derived from integrated ir-absorption intensity measurements of N3 - ions isolated in alkali-halide lattices. A value f3=+0.071 mdyn/ is calculated for the force constant of the interaction that couples such N3 vibrations of neighbor azide ions in K3[Co(CN)5N3].2H 2O. The potentiality of combined ir and Raman spectroscopic techniques for the study of intermolecular vibrational coupling in solids is here emphasized.

  8. Intermolecular interaction in TeO2 crystal.

    PubMed

    Gabuda, Svyatoslav P; Kozlova, Svetlana G

    2006-09-21

    It is shown that the abnormal long-range Te-Te intermolecular interaction in TeO(2) crystals may be related to the tunneling of electrons from the 5s(2) active lone pairs of Te(4+) ions and their partial delocalization on neighboring Te(4+). PMID:16970416

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

    SciTech Connect

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

    2006-07-15

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

  10. 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

  11. 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.

  12. Coherent dipole-dipole coupling between two single Rydberg atoms at an electrically-tuned Frster resonance

    NASA Astrophysics Data System (ADS)

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-07-01

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

  14. Studies of pilocarpine:carbomer intermolecular interactions.

    PubMed

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

    2012-05-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

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

  16. 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

  17. 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

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

    PubMed

    Yigzawe, Tesfaye M; Sadus, Richard J

    2013-05-21

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

  19. Intermolecular interactions and the thermodynamic properties of supercritical fluids

    NASA Astrophysics Data System (ADS)

    Yigzawe, Tesfaye M.; Sadus, Richard J.

    2013-05-01

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

  20. 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.

  1. 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.

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

    PubMed

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

    2006-09-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

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

  4. Near dipole-dipole effects on the propagation of few-cycle pulse in a dense two-level medium.

    PubMed

    Xia, Keyu; Gong, Shangqing; Liu, Chengpu; Song, Xiaohong; Niu, Yueping

    2005-08-01

    The propagation behaviors, which include the carrier-envelope phase, the area evolution and the solitary pulse number of few-cycle pulses in a dense two-level medium, are investigated based on full-wave Maxwell-Bloch equations by taking Lorentz local field correction (LFC) into account. Several novel features are found: the difference of the carrier-envelope phase between the cases with and without LFC can go up to pi at some location; although the area of ultrashort solitary pulses is lager than 2pi, the area of the effective Rabi frequency, which equals to that the Rabi frequency pluses the product of the strength of the near dipole-dipole (NDD) interaction and the polarization, is consistent with the standard area theorem and keeps 2pi; the large area pulse penetrating into the medium produces several solitary pulses as usual, but the number of solitary pulses changes at certain condition. PMID:19498598

  5. 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

  6. 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

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

    PubMed

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

    2002-08-01

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

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

    PubMed

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

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

    2008-01-01

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

  10. 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…

  11. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1972-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-11-01

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

  14. 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.

  15. 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)....

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

    NASA Astrophysics Data System (ADS)

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

    2001-11-01

    Refractive index (RI) measurements, depolarized collision-induced light (CILS) scattering and ab initio quantum chemical calculations are used to determine the dipole (?), dipole-quadrupole (A), and dipole-octopole polarizability (E) of adamantane, C10H16. For this molecule of symmetry group Td the three polarizabilities can be represented by a single scalar quantity. From experiment we obtain for the static dipole polarizability at T?400-500 K 107.51.1 e2a02Eh-1, and for the higher polarizabilities |A|=102.07.8 e2a03Eh-1, and |E|=72080 e2a04Eh-1. We have performed conventional ab initio and density functional theory calculations with specifically designed basis sets. A very large [4s3p3d1f/3s2p1d] basis set consisting of 574 basis functions is thought to provide near-Hartree-Fock values for ?,A and E: ?=101.72 e2a02Eh-1, A=-6.5 e2a03Eh-1, and E=-71.0 e2a04Eh-1. Our final theoretical estimates for these properties are ?=107.51.0 e2a02Eh-1, A=-8.01.5 e2a03Eh-1, and E=-76.55.5 e2a04Eh-1. Very strong electron correlation effects are found for both the first (?) and second (?) hyperpolarizability. Our estimate for ???xyz and the mean ? are 41.45.6 e3a03Eh-2 and (252)103 e4a04Eh-3, respectively. For the octopole and hexadecapole moments we propose ?=-4.40.2 ea03 and ?=-100.85.5 ea04. The basis sets constructed in this work should provide reliable computational tools for the study of intermolecular interactions of adamantane.

  17. Incisive probing of intermolecular interactions in molecular crystals: core level spectroscopy combined with density functional theory.

    PubMed

    Stevens, Joanna S; Seabourne, Che R; Jaye, Cherno; Fischer, Daniel A; Scott, Andrew J; Schroeder, Sven L M

    2014-10-23

    The ?-form of crystalline para-aminobenzoic acid (PABA) has been examined as a model system for demonstrating how the core level spectroscopies X-ray photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine-structure (NEXAFS) can be combined with CASTEP density functional theory (DFT) to provide reliable modeling of intermolecular bonding in organic molecular crystals. Through its dependence on unoccupied valence states NEXAFS is an extremely sensitive probe of variations in intermolecular bonding. Prediction of NEXAFS spectra by CASTEP, in combination with core level shifts predicted by WIEN2K, reproduced experimentally observed data very well when all significant intermolecular interactions were correctly taken into account. CASTEP-predicted NEXAFS spectra for the crystalline state were compared with those for an isolated PABA monomer to examine the impact of intermolecular interactions and local environment in the solid state. The effects of the loss of hydrogen-bonding in carboxylic acid dimers and intermolecular hydrogen bonding between amino and carboxylic acid moieties are evident, with energy shifts and intensity variations of NEXAFS features arising from the associated differences in electronic structure and bonding. PMID:25248405

  18. Intermolecular interactions of the malate synthase of Paracoccidioides spp

    PubMed Central

    2013-01-01

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

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

    PubMed

    Kajiya, Daisuke; Saitow, Ken-ichi

    2010-07-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    SciTech Connect

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

    1980-05-01

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

  2. 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.

  3. Mass Spectrometry Tools for Analysis of Intermolecular Interactions

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

  5. Atom depth analysis delineates mechanisms of protein intermolecular interactions

    SciTech Connect

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

    2013-07-12

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

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

    PubMed

    Ansorg, Kay; Tafipolsky, Maxim; Engels, Bernd

    2013-09-01

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

  7. 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.

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

    PubMed

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

    2016-07-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2005-01-01

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

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

    PubMed

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

    2016-01-01

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

  13. Determination of Intermolecular Interactions Using Polarization Compensated Heteronuclear Overhauser Effect of Hyperpolarized Spins.

    PubMed

    Kim, Jihyun; Liu, Mengxiao; Chen, Hsueh-Ying; Hilty, Christian

    2015-11-01

    The nuclear Overhauser effect (NOE) has long been used as a selective indicator for intermolecular interactions. Due to relatively small changes of signal intensity, often on the order of several percent, quantitative NOE measurements can be challenging. Hyperpolarization of nuclear spins can dramatically increase the NOE intensity by increasing population differences, but poses its own challenge in quantifying the original polarization level. Here, we demonstrate a method for the accurate measurement of intermolecular heteronuclear cross-relaxation rates by simultaneous acquisition of signals from both nuclei. Using this method, we measure cross-relaxation rates between water protons and (19)F of trifluoroacetic acid at concentrations ranging from 23 to 72 mM. A concentration-independent value of 2.46 10(-4) 1.02 10(-5) s(-1) M(-1) is obtained at a temperature of 301 K and validated using a nonhyperpolarized measurement. In a broader context, accurate measurement of heteronuclear cross-relaxation rates may enable the study of intermolecular interactions including those involving macromolecules where (19)F atoms can be introduced as site-selective labels. PMID:26426882

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Arrott, Anthony S.

    2011-04-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

    Evans, Diane

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

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

    PubMed

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

    2015-10-01

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

  19. 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

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

    PubMed Central

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

    2014-01-01

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

  1. 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

  2. A structural and theoretical study of the intermolecular interactions in 8-hydroxyquinolinium-7-carboxylate monohydrate.

    PubMed

    Kruszynski, Rafal

    2011-07-01

    In the title compound, C(10)H(7)NO(3)H(2)O, the zwitterionic organic molecules and the water molecules are connected by N-HO and O-HO hydrogen bonds to form ribbons, and ?-? stacking interactions expand these ribbons into a three-dimensional net. The energies of these hydrogen bonds adopt values typical for mildly weak interactions (3.33-7.75 kcal mol(-1); 1 kcal mol(-1) = 4.184 kJ mol(-1)). The total ?-? stacking interactions between aromatic molecules can be classified as mildly strong (energies of 15.3 and 33.9 kcal mol(-1)), and they are made up of multiple constituent ?-? interactions between six-membered rings. The short intermolecular C-HO contact between two zwitterionic molecules is nonbonding in character. PMID:21727631

  3. Intermolecular Interactions and the Release Pattern of Electrospun Curcumin-Polyvinyl(pyrrolidone) Fiber.

    PubMed

    Rahma, Annisa; Munir, Muhammad Miftahul; Khairurrijal; Prasetyo, Anton; Suendo, Veinardi; Rachmawati, Heni

    2016-01-01

    An electrospun fiber of polyvinyl(pyrrolidone) (PVP)-Tween 20 (T20) with curcumin as the encapsulated drug has been developed. A study of intermolecular interactions was performed using Raman spectroscopy, Fourier transform infrared (FT-IR), differential scanning calorimetry (DSC), and X-ray diffraction (XRD). The Raman and FT-IR studies showed that curcumin preferrably interacted with T20 and altered PVP chain packing, as supported by XRD and physical stability data. The hydroxyl stretching band in PVP shifted to a lower wavenumber with higher intenstity in the presence of curcumin and PVP, indicating that hydrogen bond formation is more intense in a curcumin or curcumin-T20 containing fiber. The thermal pattern of the fiber did not indicate phase separation. The conversion of curcumin into an amorphous state was confirmed by XRD analysis. An in vitro release study in phosphate buffer pH 6.8 showed that intermolecular interactions between each material influenced the drug release rate. However, low porosity was found to limit the hydrogen bond-mediated release. PMID:26830478

  4. 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

  5. Intermolecular potential energy surface for CS2 dimer.

    PubMed

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

    2011-04-15

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

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

    PubMed

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

    2010-01-13

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

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

    NASA Astrophysics Data System (ADS)

    Paßens, Michael; Karthäuser, Silvia

    2015-12-01

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

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

    PubMed

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

    2015-10-01

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

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

    SciTech Connect

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

    1998-07-01

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

  10. Pressure Effects on the Intermolecular Interaction Potential of Condensed Protein Solutions.

    PubMed

    Winter, Roland

    2015-01-01

    Knowledge of the intermolecular interaction potential of proteins as a function of their solution conditions is essential for understanding protein aggregation, crystallization, and the phase behavior of proteins in general. Here, we report on a combined small-angle X-ray scattering and liquid-state theoretical approach to study dense lysozyme solutions as a function of temperature and pressure, but also in the presence of salts and osmolytes of different nature. We show that the pressure-dependent interaction potential of lysozyme changes in a nonlinear fashion over a wide range of temperatures, salt and protein concentrations, indicating that changes of the bulk water structure mediate the pressure dependence of the intermolecular forces. We present also results on the effect of high hydrostatic pressure on the phase behavior of dense lysozyme solutions in the liquid-liquid phase-coexistence region. As also shown in this study, the application of pressure can be used to fine-tune the second virial coefficient of protein solutions, which can be used to control nucleation rates and hence protein crystallization, or to prevent protein aggregation. Moreover, these results are also important for understanding the hydration behavior of biological matter under extreme environmental conditions, and the high stability of dense protein solutions (as they occur intracellularly) in organisms thriving under hydrostatic pressure conditions such as in the deep sea, where pressures up to the 100MPa-level are reached. PMID:26174381

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

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

    PubMed

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

    2015-07-14

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

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

    PubMed

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Babusca, Daniela; Dorohoi, Dana Ortansa

    2016-01-01

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

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

    PubMed

    Babusca, Daniela; Dorohoi, Dana Ortansa

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Karayel, A.; zbey, S.; Ayhan-K?lc?gil, G.; Ku?, 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.

  17. Range-separated density-functional theory with random phase approximation applied to noncovalent intermolecular interactions.

    PubMed

    Zhu, Wuming; Toulouse, Julien; Savin, Andreas; Angyn, Jnos G

    2010-06-28

    Range-separated methods combining a short-range density functional with long-range random phase approximations (RPAs) with or without exchange response kernel are tested on rare-gas dimers and the S22 benchmark set of weakly interacting complexes of Jurecka et al. [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The methods are also compared to full-range RPA approaches. Both range separation and inclusion of the Hartree-Fock exchange kernel largely improve the accuracy of intermolecular interaction energies. The best results are obtained with the method called RSH+RPAx, which yields interaction energies for the S22 set with an estimated mean absolute error of about 0.5-0.6 kcal/mol, corresponding to a mean absolute percentage error of about 7%-9% depending on the reference interaction energies used. In particular, the RSH+RPAx method is found to be overall more accurate than the range-separated method based on long-range second-order Moller-Plesset (MP2) perturbation theory (RSH+MP2). PMID:20590182

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Krger, Ingo; Stadtmller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-01

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

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

    PubMed

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

    2014-08-14

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

  1. Vibrational dynamics, intermolecular interactions, and compound formation in GeH4H2 under pressure

    SciTech Connect

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

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    PubMed

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

    2010-03-14

    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. PMID:20232974

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

    SciTech Connect

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

    2012-03-13

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

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

    PubMed

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

    2015-12-01

    The compounds (2'E,2'E)-2,2'-(propane-1,2-diylidene)bis[1-(2-nitrophenyl)hydrazine], C15H14N6O4, (I), and (2Z,3Z)-ethyl 3-[2-(2-nitrophenyl)hydrazinylidene]-2-[2-(4-nitrophenyl)hydrazinylidene]butanoate tetrahydrofuran hemisolvate, C18H18N6O60.5C4H8O, (II), are puzzling outliers deviating from a general synthetic route aimed at the preparation of substituted pyrazoles. Possible reasons for this outcome, which is exceptional in an otherwise firmly established synthetic procedure, are analyzed. Compound (I) is unsolvated, while compound (II) crystallizes with a tetrahydrofuran solvent molecule lying on an inversion centre. The ethoxycarbonyl chain of (II), in turn, appears disordered into two equally populated (50%) moieties. In both structures, a plethora of different commonly occurring weak intermolecular interactions [viz. ?(phenyl)...?(phenyl), ?(C=N)...?(C=N), ?(phenyl)...?(C=N), N-H...O and C-H...O] appear responsible for the crystal stability. Much less common are the short O(nitro)...O(nitro) contacts which are observed in the structure of (I), an example of unusual `electron donor-acceptor' (EDA) interactions. PMID:26632840

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

    PubMed Central

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

    2010-01-01

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

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

    SciTech Connect

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

    2013-11-21

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

  8. 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

  9. Weak interactions in barbituric acid derivatives. Unusually steady intermolecular organic sandwich complexes. ? ? Stacking versus hydrogen bonding interactions

    NASA Astrophysics Data System (ADS)

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

    2008-04-01

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

  10. 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

  11. 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

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

    SciTech Connect

    Wannamaker, P.E.

    1985-09-01

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

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

    PubMed

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

    2016-01-11

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

  14. New monoclinic form of bovine pancreatic ribonuclease A from a salt solution and comparison of intermolecular interactions in ribonucleases A

    NASA Astrophysics Data System (ADS)

    Takusagawa, Hideaki; Yamamura, Shigefumi; Endo, Shigeru; Sugawara, Yoko; Inagaki, Toshiyuki; Nakasako, Masayoshi

    2011-03-01

    A new monoclinic form of bovine pancreatic ribonuclease A was obtained together with the known trigonal form using sodium chloride and ammonium sulfate as precipitants. The new monoclinic form was stable at high salt concentrations. Crystal structure analysis of the new monoclinic form was carried out, and the intermolecular interactions were compared with those of the trigonal form. In the new monoclinic form, there were two pairs of non-crystallographic dimers, both of which were almost equivalent to the dimer in the trigonal form. Molecular layers were formed by the dimers, and a water region was spread between the molecular layers. Although the overall crystal structures of the two crystal forms are quite different, common successive interaction between the dimers aligned along the two-fold screw axis. Analyses of the contact surfaces were carried out, together with the other crystal forms of native ribonuclease A, resulting in a qualitative understanding of the relationship between intermolecular interactions and the crystallization conditions.

  15. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Azar, Richard Julian; Head-Gordon, Martin

    2015-05-01

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

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

    SciTech Connect

    Azar, Richard Julian Head-Gordon, Martin

    2015-05-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  20. 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 (?), viscosity (?), 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 (?), acoustic impedance ( Z), viscous relaxation time (?), free length ( L f), free volume ( V f), internal pressure (?i), and Gibbs free energy (? 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.

