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1

On the theory of the proton free induction decay and Hahn echo in polymer systems: The role of intermolecular magnetic dipole-dipole interactions and the modified Anderson-Weiss approximation  

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

2

Dipole-Dipole Interactions in a Frozen Rydberg Gas.  

National Technical Information Service (NTIS)

We investigate here the characteristics of energy resonant dipole- dipole interactions between Rydberg atoms in Magneto-Optical Trap. These resonant processes occur in a kinetic energy regime in which the atoms may be considered stationary over the time s...

J. R. Lowell

1998-01-01

3

Dipole-dipole interaction in random electromagnetic fields  

NASA Astrophysics Data System (ADS)

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

Sukhov, Sergey; Douglass, Kyle M.; Dogariu, Aristide

2013-07-01

4

Dipole-dipole interaction in random electromagnetic fields.  

PubMed

We demonstrate that a nonvanishing interaction force exists between pairs of induced dipoles in a random, statistically stationary electromagnetic field. This new type of optical binding force leads to long-range interaction between dipolar particles even when placed in spatially incoherent fields. We also discuss several unique features of the dipole-dipole interaction in spatially incoherent Gaussian fields. PMID:23939056

Sukhov, Sergey; Douglass, Kyle M; Dogariu, Aristide

2013-07-15

5

Dipole-dipole interaction between rubidium Rydberg atoms  

SciTech Connect

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.

Altiere, Emily; Fahey, Donald P.; Noel, Michael W. [Physics Department, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010 (United States); Smith, Rachel J.; Carroll, Thomas J. [Department of Physics and Astronomy, Ursinus College, Collegeville, Pennsylvania 19426 (United States)

2011-11-15

6

Theory of intermolecular interactions: The long range terms in the dipole-dipole, monopoles-dipole, and monopoles-bond polarizabilities approximations  

Microsoft Academic Search

The problem of evaluating the long range terms (electrostatic, polarization, dispersion) of the interaction energy between molecules at intermediate distances (i.e. distances of the order of magnitude of the molecular dimensions) is considered. Instead of being approximated by its dipole part, the exact interaction Hamiltonian is treated as proposed by Longuet-Higgins [11], i.e. the matrix elements are interpreted as electrostatic

Pierre Claverie; Robert Rein

1969-01-01

7

Stability of quasi-two-dimensional Bose-Einstein condensates with dominant dipole-dipole interactions  

Microsoft Academic Search

We consider quasi-two-dimensional atomic or molecular Bose-Einstein condensates with both contact and dipole-dipole interactions. It is shown that as a consequence of the dimensional reduction, and within mean-field theory, the condensates do not develop unstable excitation spectra, even when the dipole-dipole interaction completely dominates the contact interaction.

Uwe R

2006-01-01

8

Measurement of the dipole-dipole interaction of Rb nsnp states by microwave Ramsey interferometry  

NASA Astrophysics Data System (ADS)

We have used the Ramsey method of separated oscillatory fields to probe the dipole-dipole interaction of Rb nsnp pair states of 33?n?41. In the Ramsey method dipole-dipole broadening in an inhomogeneous sample is manifested as a decrease in the fringe contrast with increasing density. An attractive feature of this approach compared to conventional line broadening is that the effect of the dipole-dipole interaction can be seen near the center of the Ramsey interference pattern, where the signal is large, as opposed to in the wings, where it is small. We observe dipole-dipole broadening which scales as n4, in agreement with the calculated broadening. In addition, the Ramsey method points to the existence of nsnp1/2 states which have no dipole-dipole shift.

Park, Hyunwook; Gallagher, T. F.

2012-11-01

9

Geometrical simplification of the dipole-dipole interaction formula  

Microsoft Academic Search

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

Ladislav Kocbach; Suhail Lubbad

2010-01-01

10

Geometrical Simplification of the Dipole-Dipole Interaction Formula  

ERIC Educational Resources Information Center

|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…

Kocbach, Ladislav; Lubbad, Suhail

2010-01-01

11

Geometrical Simplification of the Dipole-Dipole Interaction Formula  

ERIC Educational Resources Information Center

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…

Kocbach, Ladislav; Lubbad, Suhail

2010-01-01

12

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

Microsoft Academic Search

Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion

Motohiko Ezawa

2010-01-01

13

Role of dipole-dipole interactions for hyperthermia heating of magnetic nanoparticle ensembles  

NASA Astrophysics Data System (ADS)

For clinical hyperthermia treatment the heating efficiency of magnetic nanoparticle ensembles is a crucial element. Using efficient algorithms, this heating is studied numerically with a focus on the effects of dipole-dipole interparticle interactions. For the time evolution of realistically modeled systems an approach based on the Landau-Lifschitz-Gilbert equation of motion with Langevin dynamics is taken. Our results suggest a widely negative influence of dipole-dipole interactions on the heating power of nanoparticles. However, considering ensembles within a fixed, given sample volume an optimal particle density exists. The presented results may have important implications for the medical use of magnetic hyperthermia treatment.

Haase, C.; Nowak, U.

2012-01-01

14

Geometrical simplification of the dipole-dipole interaction formula  

NASA Astrophysics Data System (ADS)

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.

Kocbach, Ladislav; Lubbad, Suhail

2010-07-01

15

Magnetic Field of a Dipole and the Dipole-Dipole Interaction  

ERIC Educational Resources Information Center

|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…

Kraftmakher, Yaakov

2007-01-01

16

Stability of quasi-two-dimensional Bose-Einstein condensates with dominant dipole-dipole interactions  

Microsoft Academic Search

We consider quasi-two-dimensional atomic\\/molecular Bose-Einstein condensates\\u000awith both contact and dipole-dipole interactions. It is shown that, as a\\u000aconsequence of the dimensional reduction, and within mean-field theory, the\\u000acondensates do not develop unstable excitation spectra, even when the\\u000adipole-dipole interaction completely dominates the contact interaction.

Uwe R. Fischer

2006-01-01

17

Population dynamics in cold gases resulting from the long-range dipole-dipole interaction  

NASA Astrophysics Data System (ADS)

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

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

2009-11-01

18

Solitons and transients in media with near dipole-dipole interaction  

Microsoft Academic Search

This paper studies soliton regimes of light pulse propagation and transient processes in optically dense media with the near dipole-dipole interaction. It is shown that such an interaction permits the soliton propagation to be realized while the pulse duration is not only less than both irreversible relaxation times T1 and T2 but also when it falls between T2 ≪ ?p

O. K. Khasanov; G. A. Rusetskii; O. M. Fedotova; T. V. Smirnova; A. A. Afanas'ev; R. A. Vlasov

2003-01-01

19

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

NASA Astrophysics Data System (ADS)

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

Park, Hyunwook

20

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

SciTech Connect

Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion radius. The radius is controllable by the external magnetic field. It is intriguing that a Skyrmion may have already been observed as a magnetic domain. A salient feature is that a single Skyrmion can be created or destroyed experimentally. An analysis is made also on Skyrmions in chiral magnets.

Ezawa, Motohiko [Department of Applied Physics, University of Tokyo, Hongo 7-3-1, 113-8656 (Japan)

2010-11-05

21

Giant Skyrmions stabilized by dipole-dipole interactions in thin ferromagnetic films.  

PubMed

Motivated by a recent magnetization reversal experiment on a TbFeCo thin film, we study a topological excitation in the anisotropic nonlinear sigma model together with the Zeeman and magnetic dipole-dipole interactions. Dipole-dipole interactions turn a ferromagnet into a frustrated spin system, which allows a nontrivial spin texture such as a giant Skyrmion. We derive an analytic formula for the Skyrmion radius. The radius is controllable by the external magnetic field. It is intriguing that a Skyrmion may have already been observed as a magnetic domain. A salient feature is that a single Skyrmion can be created or destroyed experimentally. An analysis is made also on Skyrmions in chiral magnets. PMID:21231193