  1. 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

  2. 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...

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

    NASA Astrophysics Data System (ADS)

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

    2007-10-01

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

  4. 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 previously published state of the art theoretical potential energy curve for Xe(2), are in excellent agreement with the experiment for the first time. PMID:17979344

  5. 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}XB 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 ?-pair (C{sub 2}H{sub 4}) and two ?-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 ?-hole model. Upon formation of stable complexes, the CX bond lengths shorten, while the CX vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the ?-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

  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 forms of the newly introduced generalized potential energy functions (PEFs) describing intermolecular interactions [J. Chem. Phys. xx, yyyyy (2011)] have been used to fit the ab-initio minimum energy paths (MEPs) for the halide- and alkali metal-water systems X-(H2O), X=F, Cl, Br, I, and M+(H2O), M=Li, Na, K, Rb, Cs. These generalized forms produce fits to the ab-initio data that are between one and two orders of magnitude better in the χ2 than the original forms of the PEFs. They were found to describe both the long-range, minimum and repulsive wall of the potential energy surface quite well. Overall the 4-parameter extended Morse (eM) and generalized Buckingham exponential-6 (gB-e6) potentials were found to best fit the ab-initio data. Furthermore, a single set of parameters of the reduced form was found to describe all candidates within each class of interactions. The fact that in reduced coordinates a whole class of interactions can be represented by a single PEF, yields the simple relationship between the molecular parameters associated with energy (well depth, ε), structure (equilibrium distance, rm) and spectroscopy (anharmonic frequency, ν):€ν = A⋅ (ε /μ)1/ 2 /rm + B⋅ε /rm 3 , where A and B are constants depending on the underlying PEF. This more general case of Badger’s rule has been validated using the experimentally measured frequencies of the hydrogen bonded OH stretching vibrations in the halide-water series.

  7. Intermolecular Bonding effects on ^14N Quadrupole Interaction in RDX(cyclotrimethylene-trinitramine) and ?-HMX (Cyclotetramethylene-tetranitramine)

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Sahoo, N.; Das, T. P.; Ray, S. N.

    1998-03-01

    In contrast to the very good agreement(Ranjit Pati et. al. J. Phys. Chem. 99), 9051 (1995); 101, 8302 (1997). for the ring nitrogens, the nature of agreement between the ^14N nuclear quadrupole interaction parameters for the peripheral nitrogens in cyclotrimethylene-trinitramine and cyclotetramethylene-tetranitramine is found to be less satisfactory (the experimental coupling constants(V. S. Grechishkin, J. Struct. Chem. 32), 609 (1991). being about 50 and 60 percent respectively of the theoretical results^1). A possible reason suggested in the literature^1 for this situation is the intermolecular bonding of the peripheral oxygen atoms of the nitro groups, containing the peripheral nitrogens, to hydrogen atoms of neighboring molecules. The influence of this intermolecular bonding is expected to be much more important for the peripheral nitrogens than for the ring nitrogens which are not directly bonded to the oxygens. Results of our current investigations of the influence of the intermolecular bonding on the electron distributions around the peripheral and ring nitrogens will be reported and the influence of other possible factors will be discussed.

  8. 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.

  9. 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

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

    PubMed

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

    2015-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  12. Ethyl 4-dodecyl-3,5-dimethyl-1H-pyrrole-2-carboxylate: intermolecular interactions in an amphiphilic pyrrole.

    PubMed

    Ramos Silva, Manuela; Matos Beja, Ana; Paixo, Jose Antonio; Sobral, Abilio J F N; Lopes, Susana H; Rocha Gonsalves, A M d'A

    2002-09-01

    The title compound, C(21)H(37)NO(2), is a new amphiphilic pyrrole with a long hydrocarbon chain, which will be used as a precursor for the synthesis of Langmuir-Blodgett films of porphyrins. Molecules related by an inversion centre are joined head-to-head into dimers by strong N-H.O hydrogen bonds. The dimers pack in the structure with their carbon chains parallel to one another, thereby forming alternating layers of carbon chains and pyrrole heads. The structure is further stabilized by two weak C-H.pi intermolecular interactions, thereby saturating the hydrogen-bonding capability of the aromatic pi-electron clouds. PMID:12205393

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

    PubMed

    Odahara, Takayuki; Odahara, Koji

    2016-04-01

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

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

    PubMed

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

    2011-12-01

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

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

    PubMed

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

    2005-01-01

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

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

    PubMed

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

    2015-12-24

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

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

    NASA Astrophysics Data System (ADS)

    Hight, Lauren M.

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

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

    PubMed Central

    Scott, H L; Pearce, P A

    1989-01-01

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

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

    PubMed

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

    2013-09-16

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

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

    PubMed

    Ingrosso, Francesca; Ladanyi, Branka M

    2013-01-17

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

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

    PubMed

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

    2015-09-01

    ?-? Intermolecular interactions among adjacent conjugated azobenzenes chemisorbed on (non-)flat Au surfaces can be tuned by varying the curvature of the Au nanoparticles. Here we show that such interactions rule the thermal cis-trans isomerization kinetics, towards a better control on the azobenzene bistability for its optimal integration as a responsive material. PMID:26234482

  2. 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.

  3. 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

  4. 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

  5. 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.

  6. A structural and theoretical study of intermolecular interactions in nicotinohydrazide dihydrochloride.

    PubMed

    Kruszynski, Rafal

    2011-02-01

    In the title compound [systematic name: 3-(azaniumylcarbamoyl)pyridinium dichloride], C(6)H(9)N(3)O(2+)2Cl(-), the ions are connected by N-HCl hydrogen bonds to form layers and C-HCl interactions expand the layers into a three-dimensional net. The energies of the N-HCl interactions range from typical for very weak interactions (0.17?kcal?mol(-1)) to those observed for relatively strong interactions (29.1?kcal?mol(-1)). C-HCl interactions can be classified as weak and mildly strong (energies ranging from 2.2 to 8.2?kcal?mol(-1)). Despite the short contacts existing between the parallel aromatic rings of the cations, ?-? interactions do not occur. PMID:21285501

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

    PubMed

    Jadzyn, Jan; Swiergiel, Jolanta

    2011-05-26

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  9. Intermolecular 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.

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

    PubMed

    Huang, Yuanhang; Beran, Gregory J O

    2015-07-28

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

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

    NASA Astrophysics Data System (ADS)

    Huang, Yuanhang; Beran, Gregory J. O.

    2015-07-01

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

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

    SciTech Connect

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

    2000-11-01

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

  13. [Noncovalent cation-? interactions--their role in nature].

    PubMed

    Fink, Krzysztof; Boraty?ski, Janusz

    2014-01-01

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

  14. 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.

  15. 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.

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

    PubMed

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

    2015-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed Central

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

    2001-01-01

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

  19. Enhanced fullereneAu(111) coupling in (2?3 2?3)R30 superstructures with intermolecular interactions

    PubMed Central

    Paens, Michael; Waser, Rainer

    2015-01-01

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

  20. 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.

  1. 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

  2. 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.

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

    PubMed Central

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

    2007-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-07-01

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

  5. 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 Frster 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 endophilins membrane interactions, our measurements support a syngergistic model where these interactions are inhibited in the absence of SH3 domain binding ligands such as dynamins prolin rich domains, and where the binding of these ligands may be suppressed for non-membrane-bound endophilin. PMID:24568626

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

    PubMed Central

    Haward, Simon J.

    2014-01-01

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

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

    PubMed

    Haward, Simon J

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

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

    PubMed

    Grobelny, S; Erlkamp, M; Mller, 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. Synthesis, crystal structures and intermolecular interactions of two Mn(II) complexes with 4,4?-bipy and methyl benzoates

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

  11. 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=0.16μM). 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed

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

    2009-12-01

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

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

    PubMed

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

    2016-02-17

    The superoxide radical anion O2(-) is involved in many important chemical processes spanning different scientific disciplines (e.g., environmental and biological sciences). Characterizing its interaction with various substrates to help elucidate its rich chemistry may have far reaching implications. Herein, we investigate the interaction between O2(-) (X[combining tilde] (2)?g) and the hydrogen halides (X[combining tilde] (1)?) with coupled-cluster theory. In contrast to the short (1.324 ) 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 ) 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)?) + O2(-) (X[combining tilde] (2)?g) 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)?) + HO2 (X[combining tilde] (2)A'') are 25.7 kcal mol(-1) for X = Cl, 21.9 kcal mol(-1) for X = Br, and 17.9 kcal mol(-1) for X = I. Additionally, the heavier hydrogen halides can form weak halogen bonds H-XO2(-) (X[combining tilde] (2)A'') with interaction energies including ZPVE of -2.3 kcal mol(-1) for HCl, -8.3 kcal mol(-1) for HBr, and -16.7 kcal mol(-1) for HI. PMID:26852733

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

    NASA Astrophysics Data System (ADS)

    Taylor, Jeremy; Brandbyge, Mads; Stokbro, Kurt

    2003-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

  17. 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.

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

    PubMed

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

    2013-01-15

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

  19. 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

  20. 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 100K 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 etal. 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 HH, OH/H⋯O, CH/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.

  1. In-Plane Intermolecular Interaction Assisted Assembly and Modified Electronic States of Metallofullerene Gd@C??.

    PubMed

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

    2015-10-27

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

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

    PubMed Central

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

    2011-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Renner, Christian; Holak, Tad A.

    2000-08-01

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

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

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

    PubMed

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

    2011-08-01

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

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

    PubMed

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

    2003-06-15

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

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

    PubMed

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

    2015-10-26

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

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

    PubMed

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

    2014-01-21

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

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

    PubMed Central

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

    2010-01-01

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

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

    PubMed

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

    2010-03-01

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

  12. Nonresonant and resonant mode-specific intermolecular vibrational energy transfers in electrolyte aqueous solutions.

    PubMed

    Bian, Hongtao; Chen, Hailong; Li, Jiebo; Wen, Xiewen; Zheng, Junrong

    2011-10-27

    The donor/acceptor energy mismatch and vibrational coupling strength dependences of interionic vibrational energy transfer kinetics in electrolyte aqueous solutions were investigated with ultrafast multiple-dimensional vibrational spectroscopy. An analytical equation derived from the Fermi's Golden rule that correlates molecular structural parameters and vibrational energy transfer kinetics was found to be able to describe the intermolecular mode specific vibrational energy transfer. Under the assumption of the dipole-dipole approximation, the distance between anions in the aqueous solutions was obtained from the vibrational energy transfer measurements, confirmed with measurements on the corresponding crystalline samples. The result demonstrates that the mode-specific vibrational energy transfer method holds promise as an angstrom molecular ruler. PMID:21916443

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

    NASA Astrophysics Data System (ADS)

    Marino, Michele; Vairo, Giuseppe

    2014-12-01

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

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

    SciTech Connect

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

    2011-11-22

    We investigate the chemisorption structure of CO molecules on the quasi-one-dimensional Cu(110)-(21)-O surface by low-temperature scanning tunneling microscopy and density functional theory. Contrary to flat metal surfaces, where CO molecules adsorb in an upright geometry and interact through repulsive intermolecular interactions, we find the most stable adsorption structure of single CO molecules to be at Cu atoms of substrate CuO chains with the CuCO unit bent by?45 in two equivalent structures at low coverages. At higher coverages, CO molecules combine in the same structure into highly ordered single-molecule-wide rows perpendicular to the substrate chains in an approximately 8 1 full monolayer structure. Firstprinciples calculations attribute the unprecedented chemisorption behavior of CO molecules to lifting of the host Cu atoms by 1 from the surface CuO chains, in order to optimize the bonding and reduce the repulsive interactions with the substrate. This structural distortion enables short-range intermolecular dipoledipole attraction and creates orthogonal long-range surface-mediated repulsion leading to unusual self-assembly of CO molecules into coherent nanometer scale molecular grating structures.

  15. Intermolecular interactions of inorganic and organic molecules embedded in zeolite-type materials probed by near-infrared Fourier transform Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Wirnsberger, Gernot; Fritzer, Harald P.; Koller, Hubert; Behrens, Peter; Popitsch, Alois

    1999-05-01

    Near-infrared Fourier transform Raman spectroscopy represents an excellently suited tool to investigate spectroscopically inorganic and organic molecules occluded in zeolite-type materials as well as interactions between them. Two examples are presented: First, insertion compounds of iodine in various microporous SiO 2 modifications (deca-dodecasil 3R, all-silica theta-1 and silicalite-1) are discussed. Intermolecular interaction between the inserted molecules is prevented by occlusion of iodine in the cages of deca-dodecasil 3R, but is allowed in the insertion compounds of hosts with higher pore dimensionalities. The intermolecular coupling is confirmed by an appreciable reduction of the Raman shifts, as observed similarly for liquid and amorphous iodine. The second example deals with pyridine and n-alkylamines ( n-propyl-, n-butyl- or n-pentylamine) occluded during synthesis in all-silica ferrierite. Raman spectra reveal for all compounds, regardless of the n-alkylamine used, an interaction between the n-alkylamine and neighboring pyridine molecules, with both amines being located in the ten-membered ring channels. For this reason, it is proposed that bimolecular complexes, consisting of an n-alkylamine weakly bound to a pyridine molecule act as structure-directing agents during synthesis.

  16. Intermolecular interactions of liquid dichloromethane and equilibrium properties of liquid{endash}vapor and liquid{endash}liquid interfaces: A molecular dynamics study

    SciTech Connect

    Dang, L.X.

    1999-05-01

    Extensive molecular dynamics simulations are carried out to study the molecular interactions, liquid states, and liquid/vapor properties of dichloromethane. The study is also extended to the equilibrium properties of the liquid/liquid interface of water-dichloromethane. The intermolecular interactions among water, dichloromethane, and water-dichloromethane are described using our polarizable potential models. The equilibrium properties of liquid dichloromethane, including the radial distribution functions, the intermolecular structural factor, the self-diffusion coefficient, and the dielectric constant, are evaluated. The dielectric constant is computed using Ewald summation techniques and the computed result compared reasonably well with the available experimental data. Properties such as surface tensions and density profiles of liquid/vapor dichloromethane are evaluated. We found that the computed surface tensions for several temperatures are in excellent agreement with experimental data. The computed density profile of the liquid/liquid interface of water-dichloromethane is averaged over 1 ns and we found the computed profile to be quite smooth and stable. The effect of polarization on the liquid/liquid interfacial equilibrium properties is evaluated by computing the dipole moments of water and dichloromethane molecules as a function of the distance normal to the interface. We found that these values deviated significantly from the simulations that are based on nonpolarizable potential models. We attribute these observations to the changes in the electric fields around the water and dichloromethane molecules near the interface. {copyright} {ital 1999 American Institute of Physics.}

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

    PubMed

    Kyas, Gerold; May, Volkhard

    2011-01-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-02-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    SciTech Connect

    Xantheas, Sotiris S.; Werhahn, Jasper C.

    2014-08-14

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Kuchenbecker, Dennis; Jansen, Georg

    2012-08-01

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

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

    PubMed Central

    da Silva, Jlio Csar; Sfora, Maurcio Lus; Honorato, Rodrigo Vargas; Granato, Daniela Campos; dos Santos Migueleti, Deivid Lucas; Neves, Jorge L.; de Oliveira, Paulo Sergio Lopes; Paes-Leme, Adriana Franco; Zeri, Ana Carolina de Mattos; de Torriani, Iris Concepcion Linares; Kobarg, Jrg

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

  7. Tailored donor-acceptor polymers with an A-D1-A-D2 structure: controlling intermolecular interactions to enable enhanced polymer photovoltaic devices.