Ezawa, Motohiko

2010-11-02

22

Probing dipole-dipole interactions in a frozen Rydberg gas with millimeter waves  

NASA Astrophysics Data System (ADS)

Frozen Rydberg gases are currently of interest for two reasons. First, the atoms in such cold samples only move roughly 3% of the average interatomic spacing during the 1mus time scale of experimental interest, so the interactions between them are almost static, as in a disordered solid. Second, a frozen Rydberg gas can spontaneously evolve into an ultracold plasma, and the ultracold plasma can recombine to form Rydberg atoms. In this dissertation, I present experimental studies of these collective phenomena of cold Rydberg gases, with emphasis on the experiments done using millimeter waves. The many-body nature of the dipole-dipole interactions in a cold gas of Rydberg atoms is clearly demonstrated in the resonant energy transfer experiment by adding an additional state to the system using a microwave transition. Moreover, the microwave spectroscopy studies show that the attractive dipole-dipole interaction provides the initial ionization mechanism responsible for producing the free ions for trapping the electrons. This suggests an intimate connection between dipole-dipole interaction and plasma formation.

Li, Wenhui

23

Dissipation-induced stationary entanglement in dipole-dipole interacting atomic samples  

SciTech Connect

The dynamics of two two-level dipole-dipole interacting atoms coupled to a common electro-magnetic bath and closely located inside a lossy cavity, is reported. Initially injecting only one excitation in the two-atom cavity system, loss mechanisms asymptotically drive the matter sample toward a stationary maximally entangled state. The role played by the closeness of the two atoms, with respect to such a cooperative behavior, is carefully discussed. Stationary radiation trapping effects are found and transparently interpreted.

Nicolosi, S.; Napoli, A.; Messina, A. [INFM, MIUR, and Dipartimento di Scienze Fisiche ed Astronomiche, Universita di Palermo, Via Archirafi 36, 90123 Palermo (Italy); Petruccione, F. [School of Pure and Applied Physics University of KwaZulu-Natal Durban, 4041 Durban, South Africa, and Istituto Italiano per gli Studi Filosofici, Via Monte di Dio 14, I-80132 Naples (Italy)

2004-08-01

24

Modeling magnetic nanoparticle dipole-dipole interactions inside living cells  

NASA Astrophysics Data System (ADS)

Biomedical applications based on superparamagnetic nanoparticles injected in vivo may be affected by the cellular uptake of these nanoparticles. Living cells indeed capture and internalize nanoparticles, concentrating them into intracellular vesicles called lysosomes. As a consequence, nanoparticles interact magnetically with each other, modifying their magnetic properties. The effects of cellular uptake can be observed on the temperature dependence of zero-field cooled (ZFC) magnetization, which is known to be sensitive to magnetic interactions. In this paper, a theoretical model is proposed to account for weak magnetic interactions between nanoparticles aggregated into spherical compartments. This model suggests a new interpretation of the maximum of the ZFC curve, uncorrelated with the nanoparticle relaxation time but with the extent of interaction effects. It focuses on the local field felt by each nanoparticle, which is the sum of the applied magnetic field and the field created by all the other nanoparticles. For the considered organization of nanoparticles, only the field created by touching neighbors has to be taken into account, setting up the local nanoparticle volume fraction as the unique parameter of the model. This parameter relates the global magnetization measurements to the local distribution of nanoparticles in cells and tissues or in other complex media with aggregated organization.

Lévy, Michael; Gazeau, Florence; Bacri, Jean-Claude; Wilhelm, Claire; Devaud, Martin

2011-08-01

25

Near dipole-dipole interaction effects in dense media  

Microsoft Academic Search

The local field correction in semiclassical model of superluminescence is presented for short and pencil-like samples. We propose a new experimental technique for stability measurements based on Fourier spectroscopy of laser pulses interacting with dense self-chirped resonant media having many atoms within a cubic wavelength an d theoretical model of the two-photon Fourier spectroscopy of Cs.

Igor I. Korel; Vladimir I. Denisov

2001-01-01

26

Wigner crystal induced by dipole-dipole interaction in one-dimensional optical lattices  

NASA Astrophysics Data System (ADS)

We demonstrate that the static structure factor, momentum distribution, and density distribution provide clear signatures of the emergence of Wigner crystal for the fermionic dipolar gas with strongly repulsive dipole-dipole interactions trapped in one-dimensional optical lattices. Our numerical evidences are based on the exact diagonalization of the microscopic effective lattice Hamiltonian of few particles interacting with long-range interactions. As a comparison, we also study the system with only nearest-neighbor interactions, which displays quite different behavior from the dipolar system in the regime of strong repulsion.

Xu, Zhihao; Chen, Shu

2012-03-01

27

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

NASA Astrophysics Data System (ADS)

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

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

2006-05-01

28

Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam  

NASA Astrophysics Data System (ADS)

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion of neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.

Kutteruf, M. R.; Jones, R. R.

2010-12-01

29

Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam  

SciTech Connect

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion of neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.

Kutteruf, M. R.; Jones, R. R. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904-4714 (United States)

2010-12-15

30

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

31

Tailored electronic structure and optical properties of conjugated systems through aggregates and dipole-dipole interactions.  

PubMed

A series of PPVO (p-phenylene vinylene oligomer) derivatives with functional groups of varying electronegativity were synthesized via the Horner-Wadsworth-Emmons reaction. Subtle changes in the end group functionality significantly impact the molecular electronic and optical properties of the PPVOs, resulting in broadly tunable and efficient UV absorption and photoluminescence spectra. Of particular interest is the NO2-substituted PPVO which exhibits photoluminescence color ranging from the blue to the red, thus encompassing the entire visible spectrum. Our experimental study and electronic structure calculations suggest that the formation of aggregates and strong dipole-dipole solute-solvent interactions are responsible for the observed strong solvatochromism. Experimental and theoretical results for the NH2-, H-, and NO2-substituted PPVOs suggest that the stabilization of ground or excited state dipoles leads to the blue or red shift of the optical spectra. The electroluminescence (EL) spectra of H-, COOH-, and NO2-PPVO have maxima at 487, 518, and 587 nm, respectively, in the OLED device. This trend in the EL spectra is in excellent agreement with the end group-dependent PL spectra of the PPVO thin-films. PMID:23607446

Park, Young Il; Kuo, Cheng-Yu; Martinez, Jennifer S; Park, Young-Shin; Postupna, Olena; Zhugayevych, Andriy; Kim, Seungho; Park, Jongwook; Tretiak, Sergei; Wang, Hsing-Lin

2013-05-17

32

Teaching Ion-Ion, Ion-Dipole, and Dipole-Dipole Interactions  

ERIC Educational Resources Information Center

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)

Yoder, Claude H.

1977-01-01

33

Contributions of Exchange and Dipole–Dipole Interactions to the Shape of EPR Spectra of Free Radicals in Diluted Solutions  

Microsoft Academic Search

This report presents a comprehensive analysis of the contributions of the Heisenberg exchange and dipole–dipole interactions\\u000a in diluted solutions of nitroxide radicals to the shape of their electron paramagnetic resonance (EPR) spectra taking into\\u000a account all coherence transfer processes. It is shown that these contributions interfere. The approaches to obtain the molecular-kinetic\\u000a and exchange integral parameters by analyzing the EPR

K. M. Salikhov

2010-01-01

34

Theoretical analysis of the spin exchange and magnetic dipole-dipole interactions leading to the magnetic structure of Ni3TeO6.  