    PubMed

    Qin, Tianshi; Zajaczkowski, Wojciech; Pisula, Wojciech; Baumgarten, Martin; Chen, Ming; Gao, Mei; Wilson, Gerry; Easton, Christopher D; Mllen, Klaus; Watkins, Scott E

    2014-04-23

    Extensive efforts have been made to develop novel conjugated polymers that give improved performance in organic photovoltaic devices. The use of polymers based on alternating electron-donating and electron-accepting units not only allows the frontier molecular orbitals to be tuned to maximize the open-circuit voltage of the devices but also controls the optical band gap to increase the number of photons absorbed and thus modifies the other critical device parameter-the short circuit current. In fact, varying the nonchromophoric components of a polymer is often secondary to the efforts to adjust the intermolecular aggregates and improve the charge-carrier mobility. Here, we introduce an approach to polymer synthesis that facilitates simultaneous control over both the structural and electronic properties of the polymers. Through the use of a tailored multicomponent acceptor-donor-acceptor (A-D-A) intermediate, polymers with the unique structure A-D1-A-D2 can be prepared. This approach enables variations in the donor fragment substituents such that control over both the polymer regiochemistry and solubility is possible. This control results in improved intermolecular ?-stacking interactions and therefore enhanced charge-carrier mobility. Solar cells using the A-D1-A-D2 structural polymer show short-circuit current densities that are twice that of the simple, random analogue while still maintaining an identical open-circuit voltage. The key finding of this work is that polymers with an A-D1-A-D2 structure offer significant performance benefits over both regioregular and random A-D polymers. The chemical synthesis approach that enables the preparation of A-D1-A-D2 polymers therefore represents a promising new route to materials for high-efficiency organic photovoltaic devices. PMID:24697300

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

    NASA Astrophysics Data System (ADS)

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

    2006-09-01

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

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

    PubMed

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

    2015-04-01

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

  10. Multidimensional infrared spectroscopy for molecular vibrational modes with dipolar interactions, anharmonicity, and nonlinearity of dipole moments and polarizability

    NASA Astrophysics Data System (ADS)

    Hyeon-Deuk, Kim; Tanimura, Yoshitaka

    2005-12-01

    We present an analytical expression for the linear and nonlinear infrared spectra of interacting molecular vibrational motions. Each of the molecular modes is explicitly represented by a classical damped oscillator on an anharmonic multidimensional potential-energy surface. The two essential interactions, the dipole-dipole (DD) and the dipole-induced-dipole (DID) interactions, are taken into account, and each dipole moment and polarizability are expanded to nonlinear order with respect to the nuclear vibrational coordinate. Our analytical treatment leads to expressions for the contributions of anharmonicity, DD and DID interactions, and the nonlinearity of dipole moments and polarizability elements to the one-, two-, and three-dimensional spectra as separated terms, which allows us to discuss the relative importance of these respective contributions. We can calculate multidimensional signals for various configurations of molecules interacting through DD and DID interactions for different material parameters over the whole range of frequencies. We demonstrate that contributions from the DD and DID interactions and anharmonicity are separately detectable through the third-order three-dimensional IR spectroscopy, whereas they cannot be distinguished from each other in either the linear or the second-order IR spectroscopies. The possibility of obtaining the intra- or intermolecular structural information from multidimensional spectra is also discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

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

    SciTech Connect

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

    2013-08-29

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

  15. Weak intermolecular interactions in isomorphous 5-(2-chloroethoxy)-2,3-dihydro-1,4-benzodioxine and 5-(2-bromoethoxy)-2,3-dihydro-1,4-benzodioxine: bonding or nonbonding interactions.

    PubMed

    Kruszynski, Rafal

    2009-08-01

    The title compounds, C10H11ClO3, (I), and C10H11BrO3, (II), are isomorphous and effectively isostructural; all of the interatomic distances and angles are normal. The structures exhibit long intermolecular C-H...O and C-H...pi contacts with attractive energies ranging from 1.17 to 2.30 kJ mol(-1). Weak C-H...O hydrogen bonds form C(3) and C(4) motifs, combining to form a two-dimensional R(3)(4)(12) net. No face-to-face stacking interactions are observed. PMID:19652322

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

    NASA Astrophysics Data System (ADS)

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

    1984-03-01

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

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

    PubMed

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

    2016-03-21

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

  18. Organic nonlinear optical materials: the mechanism of intermolecular covalent bonding interactions of Kekul hydrocarbons with significant singlet biradical character.

    PubMed

    Liu, Jing; Xia, Jiarui; Song, Peng; Ding, Yong; Cui, Yanling; Liu, Xuemei; Dai, Yumei; Ma, Fengcai

    2014-08-25

    The ground- and excited-state properties of benzene-linked bisphenalenyl (B-LBP), naphthaline-linked bisphenalenyl (N-LBP), and anthracene-linked bisphenalenyl (A-LBP) Kekul molecules and their respective one-dimensional (1D) stacks are investigated using time-dependent density functional theory (TD-DFT) and a range of extensive multidimensional visualization techniques. The results reveal a covalent ?-? bonding interaction between overlapping phenalenyl radicals whose bond length is shorter than the van der Waals distance between carbon atoms. Increasing the linker length and/or number of molecules involved in the 1D stack decreases the HOMO-LUMO energy gap and increases the wavelength of the systems. The charge-transfer mechanism and electron coherence both differ with changes in the linker length and/or number of molecules involved in the 1D stack. PMID:24888700

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

    SciTech Connect

    Galbis, Elsa; Pappalardo, Rafael R.; Marcos, Enrique Snchez; Hernndez-Cobos, Jorge

    2014-06-07

    This work proposes a new methodology to build interaction potentials between a highly charged metal cation and water molecules. These potentials, which can be used in classical computer simulations, have been fitted to reproduce quantum mechanical interaction energies (MP2 and BP86) for a wide range of [M(H{sub 2}O){sub n}]{sup m+}(H{sub 2}O){sub ?} clusters (n going from 6 to 10 and ? from 0 to 18). A flexible and polarizable water shell model (Mobile Charge Density of Harmonic Oscillator) has been coupled to the cation-water potential. The simultaneous consideration of poly-hydrated clusters and the polarizability of the interacting particles allows the inclusion of the most important many-body effects in the new polarizable potential. Applications have been centered on the californium, Cf(III) the heaviest actinoid experimentally studied in solution. Two different strategies to select a set of about 2000 structures which are used for the potential building were checked. Monte Carlo simulations of Cf(III)+500 H{sub 2}O for three of the intermolecular potentials predict an aquaion structure with coordination number close to 8 and average R{sub Cf??O} in the range 2.432.48 , whereas the fourth one is closer to 9 with R{sub Cf??O} = 2.54 . Simulated EXAFS spectra derived from the structural Monte Carlo distribution compares fairly well with the available experimental spectrum for the simulations bearing 8 water molecules. An angular distribution similar to that of a square antiprism is found for the octa-coordination.

  20. Intermolecular mRNA-rRNA hybridization and the distribution of potential interaction regions in murine 18S rRNA.

    PubMed Central

    Matveeva, O V; Shabalina, S A

    1993-01-01

    Intermolecular hybridization experiments show that murine 18S rRNA and 28S rRNA are capable of forming stable hybrid structures with mRNA from genes p53, c-myc and c-mos from the same species. Both 5'-uncoding and coding oncogene p53 mRNA regions contain fragments interacting with rRNA. Computer analysis revealed 18S rRNA fragments complementary to oligonucleotides frequently met in mRNA, which are potential hybridization regions (clinger-fragments). The distribution of clinger-fragments along 18S rRNA sequence is universal at least for one hundred murine mRNA sequences analyzed. Maximal frequencies of oligonucleotides complementary to 18S rRNA clinger-fragments are reliably (2-3 times) higher for mRNA than for intron sequences and randomly generated sequences. The results obtained suggest a possible role of clinger-fragments in translation processes as universal regions of mRNA binding. Images PMID:8451167

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

    NASA Astrophysics Data System (ADS)

    Nakamura, Nobuo; Masui, Hirotsugo; Ueda, Takahiro

    2000-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Sikorski, Artur; Trzybiński, Damian

    2013-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

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

    2013-11-01

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

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

    PubMed Central

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

    1996-01-01

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

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

    PubMed Central

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

    1992-01-01

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

  7. Intermolecular interactions between salmon calcitonin, hyaluronate, and chitosan and their impact on the process of formation and properties of peptide-loaded nanoparticles.

    PubMed

    Umerska, Anita; Corrigan, Owen I; Tajber, Lidia

    2014-12-30

    The principal aim of this work was to study the formulation of a ternary complex comprising salmon calcitonin (sCT), hyaluronate (HA), and chitosan (CS) in a nanoparticle (NP) format. As interactions between the constituents are possible, their presence and component mass mixing ratio (MMR) and charge mixing ratio (CMR) were investigated to tune the properties of NPs. Intermolecular interactions between sCT and HA as well as sCT and CS were studied by infrared spectroscopy (FTIR) and dynamic viscosity. The impact of MMR, CMR, and HA molecular weight on the sCT loading capacity in NPs and in vitro release properties was determined. sCT complexes to HA via electrostatic interactions and a support for hydrophobic interactions between sCT and HA as well as sCT and CS was found by FTIR. The sCT/HA complex is soluble but, depending on the mass mixing ratio between sCT and HA, NPs and microparticles were also formed indicative of associative phase separation between HA and sCT. The negatively charged HA/CS/sCT NPs were characterized by very high values (above 90%) of peptide association for the systems tested. Also, high sCT loading up to 50% were achieved. The peptide loading capacity and in vitro release properties were dependent on the NP composition. The zeta potential of the NPs without sCT was negative and ranging from -136 to -36 mV, but increased to -84 to -19 mV when the peptide was loaded. The particle size was found to be smaller and ranging 150-230 nm for sCT/NPs in comparison to NPs without sCT (170-260 nm). Short-term storage studies in liquid dispersions showed that the colloidal stability of NPs was acceptable and no release of sCT was observed for up to 3 days. In conclusion, a range of NP systems comprising sCT, HA, and CS was successfully developed and characterized. Such NPs may be considered as a suitable nanoparticulate format for the delivery of sCT. PMID:25447822

  8. Crystal and molecular structure of 5-benzylidene-2-thiohydantoin: The SS intermolecular interactions between two C dbnd S groups

    NASA Astrophysics Data System (ADS)

    Ksi??ek, Waldemar; Kie?-Kononowicz, Katarzyna; Karolak-Wojciechowska, Janina

    2009-03-01

    The crystal structure of 5-benzylidene-2-thiohydantoin, C 10H 8N 2OS, the precursor of annelated arylidene-2-thiohydantoin derivatives with the micromolar affinity to the benzodiazepine receptor, has been determined at 293 K and 120 K. The title molecule in Z-configuration is planar within experimental error. Among two bonds between N1/N3 and C2(sp 2), N3 sbnd C2 is evidently longer than the N1 sbnd C2 one. In the structure determined at 120 K difference equals 0.019 . For that reason, in the cycloaddition reaction N3 nitrogen was privileged and the products of 2,3-substitution were obtained at a significantly higher yield than the 1,2-substitution ones. The chain of molecules joined by N sbnd HO hydrogen bonds created the main structure motive in the crystal. Hydrogen bond of N sbnd HS and intermolecular interactions of SS were noticed between two chains. With respect to the center of symmetry, sulfur atoms are 3.414(1) and 3.3745(8) apart at ambient and low temperatures, respectively. The related SS contacts, shorter than the sum of van der Waals' radii, were identified in many species deposited in CSD, all with cyclic and/or non-cyclic arrangements of C dbnd S. The statistical analysis of the geometrical distribution for such contacts suggests that there is a maximum of probability for collinear C dbnd SS dbnd C orientations. Additionally, if NH is located in close proximity of C dbnd S substituent, this contact is self-assembled with N sbnd HS weak hydrogen bonds.

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

    PubMed

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

    2012-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

    We develop the method proposed by Chernyshuk and Lev [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.81.041701 81, 041701 (2010)] for theoretical investigation of elastic interactions between colloidal particles of arbitrary shape and chirality (polar as well as azimuthal anchoring) in the confined nematic liquid crystal (NLC). General expressions for six different types of multipole elastic interactions are obtained in the confined NLC: monopole-monopole (Coulomb type), monopole-dipole, monopole-quadrupole, dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole interactions. The obtained formulas remain valid in the presence of the external electric or magnetic fields. The exact equations are found for all multipole coefficients for the weak anchoring case. For the strong anchoring coupling, the connection between the symmetry of the shape or director and multipole coefficients is obtained, which enables us to predict which multipole coefficients vanish and which remain nonzero. The particles with azimuthal helicoid anchoring are considered as an example. Dipole-dipole interactions between helicoid cylinders and cones are found in the confined NLC. In addition, the banana-shaped particles in homeotropic and planar nematic cells are considered. It is found that the dipole-dipole interaction between banana-shaped particles differs greatly from the dipole-dipole interaction between the axially symmetrical particles in the nematic cell. There is a crossover from attraction to repulsion between banana particles along some directions in nematic cells. It is shown that monopoles do not “feel” the type of nematic cell: monopole-monopole interaction turns out to be the same in homeotropic and planar nematic cells and converges to the Coulomb law as thickness increases, L→∞.

  11. Competing interactions in semiconductor quantum dots

    SciTech Connect

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

    2014-10-14

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

  12. Competing interactions in semiconductor quantum dots

    DOE PAGESBeta

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

    2014-10-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-09-01

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

  14. Disorder and intermolecular interactions in a family of tetranuclear Ni(II) complexes probed by high-frequency electron paramagnetic resonance.

    PubMed

    Lawrence, Jon; Yang, En-Che; Edwards, Rachel; Olmstead, Marilyn M; Ramsey, Chris; Dalal, Naresh S; Gantzel, Peter K; Hill, Stephen; Hendrickson, David N

    2008-03-17

    High-frequency electron paramagnetic resonance (HFEPR) data are presented for four closely related tetranuclear Ni(II) complexes, [Ni(hmp)(MeOH)Cl]4.H2O (1a), [Ni(hmp)(MeOH)Br]4.H2O (1b), [Ni(hmp)(EtOH)Cl]4.H2O (2), and [Ni(hmp)(dmb)Cl]4 (3) (where hmp(-) is the anion of 2-hydroxymethylpyridine and dmb is 3,3'-dimethyl-1-butanol), which exhibit magnetic bistability (hysteresis) and fast magnetization tunneling at low temperatures, properties which suggest they are single-molecule magnets (SMMs). The HFEPR spectra confirm spin S = 4 ground states and dominant uniaxial anisotropy (DSz(2), D < 0) for all four complexes, which are the essential ingredients for a SMM. The individual fine structure peaks (due to zero-field splitting) for complexes 1a, 1b, and 2 are rather broad. They also exhibit further (significant) splitting, which can be explained by the fact that there exists two crystallographically distinct Ni 4 sites in the lattices for these complexes, with associated differences in metal-ligand bond lengths and different zero-field splitting (ZFS) parameters. The broad EPR lines, meanwhile, may be attributed to ligand and solvent disorder, which results in additional distributions of microenvironments. In the case of complex 3, there are no solvate molecules in the structure, and only one distinct Ni 4 molecule in the lattice. Consequently, the HFEPR data for complex 3 are extremely sharp. As the temperature of a crystal of complex 3 is decreased, the HFEPR spectrum splits abruptly at approximately 46 K into two patterns with very slightly different ZFS parameters. Heat capacity data suggest that this is caused by a structural transition at 46.6 K. A single-crystal X-ray structure at 12(2) K indicates large thermal parameters on the terminal methyl groups of the dmb (3,3-dimethyl-1-butanol) ligand. Most likely there exists dynamic disorder of parts of the dmb ligand above 46.6 K; an order-disorder structural phase transition at 46.6 K then removes some of the motion. A further decrease in temperature (<6 K) leads to further fine structure splittings for complex 3. This behavior is thought to be due to the onset of short-range magnetic correlations/coherences between molecules caused by weak intermolecular magnetic exchange interactions. PMID:18284196

  15. Calculating intermolecular potentials with SIMPER

    NASA Astrophysics Data System (ADS)

    Wheatley, Richard J.; Lillestolen, Timothy C.

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

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

    PubMed

    Beck, John Frederick; Mo, Yirong

    2007-01-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

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

    PubMed

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

    2015-07-01

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

  19. Crystal structures of 4-chloropyridine-2-carbonitrile and 6-chloropyridine-2-carbonitrile exhibit different intermolecular ?-stacking, CH?Nnitrile and CH?Npyridine interactions

    PubMed Central

    Montgomery, Matthew J.; OConnor, Thomas J.; Tanski, Joseph M.

    2015-01-01

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

  20. Desensitization of metastable intermolecular composites

    DOEpatents

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

    2011-04-26

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

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

    NASA Astrophysics Data System (ADS)

    Han, Jianing; Gallagher, Tom

    2009-05-01

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

  2. Intermolecular electrostatic energies using density fitting.

    PubMed

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

    2005-07-22

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

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

    SciTech Connect

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

    2011-11-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed

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

    2015-12-01

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

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

    PubMed

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

    1989-08-15

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

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

    PubMed

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

    2009-12-01

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

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

    SciTech Connect

    Salam, A. |

    2007-12-15

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

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

    PubMed

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

    2016-01-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    SciTech Connect

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

    2007-02-09

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

  12. Mapping intermolecular bonding in C??.

    PubMed

    Sundqvist, Bertil

    2014-01-01

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

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

    PubMed

    Renaud, Nicolas; Grozema, Ferdinand C

    2015-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

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

    PubMed

    Esrafili, Mehdi D

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Cody, Vivian; Murray-Rust, Peter

    1984-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    PubMed Central

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

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  20. Metal-Arene Complexes with Indolo[3,2-c]-quinolines: Effects of Ruthenium vs Osmium and Modifications of the Lactam Unit on Intermolecular Interactions, Anticancer Activity, Cell Cycle, and Cellular Accumulation.

    PubMed

    Filak, Lukas K; Gschl, Simone; Heffeter, Petra; Ghannadzadeh Samper, Katia; Egger, Alexander E; Jakupec, Michael A; Keppler, Bernhard K; Berger, Walter; Arion, Vladimir B

    2013-02-11

    Six novel ruthenium(II)- and osmium(II)-arene complexes with three modified indolo[3,2-c]quinolines have been synthesized in situ starting from 2-aminoindoloquinolines and 2-pyridinecarboxaldehyde in the presence of [M(p-cymene)Cl(2)](2) (M = Ru, Os) in ethanol. All complexes have been characterized by elemental analysis, spectroscopic techniques ((1)H, (13)C NMR, IR, UV-vis), and ESI mass spectrometry, while four complexes were investigated by X-ray diffraction. The complexes have been tested for antiproliferative activity in vitro in A549 (non-small cell lung), SW480 (colon), and CH1 (ovarian) human cancer cell lines and showed IC(50) values between 1.3 and >80 ?M. The effects of Ru vs Os and modifications of the lactam unit on intermolecular interactions, antiproliferative activity, and cell cycle are reported. One ruthenium complex and its osmium analogue have been studied for anticancer activity in vivo applied both intraperitoneally and orally against the murine colon carcinoma model CT-26. Interestingly, the osmium(II) complex displayed significant growth-inhibitory activity in contrast to its ruthenium counterpart, providing stimuli for further investigation of this class of compounds as potential antitumor drugs. PMID:23431223

  1. MetalArene Complexes with Indolo[3,2-c]-quinolines: Effects of Ruthenium vs Osmium and Modifications of the Lactam Unit on Intermolecular Interactions, Anticancer Activity, Cell Cycle, and Cellular Accumulation

    PubMed Central

    2013-01-01

    Six novel ruthenium(II) and osmium(II)arene complexes with three modified indolo[3,2-c]quinolines have been synthesized in situ starting from 2-aminoindoloquinolines and 2-pyridinecarboxaldehyde in the presence of [M(p-cymene)Cl2]2 (M = Ru, Os) in ethanol. All complexes have been characterized by elemental analysis, spectroscopic techniques (1H, 13C NMR, IR, UVvis), and ESI mass spectrometry, while four complexes were investigated by X-ray diffraction. The complexes have been tested for antiproliferative activity in vitro in A549 (non-small cell lung), SW480 (colon), and CH1 (ovarian) human cancer cell lines and showed IC50 values between 1.3 and >80 ?M. The effects of Ru vs Os and modifications of the lactam unit on intermolecular interactions, antiproliferative activity, and cell cycle are reported. One ruthenium complex and its osmium analogue have been studied for anticancer activity in vivo applied both intraperitoneally and orally against the murine colon carcinoma model CT-26. Interestingly, the osmium(II) complex displayed significant growth-inhibitory activity in contrast to its ruthenium counterpart, providing stimuli for further investigation of this class of compounds as potential antitumor drugs. PMID:23431223

  2. Student Understanding of Intermolecular Forces: A Multimodal Study

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  3. Student Understanding of Intermolecular Forces: A Multimodal Study

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  4. Intermolecular artifacts in probe microscope images of C60 assemblies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  5. Energy exchange in systems of particles with nonreciprocal interaction

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  6. Quantum structure of the intermolecular proton bond.

    PubMed

    Roscioli, J R; McCunn, L R; Johnson, M A

    2007-04-13

    A proton shared between two closed-shell molecules, [A.H+.B], constitutes a ubiquitous soft binding motif in biological processes. The vibrational transitions associated with the shared proton, which provide a direct probe of this interaction, have been extensively studied in the condensed phase but have yielded only limited detailed information because of their diffuse character. We exploited recent advances in gas-phase ion spectroscopy to identify sharp spectral features that can be assigned to both the shared proton and the two tethered molecules in a survey of 18 cold, isolated [A.H+.B] ions. These data yield a picture of the intermolecular proton bond at a microscopic scale, facilitating analysis of its properties within the context of a floppy polyatomic molecule. PMID:17431174

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

    NASA Technical Reports Server (NTRS)

    Matsuura, Yoshiki; Chernov, Alexander A.

    2002-01-01

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

  8. The intermolecular vibrations of the water dimer

    NASA Astrophysics Data System (ADS)

    Braly, Linda Beth

    Terahertz laser spectra of water dimer intermolecular vibrations have yielded four (D2O)2 VRT bands (one previously published) and five (H2O)2 VRT bands measured with ca. 1 MHz precision and assigned between 65 and 142 cm-1. The results differ both qualitatively and quantitatively from the predictions of popular, effective pair potentials tested. The spectra also reveal an ordering of the intermolecular vibrations which differs dramatically from that predicted by a normal mode analysis. Strong coupling is indicated between the low barrier tunneling motions and the intermolecular vibrations as well as between different vibrations. In particular the 102.1 cm-1 (H2O) 2 band assigned as the acceptor wag has two types of perturbations. The first perturbation involves coupling of two of the tunneling components between the Ka = 0 and 1 levels similar to that occurring in ground state between Ka = 0 and 1 levels. This is treated with an effective Coriolis coupling constant. These seconded perturbation involves one tunneling component with Ka = 1 coupling with a tunneling component with Ka = 0 of the 108 cm-1 acceptor twist vibration. A more detailed Coriolis coupling scheme is required to deperturb these states. Also it is indicated that the 103.1 cm-1 (H2O) 2 band assigned as the donor in-plane bend is coupled to the acceptor wag resulting in a lowering of the in-plane bend frequency and raising the acceptor wag frequency. In addition the 141 cm-1 (H2O)2 band shows perturbations which could not be. resolved at this time. And the 83 cm-1 (acceptor wag) and 90 cm-1 (D2O)2 (acceptor twist) band are perturbing one another through a Coriolis interaction. A subset of the (D2O)2 data have been used in an ongoing effort to determine an accurate IPS via least-squares fitting to an analytical form. The results from the most recent fit which produced VRT(ASP- W)II are presented and compared with the experimental data. The IPS was used to calculate the eigenstates of the water dimer using the Split Wigner Psuedo Spectral (SWPS) method. The transitions could then be calculated from the eigenstates. This improved IPS reproduces the dominant features of the VRT spectra quite well. The ultimate goal of this water dimer research project is to determine the ``perfect'' water pair potential from the spectroscopic data.

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

    PubMed

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

    2009-10-22

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

  10. Desensitization and recovery of metastable intermolecular composites

    DOEpatents

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

    2010-09-07

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

  11. Quantum dynamics with strongly interacting Rydberg atoms

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  12. Intermolecular domain docking in the hairpin ribozyme

    PubMed Central

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Han, Jianing

    2010-11-01

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

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

    SciTech Connect

    Han Jianing

    2010-11-15

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

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

    PubMed

    Nagy, Peter I

    2014-01-01

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

  16. Competing Intramolecular vs. Intermolecular Hydrogen Bonds in Solution

    PubMed Central

    Nagy, Peter I.

    2014-01-01

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

  17. Tunable high-temperature thermodynamics of weakly interacting dipolar gases

    NASA Astrophysics Data System (ADS)

    Daily, K. M.; Blume, D.

    2014-01-01

    We consider dilute gases of dipolar bosons or fermions in the high-temperature limit in a spherically symmetric harmonic trapping potential. We examine the system using a virial expansion up to second order in the fugacity. Using the Born approximation and assuming purely dipolar interactions, we find that the second-order virial coefficient for both bosons and fermions depends quadratically on the dipole length and is negative at high temperatures, indicating that to lowest order in the dipole-dipole interactions the dipolar single-component quantum gases are repulsive. If the s-wave scattering length for the bosonic system is tunable and its absolute value is made small, then the s-wave interactions dominate and the dipolar gas behaves like a weakly interacting Bose gas with isotropic s-wave interactions. If the generalized scattering lengths for the fermionic system are tunable, then the dipole length can enter linearly in the virial equation of state, enhancing the dipole-dipole effects in the thermodynamic observables.

  18. Intermolecular Vibrations of Hydrophobic Amino Acids

    NASA Astrophysics Data System (ADS)

    Williams, Michael Roy Casselman

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

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

    PubMed

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

    2011-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  1. Energetics of intermolecular hydrogen bonds in a hydrophobic protein cavity.

    PubMed

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

    2014-05-01

    This work explores the energetics of intermolecular H-bonds inside a hydrophobic protein cavity. Kinetic measurements were performed on the gaseous deprotonated ions (at the -7 charge state) of complexes of bovine ?-lactoglobulin (Lg) and three monohydroxylated analogs of palmitic acid (PA): 3-hydroxypalmitic acid (3-OHPA), 7-hydroxypalmitic acid (7-OHPA), and 16-hydroxypalmitic acid (16-OHPA). From the increase in the activation energy for the dissociation of the (Lg + X-OHPA)?? ions, compared with that of the (Lg + PA)?? ion, it is concluded that the OH groups of the X-OHPA ligands participate in strong (5-11 kcal mol?) intermolecular H-bonds in the hydrophobic cavity of Lg. The results of molecular dynamics (MD) simulations suggest that the OH groups of 3-OHPA and 16-OHPA act as H-bond donors and interact with backbone carbonyl oxygens, whereas the OH group of 7-OHPA acts as both H-bond donor and acceptor with nearby side chains. The capacity for intermolecular H-bonds within the Lg cavity, as suggested by the gas-phase measurements, does not necessarily lead to enhanced binding in aqueous solution. The association constant (Ka) measured for 7-OHPA [(2.3 0.2) 10? M?] is similar to the value for the PA [(3.8 0.1) 10? M?]; Ka for 3-OHPA [(1.1 0.3) 10? M?] is approximately three-times larger, whereas Ka for 16-OHPA [(2.3 0.2) 10? M?] is an order of magnitude smaller. Taken together, the results of this study suggest that the energetic penalty to desolvating the ligand OH groups, which is necessary for complex formation, is similar in magnitude to the energetic contribution of the intermolecular H-bonds. PMID:24658798

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

    NASA Astrophysics Data System (ADS)

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

    2004-04-01

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

  3. Visualizing the orientational dependence of an intermolecular potential

    PubMed Central

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

    2016-01-01

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

  4. Visualizing the orientational dependence of an intermolecular potential.

    PubMed

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

    2016-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

  6. Mapping intermolecular bonding in C60

    NASA Astrophysics Data System (ADS)

    Sundqvist, Bertil

    2014-08-01

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

  7. Mapping intermolecular bonding in C60

    PubMed Central

    Sundqvist, Bertil

    2014-01-01

    The formation of intermolecular bonds in C60 has been investigated in detail at pressures below 2.2?GPa and up to 750?K. Fullerene samples were heated in a temperature gradient to obtain data on the formation of dimers and low-dimensional polymers along isobars. Intermolecular bonding was analyzed ex situ by Raman scattering, using both intramolecular modes and intermolecular stretching modes. Semi-quantitative reaction maps are given for the formation of dimers and chains. The activation energy for dimer formation decreases by 0.2?meV pm?1 when intermolecular distances decrease and dimer formation is noticeably affected by the rotational state of molecules. Above 400450?K larger oligomers are formed; below 1.4?GPa most of these are disordered, with small domains of linear chains, but above this the appearance of stretching modes indicates the existence of ordered one-dimensional polymers. At the highest pressures and temperatures two-dimensional polymers are also observed. PMID:25145952

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

    NASA Astrophysics Data System (ADS)

    Qian, Yachao; Zahed, Ismail

    2015-11-01

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

  9. Cs Trilobite Molecules and Rydberg atom Interactions

    NASA Astrophysics Data System (ADS)

    Booth, Donald; Jin, Yang; Shaffer, James

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

    Polat, Turgay; Bulut, Fatih; Arıcan, Ilknur; Kandemirli, Fatma; Yildirim, Gürcan

    2015-12-01

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

  11. Thermodynamic curvature for attractive and repulsive intermolecular forces.

    PubMed

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

    2013-09-01

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

  12. Intermolecular diatomic energies of a hydrogen dimer with non-Born-Oppenheimer nuclear and electron wave packets

    NASA Astrophysics Data System (ADS)

    Hyeon-Deuk, Kim; Ando, Koji

    2012-04-01

    We have developed an efficient theoretical framework of a non-Born-Oppenheimer (non-BO) nuclear and electron wave packet (NWP and EWP) method and applied it to intra- and intermolecular energies of a hydrogen dimer. The energy surface functions were derived at low computational cost. In contrast with the ordinary BO nuclear quantization on a given energy surface that reduces the effective barrier, non-trivial non-BO interactions between the EWPs and NWPs resulted in increases of intermolecular rotational and translational barriers. A direct comparison demonstrated that the non-BO effect on the intermolecular energy is significant.

  13. Direct measurements of intermolecular forces by chemical force microscopy

    NASA Astrophysics Data System (ADS)

    Vezenov, Dmitri Vitalievich

    1999-12-01

    Detailed description of intermolecular forces is key to understanding a wide range of phenomena from molecular recognition to materials failure. The unique features of atomic force microscopy (AFM) to make point contact force measurements with ultra high sensitivity and to generate spatial maps of surface topography and forces have been extended to include measurements between well-defined organic molecular groups. Chemical modification of AFM probes with self-assembled monolayers (SAMs) was used to make them sensitive to specific molecular interactions. This novel chemical force microscopy (CFM) technique was used to probe forces between different molecular groups in a range of environments (vacuum, organic liquids and aqueous solutions); measure surface energetics on a nanometer scale; determine pK values of the surface acid and base groups; measure forces to stretch and unbind a short synthetic DNA duplex and map the spatial distribution of specific functional groups and their ionization state. Studies of adhesion forces demonstrated the important contribution of hydrogen bonding to interactions between simple organic functionalities. The chemical identity of the tip and substrate surfaces as well as the medium had a dramatic effect on adhesion between model monolayers. A direct correlation between surface free energy and adhesion forces was established. The adhesion between epoxy polymer and model mixed SAMs varied with the amount of hydrogen bonding component in the monolayers. A consistent interpretation of CFM measurements in polar solvents was provided by contact mechanics models and intermolecular force components theory. Forces between tips and surfaces functionalized with SAMs terminating in acid or base groups depended on their ionization state. A novel method of force titration was introduced for highly local characterization of the pK's of surface functional groups. The pH-dependent changes in friction forces were exploited to map spatially the changes in ionization state on SAM surfaces. The phase contrast in tapping mode AFM between chemically distinct monolayer regions and corresponding adhesion forces were found to be directly correlated. Thus, both friction and intermittent contact CFM images could be interpreted in terms of the strength of intermolecular interactions. CFM was also used to probe biomolecular interactions. Separation forces between complementary oligonucleotide strands were significantly larger than the forces measured between noncomplementary strands and were consistent with the unbinding of a single DNA duplex. CFM data provided a direct measure of the forces required to elastically deform, structurally-transform and separate well-defined, synthetic duplexes into single strand oligonucleotides.

  14. Selective intermolecular amination of C-H bonds at tertiary carbon centers.

    PubMed

    Roizen, Jennifer L; Zalatan, David N; Du Bois, J

    2013-10-18

    C-H insertion: A method for intermolecular amination of tertiary C?H bonds is described that uses limiting amounts of substrate and a convenient phenol-derived nitrogen source. Structure-selectivity and mechanistic studies suggest that steric interaction between the substrate and active oxidant is the principal determinant of product selectivity. PMID:24000186

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

    PubMed

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

    2009-10-14

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

  16. Lipid intermolecular hydrogen bonding: influence on structural organization and membrane function.

    PubMed

    Boggs, J M

    1987-10-01

    The great variety of different lipids in membranes, with modifications to the hydrocarbon chains, polar groups and backbone structure suggests that many of these lipids may have unique roles in membrane structure and function. Acidic groups on lipids are clearly important, since they allow interaction with basic groups on proteins and with divalent cations. Another important property of certain lipids is their ability to interact intermolecularly with other lipids via hydrogen bonds. This interaction occurs through acidic and basic moieties in the polar head groups of phospholipids, and the amide moiety and hydroxyl groups on the acyl chain, sphingosine base and sugar groups of sphingo- and glycolipids. The putative ability of different classes of lipids to interact by intermolecular hydrogen bonding, the molecular groups which may participate and the effect of these interactions on some of their physical properties are summarized in Table IX. It is frequently questioned whether intermolecular hydrogen bonding could occur between lipids in the presence of water. Correlations of their properties with their molecular structures, however, suggest that it can. Participation in intermolecular hydrogen bonding increases the lipid phase transition temperature by approx. 8-16 Cdeg relative to the electrostatically shielded state and by 20-30 Cdeg relative to the repulsively charged state, while having variable effects on the enthalpy. It increases the packing density in monolayers, possibly also in the liquid-crystalline phase in bilayers, and decreases the lipid hydration. These effects can probably be accounted for by transient, fluctuating hydrogen bonds involving only a small percentage of the lipid at any one time. Thus, rotational and lateral diffusion of the lipids may take place but at a slower rate, and the lateral expansion is limited. Intermolecular hydrogen bonding between lipids in bilayers may be significantly stabilized, despite the presence of water, by the fact that the lipids are already intermolecularly associated as a result of the hydrophobic effect and the Van der Waals' interactions between their chains. The tendency of certain lipids to self-associate, their asymmetric distribution in SUVs, their preferential association with cholesterol in non-cocrystallizing mixtures, their temperature-induced transitions to the hexagonal phase and their inhibitory effect on penetration of hydrophobic residues of proteins partway into the bilayer can all be explained by their participation in intermolecular hydrogen bonding interactions.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3307919

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. An assay for intermolecular exchange of alpha crystallin

    NASA Technical Reports Server (NTRS)

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

    1992-01-01

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

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

    PubMed

    Madeira, Pedro P; Bessa, Ana; Loureiro, Joana A; lvares-Ribeiro, Lus; Rodrigues, Alrio E; Zaslavsky, Boris Y

    2015-08-21

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

  20. Maximizing Singlet Fission by Intermolecular Packing.

    PubMed

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

    2014-10-01

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

  1. Origin of the low-viscosity of [emim][(FSO2)2N] ionic liquid and its lithium salt mixture: experimental and theoretical study of self-diffusion coefficients, conductivities, and intermolecular interactions.