PubMed

The origin of the collinear antiferromagnetic magnetic structure of Ni(3)TeO(6) below 52 K was analyzed by calculating its spin exchanges on the basis of density functional calculations, and the cause for the parallelc-spin orientation found for this magnetic structure by calculating the spin-orbit coupling and magnetic dipole-dipole interaction energies. The calculated exchanges correctly predict the observed magnetic structure below 52 K, and lead practically to no spin frustration. The perpendicularc- and parallelc-spin orientations are predicted by the spin-orbit coupling and the magnetic dipole-dipole interactions, respectively. However, the magnetic dipole-dipole interactions are stronger than the spin-orbit coupling interactions, and hence are responsible for the spin orientation observed for Ni(3)TeO(6). PMID:20690764

Wu, Fang; Kan, Erjun; Tian, Chuan; Whangbo, Myung-Hwan

2010-08-16

35

Effects of magnetic dipole-dipole interactions in atomic Bose-Einstein condensates with tunable s-wave interactions  

NASA Astrophysics Data System (ADS)

The s-wave interaction is usually the dominant form of interactions in atomic Bose-Einstein condensates (BECs). Recently, Feshbach resonances have been employed to reduce the strength of the s-wave interaction in many atomic species. This opens the possibilities to study magnetic dipole-dipole interactions (MDDIs) in BECs, where the novel physics resulting from long-range and anisotropic dipolar interactions can be explored. Using a variational method, we study the effect of MDDIs on the statics and dynamics of atomic BECs with tunable s-wave interactions for a variety of species, including both nonalkali metals with large magnetic dipole moments (52Cr, 164Dy, 168Er) and alkali metals (with much smaller magnetic dipole moments). A parameter of magnetic Feshbach resonances, ?dd,max, is used to quantitatively indicate the feasibility of experimentally observing MDDI effects in different atomic species. We find that strong MDDI effects should be observable in both in-trap and time-of-flight behaviors, not only for the strongly magnetic dipolar species but also for the alkali-metal BECs of 7Li, 39K, and 133Cs. In addition, we predict several effects which should be experimentally observable. Our results provide a helpful guide for experimentalists to realize and study atomic dipolar quantum gases.

Olson, Abraham J.; Whitenack, Daniel L.; Chen, Yong P.

2013-10-01

36

Molecular desorption of methyl halides from GaAs(110): The role of lateral dipole--dipole interaction between adsorbates  

SciTech Connect

Temperature programmed desorption (TPD) spectra of CH[sub 3]X (X=Cl, Br, I) from GaAs(110) were recorded with a heating rate of 5 K/s for coverages from less than 0.1 to 2 ML, where methyl halides desorb molecularly, i.e., without dissociation. The shapes of the TPD spectra are strongly coverage dependent with the peak temperature of desorption decreasing with increasing coverage, especially for the submonolayer region. A model incorporating dipole--dipole repulsive interactions between the adsorbed molecules and which was previously proposed for the desorption of adsorbed molecules from metal surfaces has been employed to fit our TPD spectra. The fit gives the activation energy, effective dipole moment, and effective polarizability for the adsorbate. The resulting dipole moment and polarizability are less than the gas-phase molecular values, suggesting the importance of an ordered adsorption orientation. [copyright] [ital 1994][ital American] [ital Institute] [ital of] [ital Physics].

Lu, P.; Lasky, P.J.; Yang, Q.; Wang, Y.; Osgood, R.M. Jr. (Columbia Radiation Laboratory, Columbia University, New York, New York 10027 (United States))

1994-12-01

37

Effect of finite detection efficiency on the observation of the dipole-dipole interaction of a few Rydberg atoms  

SciTech Connect

We have developed a simple analytical model describing multiatom signals that are measured in experiments on dipole-dipole interaction at resonant collisions of a few Rydberg atoms. It has been shown that finite efficiency of the selective field-ionization detector leads to the mixing up of the spectra of resonant collisions registered for various numbers of Rydberg atoms. The formulas which help to estimate an appropriate mean Rydberg atom number for a given detection efficiency are presented. We have found that a measurement of the relation between the amplitudes of collisional resonances observed in the one- and two-atom signals provides a straightforward determination of the absolute detection efficiency and mean Rydberg atom number. We also performed a testing experiment on resonant collisions in a small excitation volume of a sodium atomic beam. The resonances observed for 1-4 detected Rydberg atoms have been analyzed and compared with theory.