    PubMed

    Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro

    2010-12-16

    The temperature-dependent viscosity, ionic conductivity, and self-diffusion coefficients of an ionic liquid, 1-ethyl-3-methylimidazolium bis(fluorosulfonyl)amide ([emim][FSA]), and its Li salt mixture were studied with reference to emim bis(trifluoromethyl-sulfonyl)amide ([emim][TFSA]) systems. The stabilization energies for the formation of the FSA(-) complexes with emim(+) and Li(+) were calculated by the MP2/6-311G** level ab initio method. The stabilization energies calculated for the FSA(-) complexes with emim(+) and Li(+) (-77.0 and -134.3 kcal/mol) were smaller than those for the corresponding TFSA(-) complexes (-78.8 and -137.2 kcal/mol). The weaker electrostatic and induction interactions are the causes of the smaller interaction energies for the FSA(-) complexes. The weaker interaction between the FSA(-) and emim(+) can be one of the causes of the lower viscosity of the [emim][FSA] ionic liquid compared with that of the [emim][TFSA] ionic liquid. The weaker interaction between the FSA(-) and Li(+) compared with that between the TFSA(-) and Li(+) explains the fact that the addition of Li salt to the [emim][FSA] ionic liquid induces a little increase of the viscosity and a little decrease of the ionic conductivity and self-diffusion coefficients of ions. The FSA(-) in the Li[FSA] complex prefers the cis form due to the stronger attraction and smaller deformation energy of the cis-FSA(-) compared with the trans-FSA(-). PMID:21080680

  2. Some mathematical models of intermolecular autophosphorylation.

    PubMed

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

    2015-04-01

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

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

    SciTech Connect

    Muenter, J.S.

    1992-01-01

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

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

    PubMed

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

    2016-02-01

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

  5. Genome wide expression profiling and mutagenesis studies reveal that LPS responsiveness appears to be absolutely dependent on TLR4 and MD-2 expression and is dependent upon intermolecular ionic interactions

    PubMed Central

    Meng, Jianmin; Gong, Mei; Bjrkbacka, Harry; Golenbock, Douglas T.

    2011-01-01

    Lipid A (a hexaacylated 1,4 bis-phosphate) is a potent immune stimulant for TLR4/MD-2. Upon lipid A ligation, the TLR4/MD-2 complex dimerizes and initiates signal transduction. Historically, studies also suggested the existence of TLR4/MD-2-independent LPS signaling. Here we define the role of TLR4 and MD-2 in LPS signaling by using genome wide expression profiling in TLR4- and MD-2-deficient macrophages after stimulations with peptidoglycan-free LPS and synthetic E. coli lipid A. Of the 1,396 genes found significantly induced or repressed by any one of the treatments in the wildtype macrophages, none was present in the TLR4-or MD-2-deficient macrophages, confirming that the TLR4/MD-2 complex is the only receptor for endotoxin, and are both absolutely required for responses to LPS. Using a molecular genetics approach, we investigated the mechanism of TLR4/MD-2 activation by combining the known crystal structure of TLR4/MD-2 with computer modeling. The two phosphates on lipid A were predicted to interact extensively with the two positively charged patches on mouse TLR4 according to our murine TLR4/MD-2 activation model. When either positive patch was abolished by mutagenesis into Ala, the responses to LPS and lipid A were almost abrogated. However, the MyD88-dependent and independent pathways were impaired to the same extent, indicating that the adjuvant activity of monophosphorylated lipid A most likely arises from its decreased potential to induce an active receptor complex, and not more downstream signaling events. Hence, we conclude that ionic interactions between lipid A and TLR4 are essential for optimal LPS receptor activation. PMID:21865549

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

    PubMed

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

    2015-02-14

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

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

    PubMed

    Godlewska, P; Ja?czak, J; Kucharska, E; Hanuza, J; Lorenc, J; Michalski, J; Dymi?ska, L; W?gli?ski, Z

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

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

    PubMed

    Balraj, Chellamuthu; Elango, Kuppanagounder P

    2012-02-01

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

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

    PubMed Central

    Jarvis, Samuel Paul

    2015-01-01

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

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

    SciTech Connect

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

    2015-02-14

    We clarify the role of the critical imidazolium C{sub (2)}H position (the central C between N atoms in the heterocycle) in the assembly motif of the [EMIM][BF{sub 4}] ionic liquid by analyzing the vibrational spectra of the bare EMIM{sup +} ion as well as that of the cationic [EMIM]{sub 2}[BF{sub 4}]{sup +} (EMIM{sup +} = 1-ethyl-3-methylimidazolium, C{sub 6}H{sub 11}N{sub 2}{sup +}) cluster. Vibrational spectra of the cold, mass-selected ions are obtained using cryogenic ion vibrational predissociation of weakly bound D{sub 2} molecules formed in a 10 K ion trap. The C{sub (2)}H behavior is isolated by following the evolution of key vibrational features when the C{sub (2)} hydrogen, the proposed binding location of the anion to the imidazolium ring, is replaced by either deuterium or a methyl group (i.e., in the EMMIM{sup +} analogue). Strong features in the ring CH stretching region of the bare ion are traced to Fermi resonances with overtones of lower frequency modes. Upon incorporation into the EMIM{sup +} ? ? ? BF{sub 4}{sup ?} ? ? ? EMIM{sup +} ternary complex, the C{sub (2)}H oscillator strength is dramatically increased, accounting for the much more complicated patterns derived from the EMIM{sup +} ring CH stretches in the light isotopomer, which are strongly suppressed in the deuterated analogue. Further changes in the spectra that occur when the C{sub (2)}H is replaced by a methyl group are consistent with BF{sub 4}{sup ?} attachment directly to the imidazolium ring in an arrangement that maximizes the electrostatic interaction between the molecular ions.

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

    SciTech Connect

    Ghazzali, Mohamed Langer, Vratislav; Ohrstroem, Lars

    2008-09-15

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

  13. Hyper-chaotic Magnetisation Dynamics of Two Interacting Dipoles

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. Photon-mediated interaction between two distant atoms

    NASA Astrophysics Data System (ADS)

    Rist, Stefan; Eschner, Jrgen; Hennrich, Markus; Morigi, Giovanna

    2008-07-01

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

  15. Strongly interacting photons in hollow-core waveguides

    SciTech Connect

    Shahmoon, Ephraim; Kurizki, Gershon; Fleischhauer, Michael; Petrosyan, David

    2011-03-15

    Hollow-core photonic-crystal waveguides filled with cold atoms can support giant optical nonlinearities through nondispersive propagation of light tightly confined in the transverse direction. Here we explore electromagnetically induced transparency is such structures, considering a pair of counterpropagating weak quantum fields in the medium of coherently driven atoms in the ladder configuration. Strong dipole-dipole interactions between optically excited, polarized Rydberg states of the atoms translate into a large dispersive interaction between the two fields. This can be used to attain a spatially homogeneous conditional phase shift of {pi} for two single-photon pulses, realizing a deterministic photonic phase gate, or to implement a quantum nondemolition measurement of the photon number in the signal pulse by a coherent probe, thereby achieving a heralded source of single- or few-photon pulses.

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    SciTech Connect

    Salam, A.

    2013-12-28

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

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

    PubMed

    Salam, A

    2013-12-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

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

    SciTech Connect

    Venkattraman, Ayyaswamy

    2014-12-09

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

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

    NASA Astrophysics Data System (ADS)

    Venkattraman, Ayyaswamy

    2014-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  4. Mechanism of Intermolecular Electron Transfer in Bionanostructures

    NASA Astrophysics Data System (ADS)

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

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

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

    SciTech Connect

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

    2002-01-01

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

  6. Rh-Catalyzed Intermolecular Reactions of ?-Alkyl-?-Diazo Carbonyl Compounds with Selectivity over ?-Hydride Migration.

    PubMed

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

    2016-01-19

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

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

    SciTech Connect

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

    2008-11-13

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

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

    NASA Astrophysics Data System (ADS)

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

    1998-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Aquilanti, Vincenzo

    2005-05-01

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

  11. Phosphorescence quenching of fac-tris(2-phenylpyridyl)iridium(iii) complexes in thin films on dielectric surfaces.

    PubMed

    Ribierre, J C; Ruseckas, A; Staton, S V; Knights, K; Cumpstey, N; Burn, P L; Samuel, I D W

    2016-02-01

    We study the influence of the film thickness on the time-resolved phosphorescence and the luminescence quantum yield of fac-tris(2-phenylpyridyl)iridium(iii) [Ir(ppy)3]-cored dendrimers deposited on dielectric substrates. A correlation is observed between the surface quenching velocity and the quenching rate by intermolecular interactions in the bulk film, which suggests that both processes are controlled by dipole-dipole interactions between Ir(ppy)3 complexes at the core of the dendrimers. It is also found that the surface quenching velocity decreases as the refractive index of the substrate is increased. This can be explained by partial screening of dipole-dipole interactions by the dielectric environment. PMID:26750542

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

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

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

  13. Induced delocalization by correlation and interaction in the one-dimensional Anderson model

    NASA Astrophysics Data System (ADS)

    Albrecht, Conrad; Wimberger, Sandro

    2012-01-01

    We consider long-range correlated disorder and mutual interacting particles according to a dipole-dipole coupling as modifications to the one-dimensional Anderson model. Technically, we rely on the numerical exact diagonalization of the system's Hamilitonian. From the perspective of different localization measures, we confirm and extend the picture of the emergence of delocalized states with increasing correlations. Besides these studies, a definition for multiparticle localization is proposed. In the case of two interacting bosons, we observe a sensitivity of localization with respect to the range of the particle-particle interaction and insensitivity to the coupling's sign, which should stimulate new theoretical approaches and experimental investigations with, e.g., dipolar cold quantum gases.

  14. 1H NMR Relaxation Investigation of Inhibitors Interacting with Torpedo californica Acetylcholinesterase

    NASA Astrophysics Data System (ADS)

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

    2000-05-01

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

  15. Role of Silver Ions in Destabilization of Intermolecular Adhesion Forces Measured by Atomic Force Microscopy in Staphylococcus epidermidis Biofilms

    PubMed Central

    Chaw, K. C.; Manimaran, M.; Tay, Francis E. H.

    2005-01-01

    In this paper, we report on the potential use of atomic force microscopy (AFM) as a tool to measure the intermolecular forces in biofilm structures and to study the effect of silver ions on sessile Staphylococcus epidermidis cell viability and stability. We propose a strategy of destabilizing the biofilm matrix by reducing the intermolecular forces within the extracellular polymeric substances (EPSs) using a low concentration (50 ppb) of silver ions. Our AFM studies on the intermolecular forces within the EPSs of S. epidermidis RP62A and S.epidermidis 1457 biofilms suggest that the silver ions can destabilize the biofilm matrix by binding to electron donor groups of the biological molecules. This leads to reductions in the number of binding sites for hydrogen bonds and electrostatic and hydrophobic interactions and, hence, the destabilization of the biofilm structure. PMID:16304145

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Qiu, Xiaohui

    2014-03-01

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

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

    PubMed

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

    2010-09-01

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

  19. Effect of intermolecular potential on compressible Couette flow in slip and transitional regimes

    NASA Astrophysics Data System (ADS)

    Weaver, Andrew B.; Venkattraman, A.; Alexeenko, Alina A.

    2014-10-01

    The effect of intermolecular potentials on compressible, planar flow in slip and transitional regimes is investigated using the direct simulation Monte Carlo method. Two intermolecular interaction models, the variable hard sphere (VHS) and the Lennard-Jones (LJ) models, are first compared for subsonic and supersonic Couette flows of argon at temperatures of 40, 273, and 1,000 K, and then for Couette flows in the transitional regime ranging from Knudsen numbers (Kn) of 0.0051 to 1. The binary scattering model for elastic scattering using the Lennard-Jones (LJ) intermolecular potential proposed recently [A. Venkattraman and A. Alexeenko, "Binary scattering model for Lennard-Jones potential: Transport coefficients and collision integrals for non-equilibrium gas flow simulations," Phys. Fluids 24, 027101 (2012)] is shown to accurately reproduce both the theoretical collision frequency in an equilibrium gas as well as the theoretical viscosity variation with temperature. The use of a repulsive-attractive instead of a purely repulsive potential is found to be most important in the continuum and slip regimes as well as in flows with large temperature variations. Differences in shear stress of up to 28% between the VHS and LJ models is observed at Kn=0.0051 and is attributed to differences in collision frequencies, ultimately affecting velocity gradients at the wall. For Kn=1 where the Knudsen layer expands the entire domain, the effect of the larger collision frequency in the LJ model relative to VHS diminishes, and a 7% difference in shear stress is observed.

  20. The novel behaviour of interactions between Ni2+ ion and human or bovine serum albumin.

    PubMed Central

    Zhou, Y; Hu, X; Ouyang, D; Huang, J; Wang, Y

    1994-01-01

    We discovered a series of novel behaviours of interactions between Ni2+ ion and human or bovine serum albumin. Our results indicated that there exist two closely neighbouring identical prior binding sites in the binding of human or bovine serum albumin with Ni2+ ions, not only one. It is very likely that, after the binding of the first Ni2+ ion, an induced slow conformational transition happens, which leads to the binding of the second Ni2+ ion and shows itself as a hysteretic effect for a process of non-enzymic protein binding with metal ions. As the concentrations of the 1:1 (molar ratio of Ni2+ ion to protein) system increase, an increasing hypochromic effect is observed. Such a hypochromic effect has not been reported previously; however, it is in accord with the mechanism of dipole-dipole interactions between the electric dipole transition moments of chromophores. PMID:7998938

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

    PubMed

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

    2012-08-01

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

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

    PubMed

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

    2013-12-13

    We report measurements of discrete excitation-induced frequency shifts on the 7F0?5D0 transition of the Eu+ center in La:Lu:EuCl36D2O resulting from the optical excitation of neighboring Eu3+ ions. Shifts of up to 46.0810.005??MHz were observed. The magnitude of the interaction between neighboring ions was found to be significantly larger than expected from the electric dipole-dipole mechanism often observed in rare earth systems. We show that a large network of interacting and individually addressable centers can be created by lightly doping crystals otherwise stoichiometric in the optically active rare earth ion, and that this network could be used to implement a quantum processor with more than ten qubits. PMID:24483634

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

    SciTech Connect

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

    1994-12-01

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

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

    PubMed

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-21

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

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

    NASA Astrophysics Data System (ADS)

    Ito, Hironobu; Tanimura, Yoshitaka

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Heßelmann, Andreas; Korona, Tatiana

    2014-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1994-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Lebedev, A. V.

    2015-01-01

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

  10. Chiral Brnsted acid catalyzed enantioselective intermolecular allylic aminations.

    PubMed

    Zhuang, Minyang; Du, Haifeng

    2014-07-14

    This paper describes an enantioselective intermolecular allylic amination catalyzed by a chiral Brnsted acid via a possible chiral contact ion pair intermediate. A variety of symmetrical or unsymmetrical allylic alcohols can be smoothly aminated to afford the desired products in moderate to high yields with good enantioselectivities and/or regioselectivities. PMID:24872122

  11. Dancing Crystals: A Dramatic Illustration of Intermolecular Forces

    ERIC Educational Resources Information Center

    Mundell, Donald W.

    2007-01-01

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

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

    PubMed

    Collins, Karl D; Glorius, Frank

    2015-03-17

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

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

    SciTech Connect

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

    2006-02-15

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

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

    PubMed

    Ogawa, Kazuyoshi

    2015-12-01

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

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

    PubMed Central

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

    2014-01-01

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

  16. Spatio-spectral infrared vibrational nano-imaging of intermolecular coupling

    NASA Astrophysics Data System (ADS)

    Pollard, Benjamin; Muller, Eric; Raschke, Markus

    2014-03-01

    Molecular self-assembly, the function of biomembranes, and the performance of organic solar cells rely on molecular interactions on the nanoscale. The understanding and design of such heterogeneous functional soft matter has long been impeded by a lack of spectroscopic tools with sufficient nanometer spatial resolution, attomolar sensitivity, and intermolecular spectroscopic specificity. We implement vibrational scattering-scanning near-field optical microscopy (s-SNOM) in a multi-spectral modality to investigate the structure-function relationship in PS- b-PMMA block copolymers. Using a vibrational resonance as a sensitive reporter of local structure, coupling, and dynamics, we resolve spectral Stark shifts and line broadening correlated with molecular-scale morphologies. By creating images of solvatochromic vibrational shifts we discriminate local variations in electric fields between nanoscale bulk and interface regions, with quantitative agreement to dielectric continuum models. This new nano-chemometric ability to directly resolve nanoscale morphology and associated intermolecular interactions can form a basis for the systematic control of functionality in multicomponent soft matter systems.

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

    SciTech Connect

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

    2014-09-01

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

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

    PubMed

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

    2014-09-01

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

  19. A polarizable water model for intramolecular and intermolecular vibrational spectroscopies.

    PubMed

    Hasegawa, Taisuke; Tanimura, Yoshitaka

    2011-05-12

    We have developed a polarizable water model for classical molecular dynamics simulations of vibrational spectroscopies, which covers from low-frequency intermolecular modes to high-frequency intramolecular vibrational modes. The model utilizes the ab initio derived geometry-dependent multipole moment surfaces to depict the instantaneous charge density of a water molecule. Multipoles up to quadrupole are included for the permanent multipoles, while those up to dipole are included for the induced multipoles. The polarization of molecules is described by a distributed polarizability model. At room temperature, the present model is able to reproduce experimental infrared and Raman spectra of intramolecular vibrational modes, except for the blue peak shift due to a limitation of the classical simulation based on a quantum mechanical potential. The calculated infrared spectrum for low-frequency intermolecular modes agreed reasonably well with the experimental signals. PMID:21486049

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

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

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

    PubMed

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

    2015-11-13

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

  2. An intermolecular heterobimetallic system for photocatalytic water reduction.

    PubMed

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

    2012-04-01

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

  3. Calculations of helical twisting powers from intermolecular torques

    NASA Astrophysics Data System (ADS)

    Earl, David J.; Wilson, Mark R.

    2004-05-01

    We present a Monte Carlo molecular simulation method that calculates the helical twisting power of a chiral molecule by sampling intermolecular torques. The approach is applied to an achiral nematic liquid crystalline system, composed of Gay-Berne particles, that is doped with chiral molecules. Calculations are presented for six chiral dopant molecules and the results show a good correlation with the sign and magnitude of experimentally determined helical twisting powers.

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

    PubMed

    Glock, Carsten; Grls, Helmar; Westerhausen, Matthias

    2012-07-18

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

  5. Dielectric spectroscopy investigation of ion-containing and intermolecular hydrogen-bonded polymer systems

    NASA Astrophysics Data System (ADS)

    Atorngitjawat, Pornpen

    Ion-containing and intermolecular hydrogen-bonded polymers are used widely in a variety of industrial and commercial applications, from food packaging to battery electrolytes to pharmaceuticals. Yet the dynamics of these polymers, which are both complex and important to the application, are poorly understood. This thesis provides the first systematic study of the dynamics of several ion-containing and intermolecular hydrogen-bonded polymers by broadband dielectric relaxation spectroscopy. The systems under consideration include sulfonated polystyrene (SPS) in acid (SPS-H) and neutralized forms, and mixtures of poly(2-vinylpyridine) (P2VPy) with lithium perchlorate (LiClO4) and low molecular weight phenolic molecules. Dynamic mechanical analysis, Fourier transform infrared spectroscopy, differential scanning calorimetry, small-angle X-ray scattering and wide-angle X-ray diffraction were employed in a complementary role. Multiple relaxations were generally observed at high temperatures. For SPS ionomers, the segmental process, Maxwell-Wagner-Sillars interfacial polarization, and electrode polarization were detected. Three relaxations were also found in spectra of SPS-H, attributed to the segmental process, hydrogen bond association/dissociation, and electrode polarization. Three dielectric relaxations above the segmental process were observed for P2VPy-LiClO4 mixtures: ion-mode relaxation, slow hindered segmental relaxation and electrode polarization. However, only electrode polarization was observed above the segmental relaxation for all P2VPy--small phenolic molecule mixtures, except P2VPy + 10 mol% 2,3,3,4,4,5-hexahydroxybenzophenone. This mixture exhibited an additional relaxation due to Maxwell-Wagner-Sillars interfacial polarization, arising from the existence of phase-separated complexes within the P2VPy matrix. Sub-Tg local relaxations were suppressed by ionic intermolecular interactions for SPS ionomers and P2VPy-LiClO4 mixtures. Intermolecular hydrogen bonding also suppressed the local relaxation in P2VPy-small phenolic molecule mixtures by decreasing the mobility of the pyridine-side groups. Both the concentration of small phenolic molecules and the number of hydroxyl groups per molecule played an important role in suppression of the local relaxation, which was significant for all mixtures where the small molecules contained more than one hydroxyl group per molecule.

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

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

    PubMed

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

    2013-03-14

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

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

    PubMed

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

    2007-07-01

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

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

    PubMed

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

    2014-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-07-01

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

  13. Strong orbital interaction in a weak CH-? hydrogen bonding system.

    PubMed

    Li, Jianfu; Zhang, Rui-Qin

    2016-01-01

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

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

    PubMed

    Ji, Yining; Riera, Antoni; Verdaguer, Xavier

    2009-10-01

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

  15. Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif.

    PubMed

    Thevarpadam, Julie; Bessi, Irene; Binas, Oliver; Gonalves, Diana P N; Slavov, Chavdar; Jonker, Hendrik R A; Richter, Christian; Wachtveitl, Josef; Schwalbe, Harald; Heckel, Alexander

    2016-02-01

    The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+) ?ions at room temperature in all three cases with the corresponding azobenzene linker in an E?conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z?isomerization. PMID:26805928

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

    PubMed

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

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Li, Jun; Guo, Hua

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2002-04-01

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

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

    PubMed

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

    2004-06-01

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

  1. Pom1 gradient buffering through intermolecular auto-phosphorylation

    PubMed Central

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

    2015-01-01

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

  2. Pom1 gradient buffering through intermolecular auto-phosphorylation.

    PubMed

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

    2015-07-01

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

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

    SciTech Connect

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

    2013-11-21

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

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

    SciTech Connect

    Minami, Takuya; Nakano, Masayoshi

    2015-01-22

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

  5. Nonlinear dynamics of globular proteins

    SciTech Connect

    Lomdahl, P.S.

    1983-01-01

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

  6. Intermolecular dynamics in liquids studied by a third order nonlinear spectroscopy

    NASA Astrophysics Data System (ADS)

    Shirota, Hideaki

    2015-01-01

    Intermolecular dynamics, particularly intermolecular vibrational dynamics, in simple aprotic molecular liquids including both nonaromatic and aromatic molecular liquids measured using femtosecond Raman-induced Kerr effect spectroscopy is discussed. A correlation between the first moment of the intermolecular vibrational band and the value of the static physical properties, the square root of surface tension divided by liquid density, is shown. The data of the aprotic molecular liquids are also compared to that of room temperature ionic liquids.

  7. Average and extreme multi-atom Van der Waals interactions: Strong coupling of multi-atom Van der Waals interactions with covalent bonding

    PubMed Central

    Finkelstein, Alexei V

    2007-01-01

    Background The prediction of ligand binding or protein structure requires very accurate force field potentials even small errors in force field potentials can make a 'wrong' structure (from the billions possible) more stable than the single, 'correct' one. However, despite huge efforts to optimize them, currently-used all-atom force fields are still not able, in a vast majority of cases, even to keep a protein molecule in its native conformation in the course of molecular dynamics simulations or to bring an approximate, homology-based model of protein structure closer to its native conformation. Results A strict analysis shows that a specific coupling of multi-atom Van der Waals interactions with covalent bonding can, in extreme cases, increase (or decrease) the interaction energy by about 2040% at certain angles between the direction of interaction and the covalent bond. It is also shown that on average multi-body effects decrease the total Van der Waals energy in proportion to the square root of the electronic component of dielectric permittivity corresponding to dipole-dipole interactions at small distances, where Van der Waals interactions take place. Conclusion The study shows that currently-ignored multi-atom Van der Waals interactions can, in certain instances, lead to significant energy effects, comparable to those caused by the replacement of atoms (for instance, C by N) in conventional pairwise Van der Waals interactions. PMID:17880673

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

    PubMed

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

    2011-06-15

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

  9. Intermolecular complexes of singly linked bisporphyrins with trinitrobenzene

    NASA Astrophysics Data System (ADS)

    Jeyakumar, D.; Krishnan, V.

    1992-12-01

    Several covalently linked bisporphyrin systems, free-base (H 2P---H 2P), hybrid bisporphyrins (Zn---H 2P) and Zn(II) dimers (ZnP---ZnP) and their 1:1 molecular complexes with sym 1,3,5-trinitrobenzene have been investigated by optical absorption and emission, and magnetic resonance spectroscopic methods. In these systems, two porphyrin units are linked singly through one of the meso aryl groups via ether linkages of variable length. The bisporphyrins cooperatively bind a molecule of a ?-acceptor; 1,3,5-trinitrobenzene (TNB). The binding constant values vary with interchromophore separation. Maximum binding is observed in the bisporphyrin bearing a two-ether covalent linkage. It is found that TNB quenches the fluorescence of the two porphyrine units in a selective manner. It is suggested that a critical distance between the two porphyrin units is necessary for the observance of maximum cooperative intermolecular binding with an acceptor.

  10. Intermolecular vibrations and fast relaxations in supercooled ionic liquids

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.

    2011-06-01

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

  11. Dispersive light-matter interaction in programmable optical tweezers

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

  12. Supramolecular interactions in the solid state

    PubMed Central

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

    2015-01-01

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

  13. Supramolecular interactions in the solid state.

    PubMed

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

    2015-11-01

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

  14. Ground state analytical ab initio intermolecular potential for the Cl2-water system

    NASA Astrophysics Data System (ADS)

    Hormain, Laureline; Monnerville, Maurice; Toubin, Cline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stphane; Bernal-Uruchurtu, Margarita I.; Hernndez-Lamoneda, Ramn

    2015-04-01

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl2 molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl2 - H2O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl2 interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl2 on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

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

    SciTech Connect

    Hormain, Laureline; Monnerville, Maurice Toubin, Cline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stphane; Bernal-Uruchurtu, Margarita I.; Hernndez-Lamoneda, Ramn

    2015-04-14

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

    The origin and strength of intra- and inter-molecular vibrational coupling is difficult to probe by direct experimental observations. However, explicitly including or not including some specific intramolecular vibrational modes to study intermolecular interaction provides a precise theoretical way to examine the effects of anharmonic coupling between modes. In this work, a full-dimension intra- and inter-molecular ab initio potential energy surface (PES) for H2O-Ar, which explicitly incorporates interdependence on the intramolecular (Q1, ?Q2, ?Q3) normal-mode coordinates of the H2O monomer, has been calculated. In addition, four analytic vibrational-quantum-state-specific PESs are obtained by least-squares fitting vibrationally averaged interaction energies for the (v1, ?v2, ?v3) = ?(0, ?0, ?0), (0, ?0, ?1), (1, ?0, ?0), (0, ?1, ?0) states of H2O to the three-dimensional Morse/long-range potential function. Each vibrationally averaged PES fitted to 442 points has root-mean-square (rms) deviation smaller than 0.15 cm(-1), and required only 58 parameters. With the 3D PESs of H2O-Ar dimer system, we employed the combined radial discrete variable representation/angular finite basis representation method and Lanczos algorithm to calculate rovibrational energy levels. This showed that the resulting vibrationally averaged PESs provide good representations of the experimental infrared data, with rms discrepancies smaller than 0.02 cm(-1) for all three rotational branches of the asymmetric stretch fundamental transitions. The infrared band origin shifts associated with three fundamental bands of H2O in H2O-Ar complex are predicted for the first time and are found to be in good agreement with the (extrapolated) experimental values. Upon introduction of additional intramolecular degrees of freedom into the intermolecular potential energy surface, there is clear spectroscopic evidence of intra- and intermolecular vibrational couplings. PMID:26747800

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

    PubMed

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

    2007-01-01

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

  19. Direct Probing of the Local Solvent Response During Intermolecular Electron Transfer

    NASA Astrophysics Data System (ADS)

    Underwood, David F.; Blank, David A.

    Following resonant photo-excitation of coumarin 152 in the electron donating solvents aniline and dimethylaniline, dramatic changes the local intermolecular solvent response are monitored directly as a function of time during intermolecular electron transfer using third-order non-resonant Raman spectroscopy.

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

    Stiegler, Thomas; Sadus, Richard J.

    2015-02-28

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

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

    NASA Astrophysics Data System (ADS)

    Stiegler, Thomas; Sadus, Richard J.

    2015-02-01

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

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

    PubMed

    Stiegler, Thomas; Sadus, Richard J

    2015-02-28

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

  4. Protein-Protein Interactions during Bacterial Chemotaxis using Methyl TROSY Nuclear Magnetic Resonance.

    NASA Astrophysics Data System (ADS)

    Hamel, Damon; Dahlquist, Frederick

    2006-03-01

    During bacterial chemotaxis, the histidine autokinase CheA interacts with the chemotaxis receptors with the help of the coupling protein CheW. The CheA-CheW interaction is typical of many macromolecular complexes where protein-protein interactions play an important role. In this case a relatively small protein, CheW (18 kDalton), becomes part of a much larger complex. Here we describe a new method to map the residues at a protein-protein interface for macromolecular complexes of molecular weight greater than 100 kDalton. The method exploits the C13 methyl TROSY methodology developed in Lewis Kay's laboratory. The essence of the Kay approach is that a portion of the intensity of HMQC spectra of individual -(13)CH3 resonances in an otherwise deuterated macromolecule have much reduced dipole-dipole relaxation and remain sharp and relatively easy to detect , even in macromolecules of molecular mass 100 kD or greater. The reduction in dipolar interactions is lost if a given methyl group comes in close contact with other protons such as those supplied by the interface of a protonated interaction partner. Comparing the -(13)CH3 resonances of a protein of interest in the presence of a protonated versus deuterated interaction partner allows the methyls at the interface can be identified. The application of the approach for establishing points of contact between CheA and CheW will be discussed.

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

    SciTech Connect

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

    2015-03-01

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

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

    PubMed

    Zsila, Ferenc

    2015-09-01

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

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

    PubMed Central

    Wong, Jaslyn E. M. M.; Midtgaard, Sren Roi; Gysel, Kira; Thygesen, Mikkel B.; Srensen, Kasper K.; Jensen, Knud J.; Stougaard, Jens; Thirup, Sren; Blaise, Mickal

    2015-01-01

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

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

    PubMed

    Wong, Jaslyn E M M; Midtgaard, Sren Roi; Gysel, Kira; Thygesen, Mikkel B; Srensen, Kasper K; Jensen, Knud J; Stougaard, Jens; Thirup, Sren; Blaise, Mickal

    2015-03-01

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

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

    SciTech Connect

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

    2010-12-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  11. Magnetophotoluminescence line-shape narrowing through interactions between excited states in organic semiconducting materials

    NASA Astrophysics Data System (ADS)

    He, Lei; Li, Mingxing; Urbas, Augustine; Hu, Bin

    2014-04-01

    We find that interactions between intermolecular excited states can cause a line-shape narrowing in magnetophotoluminescence in an organic composite containing N,N-dimethylaniline and pyrene in the liquid state. The line-shape narrowing indicates that interactions between intermolecular excited states can decrease the spin-exchange interaction within intermolecular excited states. Our analysis shows that interactions between intermolecular excited states can occur through long-range Coulomb interaction, midrange spin-orbital interaction, and short-range spin interaction, with the consequence of line-shape modification in the development of magnetic field effects. Our experimental results reveal a parameter, the interactions between intermolecular excited states, involved in the development of magnetic field effects in organic semiconducting materials.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    PubMed

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

    2016-01-01

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

  14. Determination of stepsize parameters for intermolecular vibrational energy transfer

    SciTech Connect

    Tardy, D.C.

    1992-03-01

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

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

    PubMed

    Tiwari, Shraeddha; Kumar, Anil

    2012-02-01

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

  16. Thermal selectivity of intermolecular versus intramolecular reactions on surfaces

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Suponitsky, Kyrill Yu; Masunov, Artëm E.

    2013-09-01

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

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

    PubMed

    Suponitsky, Kyrill Yu; Masunov, Artm E

    2013-09-01

    Theoretical estimation of nonlinear optical (NLO) properties is an important step in systematic search for optoelectronic materials. Density functional theory methods are often used to predict first molecular hyperpolarizability for compounds in advance of their synthesis. However, design of molecular NLO materials require an estimation of the bulk properties, which are often approximated as additive superposition of molecular tensors. It is therefore important to evaluate the accuracy of this additive approximation and estimate the extent by which intermolecular interactions influence the first molecular hyperpolarizability ?. Here we focused on the stacking aggregates, including up to 12 model molecules (pNA and ANS) and observed enhancement and suppression of molecular hyperpolarizability relative to the additive sum. We found that degree of nonadditivity depends on relative orientation of the molecular dipole moments and does not correlate with intermolecular interaction energy. Frenkel exciton model, based on dipole-dipole approximation can be used for qualitative prediction of intermolecular effects. We report on inaccuracy of this model for the molecules with long ?-systems that are significantly shifted relative to each other, when dipole-dipole approximation becomes inaccurate. To obtain more detailed information on the effect of intermolecular interactions on ? we proposed electrostatic approach which accounts for the mutual polarization of the molecules by each other. We measure the induced polarization of each molecule in the aggregate by the charge of its donor (or acceptor) group. The proposed approach demonstrates linear correlation ?(FF) vs ?(elm) (estimated by finite field theory and electrostatic model, respectively) and allows decomposition of the hyperpolarizability for a molecular aggregate into separate molecular contributions. We used this decomposition to analyze the reasons of deviation of aggregate ? from additivity, as well as the cooperative effect of intermolecular interactions on hyperpolarizability for stacks of growing size. In cases of positive cooperativity (enhancement), we found 6-8 molecules to be necessary to reach the asymptotic limit. In more frequent cases of negative cooperativity two opposite factors play role. The first one consists of direct lowering of ? due to repulsive dipole-dipole interactions. The second factor is originated in a decrease of molecular dipole moments, which in turn leads to a decrease of dipole-dipole repulsion, and therefore increases ?. For strong intermolecular repulsive dipole-dipole interactions these effects nearly cancel each other. In such cases the trimers and even dimers are sufficient to reach the asymptotic limit of the infinite stacks. Based on the observed trends we estimated non-additive correction to ? for well known NLO crystals NPAN and MNMA. In the case of NPAN, stacking effect on molecular hyperpolarizability represents the leading component of the crystal packing effect and improves the agreement between calculated and experimental data which is further improved when frequency dependence is taken in account. PMID:24028120

  19. Estrogen receptor alpha/co-activator interaction assay: TR-FRET.

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-02-01

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

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

    PubMed

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

    2015-09-01

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

  2. Structure and intermolecular vibrations of perylenetrans-1,2-dichloroethene, a weak charge-transfer complex.

    PubMed

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

    2013-10-17

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

  3. Determining the Intermolecular Potential Energy in a Gas: A Physical Chemistry Experiment

    ERIC Educational Resources Information Center

    Olbregts, J.; Walgraeve, J. P.

    1976-01-01

    Describes an experiment in which gas viscosity coefficients over a large temperature range are used to determine the parameters of the intermolecular potential energy and other properties such as virial coefficients. (MLH)

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

    SciTech Connect

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

    1995-06-01

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

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

    PubMed

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

    2014-10-28

    Structural bioinformatics and van der Waals density functional theory are combined to investigate the mechanochemical impact of a major class of histone-DNA interactions, namely, the formation of salt bridges between arginine residues in histones and phosphate groups on the DNA backbone. Principal component analysis reveals that the configurational fluctuations of the sugar-phosphate backbone display sequence-specific directionality and variability, and clustering of nucleosome crystal structures identifies two major salt-bridge configurations: a monodentate form in which the arginine end-group guanidinium only forms one hydrogen bond with the phosphate, and a bidentate form in which it forms two. Density functional theory calculations highlight that the combination of sequence, denticity, and salt-bridge positioning enables the histones to apply a tunable mechanochemical stress to the DNA via precise and specific activation of backbone deformations. The results suggest that selection for specific placements of van der Waals contacts, with high-precision control of the spatial distribution of intermolecular forces, may serve as an underlying evolutionary design principle for the structure and function of nucleosomes, a conjecture that is corroborated by previous experimental studies. PMID:25362343

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

    NASA Astrophysics Data System (ADS)

    Shvab, I.; Sadus, Richard J.

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  9. Structure and polarization properties of water: molecular dynamics with a nonadditive intermolecular potential.

    PubMed

    Shvab, I; Sadus, Richard J

    2012-05-01

    The temperature and density dependence of the structure and polarization properties of bulk water were systematically investigated using the ab initio MCYna potential [Li et al., J. Chem. Phys. 127, 154509 (2007)], which includes nonadditive contributions to intermolecular interactions. Molecular dynamics simulations were conducted for isochores of 1, 0.8, and 0.6 g/cm^{3} and temperatures from 278 to 750 K. Special attention was paid to the structural change of water in the range from the normal boiling point to supercritical temperatures. At temperatures below the normal boiling temperature, water exhibits a tetrahedral structure along the 0.8 and 0.6 g/cm^{3} isochores. A significant collapse of the hydrogen bonding network was observed at temperatures of 450, 550, and 650 K. The MCYna potential was able to successfully reproduce the experimental dielectric constant. The dielectric constant and average dipole moments decrease with increasing temperature and decreasing density due to weakened polarization. A comparison is also made with SPC-based models. PMID:23004769

  10. Intermolecular vibrations of fluorobenzene-Ar up to 130 cm(-1) in the ground electronic state.

    PubMed

    Gascooke, Jason R; Alexander, Ula N; Lawrance, Warren D

    2012-08-28

    Sixteen intermolecular vibrational levels of the S(0) state of the fluorobenzene-Ar van der Waals complex have been observed using dispersed fluorescence. The levels range up to ~130 cm(-1) in vibrational energy. The vibrational energies have been modelled using a complete set of harmonic and quartic anharmonic constants and a cubic anharmonic coupling between the stretch and long axis bend overtone that becomes near ubiquitous at higher energies. The constants predict the observed band positions with a root mean square deviation of 0.04 cm(-1). The set of vibrational levels predicted by the constants, which includes unobserved bands, has been compared with the predictions of ab initio calculations, which include all vibrational levels up to 70-75 cm(-1). There are small differences in energy, particularly above 60 cm(-1), however, the main differences are in the assignments and are largely due to the limitations of assigning the ab initio wavefunctions to a simple stretch, bend, or combination when the states are mixed by the cubic anharmonic coupling. The availability of these experimental data presents an opportunity to extend ab initio calculations to higher vibrational energies to provide an assessment of the accuracy of the calculated potential surface away from the minimum. The intermolecular modes of the fluorobenzene-Ar(2) trimer complex have also been investigated by dispersed fluorescence. The dominant structure is a pair of bands with a ~35 cm(-1) displacement from the origin band. Based on the set of vibrational modes calculated from the fluorobenzene-Ar frequencies, they are assigned to a Fermi resonance between the symmetric stretch and symmetric short axis bend overtone. The analysis of this resonance provides a measurement of the coupling strength between the stretch and short axis bend overtone in the dimer, an interaction that is not directly observed. The coupling matrix elements determined for the fluorobenzene-Ar stretch-long axis bend overtone and stretch-short axis bend overtone couplings are remarkably similar (3.8 cm(-1) cf. 3.2 cm(-1)). Several weak features seen in the fluorobenzene-Ar(2) spectrum have also been assigned. PMID:22938231

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

    PubMed Central

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

    2005-01-01

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

  12. Intermolecular spin relaxation and translation diffusion in liquids and polymer melts: insight from field-cycling 1H NMR relaxometry.

    PubMed

    Meier, Roman; Kruk, Danuta; Rssler, Ernst A

    2013-09-16

    With the advent of commercial field-cycling (FC) spectrometers, NMR relaxometry has gained new momentum as a method of investigating dynamics in liquids and polymers. The outcome of FC NMR experiments is spin-lattice relaxation time versus frequency (relaxation dispersion). In the case of protons, due to the intra- and intermolecular origin of dipolar interactions, the relaxation dispersion reflects rotational as well as translational dynamics. The latter shows a universal dispersion law at low frequencies, which allows determination of the diffusion coefficient D(T) in addition to the rotational correlation time ?(rot)(T), that is, FC (1)H NMR becomes an alternative to field-gradient NMR spectroscopy. Subdiffusive translation found in polymers can be accessed by singling out the intermolecular relaxation through isotope dilution experiments, and the mean square displacement can then be revealed as a function of time, thus complementing neutron scattering experiments. Likewise, information on reorientational dynamics is provided by the intramolecular relaxation. Assuming frequency-temperature superposition the corresponding correlation functions can be monitored up to eight decades in amplitude and time, which allows thorough testing of current polymer theories. PMID:23881836

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

    SciTech Connect

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

    1996-02-29

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

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

    NASA Astrophysics Data System (ADS)

    Jahnke, T.

    2015-04-01

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

  15. Optimizing Noncovalent Interactions Between Lignin and Synthetic Polymers to Develop Effective Compatibilizers

    SciTech Connect

    Henry, Nathan; Harper, David; Dadmun, Mark D

    2012-01-01

    Experiments are designed and completed to identify an effective polymeric compatibilizer for lignin polystyrene blends. Copolymers of styrene and vinylphenol are chosen as the structure of the compatibilizer as the VPh unit can readily form intermolecular hydrogen bonds with the lignin molecule. Electron microscopy, thermal analysis, and neutron refl ectivity results demonstrate that among these compatibilizers, a copolymer of styrene and VPh with 20% 30% VPh most readily forms intermolecular interactions with the lignin molecule and results in the most well-dispersed blends with lignin. This behavior is explained by invoking the competition of intra- and intermolecular hydrogen bonding and functional group accessibility in forming intermolecular interactions.

  16. Anisotropy of the magnetoviscous effect in a cobalt ferrofluid with strong interparticle interaction

    NASA Astrophysics Data System (ADS)

    Linke, J. M.; Odenbach, S.

    2015-12-01

    The anisotropy of the magnetoviscous effect (MVE) of a cobalt ferrofluid has been studied in a slit die viscometer for three orientations of the applied magnetic field: in the direction of the fluid flow (??1), the velocity gradient (??2), and the vorticity (??3). The majority of the cobalt particles in the ferrofluid exhibit a strong dipole-dipole interaction, which corresponds to a weighted interaction parameter of ?w?10.6. Thus the particles form extended microstructures inside the fluid which lead to enhanced MVE ratios ??2/??1>3 and ??3/??1>0.3 even for strong shearing and weak magnetic fields compared to fluids which contain non-interacting spherical particles with ??2/??1?1 and ??3/??1=0. Furthermore, a non-monotonic increase has been observed in the shear thinning behavior of ??2 for weak magnetic fields <10 kA/m, which cannot be explained solely by the magnetization of individual particles and the formation and disintegration of linear particle chains but indicates the presence of heterophase structures.

  17. Interaction between colloidal particles on an oil-water interface in dilute and dense phases.

    PubMed

    Parolini, Lucia; Law, Adam D; Maestro, Armando; Buzza, D Martin A; Cicuta, Pietro

    2015-05-20

    The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system. PMID:25924056

  18. Interaction between colloidal particles on an oil-water interface in dilute and dense phases

    NASA Astrophysics Data System (ADS)

    Parolini, Lucia; Law, Adam D.; Maestro, Armando; Buzza, D. Martin A.; Cicuta, Pietro

    2015-05-01

    The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system.

  19. A comparison of numerical simulations and analytical theory of the dynamics of interacting magnetic vortices

    SciTech Connect

    Asmat-Uceda, Martin; Buchanan, Kristen S.; Cheng, Xuemei; Wang, Xiao; Clarke, David J.; Tchernyshyov, Oleg

    2015-03-28

    Magnetostatic interactions between vortices in closely spaced planar structures are important for applications including vortex-based magnonic crystals and spin torque oscillator networks. Analytical theories that include magnetostatic interaction effects have been proposed but have not yet been rigorously tested. Here, we compare micromagnetic simulations of the dynamics of magnetic vortices confined in three disks in an equilateral triangle configuration to analytical theories that include coupling. Micromagnetic simulations show that the magnetostatic coupling between the disks leads to splitting of the gyrotropic resonance into three modes and that the frequency splitting increases with decreasing separation. The temporal profiles of the magnetization depend on the vortex polarities and chiralities; however, the frequencies depend only on the polarity combinations and will fall into one of two categories: all polarities equal or one polarity opposite to the others, where the latter leads to a larger frequency splitting. Although the magnitude of the splitting observed in the simulations is larger than what is expected based on purely dipolar interactions, a simple analytical model that assumes dipole-dipole coupling captures the functional form of the frequency splitting and the motion patterns just as well as more complex models.

  20. A comparison of numerical simulations and analytical theory of the dynamics of interacting magnetic vortices

    NASA Astrophysics Data System (ADS)

    Asmat-Uceda, Martin; Cheng, Xuemei; Wang, Xiao; Clarke, David J.; Tchernyshyov, Oleg; Buchanan, Kristen S.

    2015-03-01

    Magnetostatic interactions between vortices in closely spaced planar structures are important for applications including vortex-based magnonic crystals and spin torque oscillator networks. Analytical theories that include magnetostatic interaction effects have been proposed but have not yet been rigorously tested. Here, we compare micromagnetic simulations of the dynamics of magnetic vortices confined in three disks in an equilateral triangle configuration to analytical theories that include coupling. Micromagnetic simulations show that the magnetostatic coupling between the disks leads to splitting of the gyrotropic resonance into three modes and that the frequency splitting increases with decreasing separation. The temporal profiles of the magnetization depend on the vortex polarities and chiralities; however, the frequencies depend only on the polarity combinations and will fall into one of two categories: all polarities equal or one polarity opposite to the others, where the latter leads to a larger frequency splitting. Although the magnitude of the splitting observed in the simulations is larger than what is expected based on purely dipolar interactions, a simple analytical model that assumes dipole-dipole coupling captures the functional form of the frequency splitting and the motion patterns just as well as more complex models.

  1. Separation of the attractive and repulsive contributions to the adsorbate-adsorbate interactions of polar adsorbates on Si(100)

    NASA Astrophysics Data System (ADS)

    Lin, Ying-Hsiu; Jeng, Horng-Tay; Lin, Deng-Sung

    2015-11-01

    Dissociative adsorption of H2O, NH3, CH3OH and CH3NH2 polar molecules on the Si(100) surface results in a 1:1 mixture of two adsorbates (H and multi-atomic fragment A = OH, NH2, CH3O, CH3NH, respectively) on the surface. By using density functional theory (DFT) calculations, the adsorption geometry, the total energies and the charge densities for various possible ordered structures of the mixed adsorbate layer have been found. Analyzing the systematic trends in the total energies unveils concurrently the nearest-neighbor interactions ENN and the next nearest-neighbor interactions ENNN between two polar adsorbates A. In going from small to large polar adsorbates, ENN's exhibit an attractive-to-repulsive crossover behavior, indicating that they include competing attractive and repulsive contributions. Exploration of the charge density distributions allows the estimation of the degree of charge overlapping between immediately neighboring A's, the resulting contribution of the steric repulsions, and that of the attractive interactions to the corresponding ENN's. The attractive contributions to nearest neighboring adsorbate-adsorbate interactions between the polar adsorbates under study are shown to result from hydrogen bonds or dipole-dipole interactions.

  2. Shaping interactions between polar molecules with far-off-resonant light

    SciTech Connect

    Lemeshko, Mikhail

    2011-05-15

    We show that dressing polar molecules with a far-off-resonant optical field leads to new types of intermolecular potentials, which undergo a crossover from the inverse power to oscillating behavior depending on the intermolecular distance, and whose parameters can be tuned by varying the laser intensity and wavelength. We present analytic expressions for the potential energy surfaces, thereby providing direct access to the parameters of an optical field required to design intermolecular interactions experimentally.

  3. Influence of Interactions between Excited States on Magnetic Field Effects in Organic Semiconducting Materials

    NASA Astrophysics Data System (ADS)

    He, Lei; Hu, Bin; Li, Mingxing; Urbas, Augustine

    2014-03-01

    The magnetic field effects in organic semiconducting materials are essentially determined by spin-exchange interaction and hyperfine interaction within individual intermolecular excited states. Intermolecular excited states can inevitably experience interactions between them due to their spatially extended wavefunctions. This interaction can be involved in the development of magnetic field effects, but this important issue has not been discussed. We study the influence of interactions between intermolecular excited states on magnetic field effects by using magneto-photoluminescence based on well-controlled organic composite containing N,N-dimethylaniline and pyrene in liquid state. We find that the interactions between intermolecular excited states can cause a line-shape narrowing in magneto-photoluminescence. The line-shape narrowing indicates that the interactions between the intermolecular excited states can decrease the force-constant of magnetic field-dependent singlet-triplet intersystem crossing within individual intermolecular excited states. Our studies show that the interactions between the excited states can occur through three different regimes, namely long-range Coulomb interaction, mid-range spin-orbital interaction, and short-range spin interaction, and consequently influence the spin-conserving and spin-dephasing processes within individual intermolecular excited states in the development of magnetic field effects in organic semiconducting materials.

  4. Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force

    NASA Astrophysics Data System (ADS)

    Ghoufi, Aziz; Malfreyt, Patrice

    2006-12-01

    The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum.

  5. Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force.

    PubMed

    Ghoufi, Aziz; Malfreyt, Patrice

    2006-12-14

    The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum. PMID:17176145

  6. Intra- and intermolecular hydrogen bonding and conformation in 1-acyl thioureas: An experimental and theoretical approach on 1-(2-chlorobenzoyl)thiourea

    NASA Astrophysics Data System (ADS)

    Saeed, Aamer; Khurshid, Asma; Bolte, Michael; Fantoni, Adolfo C.; Erben, Mauricio F.

    2015-05-01

    The vibrational analysis (FT-IR and FT-Raman) for the new 1-(2-chlorobenzoyl)thiourea species suggests that strong intramolecular interactions affect the conformational properties. The X-ray structure determination corroborates that an intramolecular N-H⋯Odbnd C hydrogen bond occurs between the carbonyl (-Cdbnd O) and thioamide (-NH2) groups. Moreover, periodic system electron density and topological analysis have been applied to characterize the intermolecular interactions in the crystal. Extended N-H⋯Sdbnd C hydrogen-bonding networks between both the thioamide (N-H) and carbamide (NH2) groups and the thiocarbonyl bond (Cdbnd S) determine the crystal packing. The Natural Bond Orbital (NBO) population analysis demonstrates that strong hyperconjugative remote interactions are responsible for both, intra and intermolecular interactions. The Atom in Molecule (AIM) results also show that the N-H⋯Cl intramolecular hydrogen bond between the 2-Cl-phenyl ring and the amide group characterized in the free molecule changes to an N⋯Cl interaction as a consequence of crystal packing.

  7. Role of Backbone Dipole Interactions in the Formation of Secondary and Supersecondary Structures of Proteins

    PubMed Central

    2015-01-01

    We present a generic solvated coarse-grained protein model that can be used to characterize the driving forces behind protein folding. Each amino acid is coarse-grained with two beads, a backbone, and a side chain. Although the backbone beads are modeled as polar entities, side chains are hydrophobic, polar, or charged, thus allowing the exploration of how sequence patterning determines a protein fold. The change in orientation of the atoms of the coarse-grained unit is captured by the addition of two oppositely charged dummy particles inside the backbone coarse-grained bead. These two dummy charges represent a dipole that can fluctuate, thus introducing structural polarization into the coarse-grained model. Realistic ?/? content is achieved de novo without any biases in the force field toward a particular secondary structure. The dipoles created by the dummy particles interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. We have also characterized the role of dipoledipole and dipolecharge interactions in shaping the secondary and supersecondary structure of proteins. Formation of helix bundles and ?-strands are also discussed. PMID:24932137

  8. Intermolecular Casimir-Polder forces in water and near surfaces.

    PubMed

    Thiyam, Priyadarshini; Persson, Clas; Sernelius, Bo E; Parsons, Drew F; Malthe-Srenssen, Anders; Bostrm, Mathias

    2014-09-01

    The Casimir-Polder force is an important long-range interaction involved in adsorption and desorption of molecules in fluids. We explore Casimir-Polder interactions between methane molecules in water, and between a molecule in water near SiO(2) and hexane surfaces. Inclusion of the finite molecular size in the expression for the Casimir-Polder energy leads to estimates of the dispersion contribution to the binding energies between molecules and between one molecule and a planar surface. PMID:25314410

  9. Photoinduced intra- and intermolecular electron transfer in solutions and in solid organized molecular assemblies.

    PubMed

    Lemmetyinen, Helge; Tkachenko, Nikolai V; Efimov, Alexander; Niemi, Marja

    2011-01-14

    The present paper highlights results of a systematic study of photoinduced electron transfer, where the fundamental aspects of the photochemistry occurring in solutions and in artificially or self-assembled molecular systems are combined and compared. In photochemical electron transfer (ET) reactions in solutions the electron donor, D, and acceptor, A, have to be or to diffuse to a short distance, which requires a high concentration of quencher molecules and/or long lifetimes of the excited donor or acceptor, which cannot always be arranged. The problem can partly be avoided by linking the donor and acceptor moieties covalently by a single bond, molecular chain or chains, or rigid bridge, forming D-A dyads. The covalent combination of porphyrin or phthalocyanine donors with an efficient electron acceptor, e.g. fullerene, has a two-fold effect on the electron transfer properties. Firstly, the electronic systems of the D-A pair result in a formation of an exciplex intermediate upon excitation both in solutions and in solid phases. The formation of the exciplex accelerates the ET rate, which was found to be as fast as >10(12) s(-1). Secondly, the total reorganization energy can be as small as 0.3 eV, even in polar solvents, which allows nanosecond lifetimes for the charge separated (CS) state. Molecular assemblies can form solid heterogeneous, but organized systems, e.g. molecular layers. This results in more complex charge separation and recombination dynamics. A distinct feature of the ET in organized assemblies is intermolecular interactions, which open a possibility for a charge migration both in the acceptor and in the donor layers, after the primary intramolecular exciplex formation and charge separation in the D-A dyad. The intramolecular ET is fast (35 ps) and efficient, but the formed interlayer CS states have lifetimes in microsecond or even second time domain. This is an important result considering possible applications. PMID:21031207

  10. Using triazine as coupling unit for intra and intermolecular ferromagnetic coupling I

    NASA Astrophysics Data System (ADS)

    Zhang, Jingping; Baumgarten, Martin

    1997-01-01

    Novel high spin bi- and triradicals composed of triazine coupling units and different kinds of radical centers ( +NH 2, .NH, .CH 2, HNO ., :N, :C), are predicted from AM1-CI calculations. It is found that when +.NH, and .N serve as spin centers, the high spin ground states of bi- and triradicals with triazine coupling units are more stable than those with phenylene and benzenetriyl ones, respectively. For a biradical with triazine coupling unit and +NH spin center, intermolecular hydrogen bonds can be formed between this biradical and a diamagnetic cyanuric acid or between two biradicals themselves as well, which may be considered as the basic units of supramolecular aggregates. For these two cases, it is shown that intermolecular hydrogen bonds between high spin molecules and diamagnetic molecules reduce the stability of high spin ground state, but the intermolecular ferromagnetic coupling of biradical dimer can be transferred although weakly through hydrogen bonds.

  11. Probing Intramolecular versus Intermolecular CO2 Adsorption on Amine-Grafted SBA-15.

    PubMed

    Yoo, Chun-Jae; Lee, Li-Chen; Jones, Christopher W

    2015-12-15

    A mesoporous silica SBA-15 is modified with an array of amine-containing organosilanes including (i) propylamine, SiCH2CH2CH2NH2 (MONO), (ii) propylethylenediamine, SiCH2CH2CH2NHCH2CH2NH2 (DI), (iii) propyldiethylenetriamine, SiCH2CH2CH2NHCH2CH2NHCH2CH2NH2 (TRI), and (iv) propyltriethylenetetramine, SiCH2CH2CH2NHCH2CH2N(CH2CH2NH2)2 (TREN) and the low loading silane adsorbents (?0.45 mmol silane/g) are evaluated for their CO2 adsorption properties, with a focus on gaining insight into the propensity for intramolecular vs intermolecular CO2 adsorption. Adsorption isotherms at low CO2 coverages are measured while simultaneously recording the heat evolved via a Tian-Calvet calorimeter. The results are compared on a silane molecule efficiency basis (mol CO2 adsorbed/mol silane) to assess the potential for intramolecular CO2 adsorption, employing two amine groups in a single silane molecule. As the number of amines in the silane molecule increases (MONO < DI < TREN ? TRI), the silane molecule efficiency is enhanced owing to the ability to intramolecularly capture CO2. Analysis of the CO2 uptake for samples with the surface silanols removed by capping demonstrates that cooperative uptake due to amine-CO2-silanol interactions is also possible over these adsorbents and is the primary mode of sorption for the MONO material at the studied low silane loading. As the propensity for intramolecular CO2 capture increases due to the presence of multiple amines in a single silane molecule (MONO < DI < TREN ? TRI), the measured heat of adsorption also increases. This study of various amine-containing silanes at low coverage is the first to provide significant, direct evidence for intramolecular CO2 capture in a single silane molecule. Furthermore, it provides evidence for the relative heats of adsorption for physisorption on a silanol laden surface (ca. 37 kJ/mol), a silanol-capped surface (ca. 25 kJ/mol), via amine-CO2-silanol interactions (ca. 46 kJ/mol), and via amine-CO2-amine interactions at low surface coverages (ca. 65 kJ/mol). PMID:26602305

  12. Pd(II) -Catalyzed Intermolecular Amination of Unactivated C(sp(3) )-H Bonds.

    PubMed

    Gou, Quan; Liu, Gang; Liu, Zi-Ning; Qin, Jun

    2015-10-26

    Pd(II) -catalyzed intermolecular amination of unactivated C(sp(3) )-H bonds has been successfully developed for the first time. This method provides a new way to achieve the challenging intermolecular amination of unactivated C(sp(3) )-H bonds, producing a variety of unnatural ?(2) -amino carboxylic acid analogues. This C(sp(3) )-H amination protocol is demonstrated with a broad substrate scope, good functional-group tolerance, and chemoselectivity. It is operated without use of phosphine ligand or external oxidant. PMID:26359788

  13. Infrared spectra of ice and water from first principles: intra vs. intermolecular dipole correlations

    NASA Astrophysics Data System (ADS)

    Chen, Wei; Sharma, Manu; Resta, Raffaele; Galli, Giulia; Car, Roberto

    2008-03-01

    We report simulated infrared (IR) spectra of deuterated ice and water using Car-Parrinello molecular dynamics with maximally localized Wannier functions. Experimental features of both ice and water are accurately reproduced within the harmonic approximation. Calculated line shapes are further decomposed in terms of intra and intermolecular dipole correlation functions with spatial resolution. This approach proves to be very useful to understand the origin of spectral features and the nature of the underlying hydrogen-bond (H-bond) network. We find that intermolecular dynamic charge fluctuations play a crucial role over the entire frequency range.

  14. Localized excitations in discrete nonlinear Schrödinger systems: Effects of nonlocal dispersive interactions and noise

    NASA Astrophysics Data System (ADS)

    Rasmussen, K. Ø.; Christiansen, P. L.; Johansson, M.; Gaididei, Yu. B.; Mingaleev, S. F.

    1998-03-01

    A one-dimensional discrete nonlinear Schrödinger (DNLS) model with the power dependence, r- s on the distance r, of dispersive interactions is proposed. The stationary states of the system are studied both analytically and numerically. Two kinds of trial functions, exp-like and sech-like are exploited and the results of both approaches are compared. Both on-site and inter-site stationary states are investigated. It is shown that for s sufficiently large all features of the model are qualitatively the same as in the DNLS model with nearest-neighbor interaction. For s less than some critical value, scr, there is an interval of bistability where two stable stationary states exist at each excitation number. The bistability of on-site solitons may occur for dipole-dipole dispersive interaction ( s = 3), while scr for inter-site solitions is close to 2.1. In the framework of the DNLS equation with nearest-neighbor coupling we discuss the stability of highly localized, “breather-like”, excitations under the influence of thermal fluctuations. Numerical analysis shows that the lifetime of the breather is always finite and in a large parameter region inversely proportional to the noise variance for fixed damping and nonlinearity. We also find that the decay rate of the breather decreases with increasing nonlinearity and with increasing damping.

  15. C60 chain phases on ZnPc/Ag(111) surfaces: Supramolecular organization driven by competing interactions

    NASA Astrophysics Data System (ADS)

    Jin, W.; Liu, Q.; Dougherty, D. B.; Cullen, W. G.; Reutt-Robey, J. E.; Weeks, J.; Robey, S. W.

    2015-03-01

    Serpentine chain C60 phases were observed in scanning tunneling microscopy (STM) images of C60 layers on zinc phthalocyanine (ZnPc) or pentacene covered Ag(111) and Au(111) surfaces. This low-density, quasi-one-dimensional organization contrasts starkly with the close-packed hexagonal phases observed for C60 layers on bare metal substrates. STM was employed to perform a detailed investigation of these chain structures for C60/ZnPc/Ag(111) heterolayers. Motivated by the similarity of these chain phases, and the chain and stripe organization occurring in dipole-fluid systems, we investigated a model based on competing van der Waals attractions and electrostatic repulsions between C60 molecules as an explanation for the driving force behind these monolayer phases. Density functional theory (DFT) calculations revealed significant charge transfer to C60 from the Ag(111) substrate, through the intervening ZnPc layer, inducing electrostatic interactions between C60 molecules. Molecular dynamics simulations performed with attractive van der Waals interactions plus repulsive dipole-dipole interactions reproduced the C60 chain phases with dipole magnitudes consistent with DFT calculations.

  16. C60 chain phases on ZnPc/Ag(111) surfaces: Supramolecular organization driven by competing interactions.

    PubMed

    Jin, W; Liu, Q; Dougherty, D B; Cullen, W G; Reutt-Robey, J E; Weeks, J; Robey, S W

    2015-03-14

    Serpentine chain C60 phases were observed in scanning tunneling microscopy (STM) images of C60 layers on zinc phthalocyanine (ZnPc) or pentacene covered Ag(111) and Au(111) surfaces. This low-density, quasi-one-dimensional organization contrasts starkly with the close-packed hexagonal phases observed for C60 layers on bare metal substrates. STM was employed to perform a detailed investigation of these chain structures for C60/ZnPc/Ag(111) heterolayers. Motivated by the similarity of these chain phases, and the chain and stripe organization occurring in dipole-fluid systems, we investigated a model based on competing van der Waals attractions and electrostatic repulsions between C60 molecules as an explanation for the driving force behind these monolayer phases. Density functional theory (DFT) calculations revealed significant charge transfer to C60 from the Ag(111) substrate, through the intervening ZnPc layer, inducing electrostatic interactions between C60 molecules. Molecular dynamics simulations performed with attractive van der Waals interactions plus repulsive dipole-dipole interactions reproduced the C60 chain phases with dipole magnitudes consistent with DFT calculations. PMID:25770499

  17. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    SciTech Connect

    Crusius, Johann-Philipp Hassel, Egon; Hellmann, Robert; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  18. MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

    EPA Science Inventory

    Abstract
    One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

  19. Intermolecular potential functions from spectroscopic properties of weakly bound complexes. Third progress report, July 1, 1991--June 30, 1992

    SciTech Connect

    Muenter, J.S.

    1992-08-01

    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  20. Explosives sensing by using electron-rich supramolecular polymers: role of intermolecular hydrogen bonding in significant enhancement of sensitivity.

    PubMed

    Gole, Bappaditya; Song, Wentao; Lackinger, Markus; Mukherjee, Partha Sarathi

    2014-10-13

    We demonstrate here that supramolecular interactions enhance the sensitivity towards detection of electron-deficient nitro-aromatic compounds (NACs) over discrete analogues. NACs are the most commonly used explosive ingredients and are common constituents of many unexploded landmines used during World War II. In this study, we have synthesised a series of pyrene-based polycarboxylic acids along with their corresponding discrete esters. Due to the electron richness and the fluorescent behaviour of the pyrene moiety, all the compounds act as sensors for electron-deficient NACs through a fluorescence quenching mechanism. A Stern-Volmer quenching constant determination revealed that the carboxylic acids are more sensitive than the corresponding esters towards NACs in solution. The high sensitivity of the acids was attributed to supramolecular polymer formation through hydrogen bonding in the case of the acids, and the enhancement mechanism is based on an exciton energy migration upon excitation along the hydrogen-bond backbone. The presence of intermolecular hydrogen bonding in the acids in solution was established by solvent-dependent fluorescence studies and dynamic light scattering (DLS) experiments. In addition, the importance of intermolecular hydrogen bonds in solid-state sensing was further explored by scanning tunnelling microscopy (STM) experiments at the liquid-solid interface, in which structures of self-assembled monolayer of the acids and the corresponding esters were compared. The sensitivity tests revealed that these supramolecular sensors can even detect picric acid and trinitrotoluene in solution at levels as low as parts per trillion (ppt), which is much below the recommended permissible level of these constituents in drinking water. PMID:25187022