Ryabtsev, I. I.; Tretyakov, D. B.; Beterov, I. I.; Entin, V. M. [Institute of Semiconductor Physics, Prospekt Lavrentyeva 13, 630090 Novosibirsk (Russian Federation)

2007-07-15

38

Dipole-dipole-interaction-induced line narrowing in thin-film vibrational-mode spectra  

NASA Astrophysics Data System (ADS)

Under certain circumstances the electric dipole interaction can reduce or eliminate the effects of spectral inhomogeneous broadening on an infrared absorption line of a thin film. The oscillating electric dipole moment must be oriented perpendicular to the film surface, and the dipole interaction, as measured by the frequency shift that it induces, must be larger than the width of the inhomogeneous frequency distribution. An example of this interaction-induced line narrowing is presented for a vibrational mode of a KReO4 film, and the relevance of this mechanism to two-dimensional electron-gas subband transitions and adsorbate vibrational modes is considered.

Schlesinger, Z.; Green, L. H.; Sievers, A. J.

1985-08-01

39

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

NASA Astrophysics Data System (ADS)

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

Sturniolo, Simone; Pieruccini, Marco

2012-10-01

40

Role of charge transfer, dipole-dipole interactions, and electrostatics in Fermi-level pinning at a molecular heterojunction on a metal surface  

NASA Astrophysics Data System (ADS)

Recently, Niederhausen [Phys. Rev. BPRBMDO0163-182910.1103/PhysRevB.86.081411 86, 081411(R) (2012)] have reported on the energy level alignment of C60 adsorbed on a bilayer ?-sexithiophene (6T) film on Ag(111). The possibility of charge transfer from the metal to the C60 through the bilayer 6T as discussed by the authors may have a strong impact on understanding the energy level alignment (ELA) at organic-organic (O-O) heterojunctions grown on electrodes. In this paper, we aim at a comprehensive picture of the ELA at O-O interfaces on a metal. We carry out a detailed investigation of the same pair of materials on Ag(111) as employed previously, however, with varying 6T interlayer thickness. The results allow unambiguous identification of integer charge transfer towards a fraction of the C60 molecules as the mechanism leading to the formation of interface dipoles. Varying the 6T interlayer thickness also reveals the dependence of the observed features on the C60-metal distance. This dependence is quantitatively addressed by electrostatic considerations involving a metal-to-overlayer charge transfer. From this, we demonstrate the important role of dipole-dipole interaction potentials in the molecular layer and electric fields resulting from interface dipole formation for the energy level alignment. These findings provide a deeper understanding of the fundamental mechanisms that establish electronic equilibrium at molecular heterojunctions and will aid the prediction of an accurate energy level alignment at device relevant heterojunctions, e.g. in organic opto-electronic devices.

Amsalem, P.; Niederhausen, J.; Wilke, A.; Heimel, G.; Schlesinger, R.; Winkler, S.; Vollmer, A.; Rabe, J. P.; Koch, N.

2013-01-01

41

Pulsed Electric Current Dipole/Dipole Interference.  

National Technical Information Service (NTIS)

A time-domain analysis of electromagnetic, pulsed electric current dipole/dipole interference is presented. The emitting and suscepting dipoles may be either 'electric dipoles' (short segments of electric current carrying wire) or 'magnetic dipoles' (smal...

D. Quak A. T. de Hoop

1998-01-01

42

DQ-DRENAR: a new NMR technique to measure site-resolved magnetic dipole-dipole interactions in multispin-1?2 systems: theory and validation on crystalline phosphates.  

PubMed

A new solid state NMR technique is described for measuring homonuclear dipole-dipole interactions in multi-spin-1?2 systems under magic-angle spinning conditions. Re-coupling is accomplished in the form of an effective double quantum (DQ) Hamiltonian created by a symmetry-based POST-C7 sequence consisting of two excitation blocks, attenuating the signal (intensity S'). For comparison, a reference signal S0 with the dipolar re-coupling absent is generated by shifting the phase of the second block by 90° relative to the first block. As in rotational echo double resonance, the homonuclear dipole-dipole coupling constant can then be extracted from a plot of the normalized difference signal (S0 - S')?S0 versus dipolar mixing time. The method is given the acronym DQ-DRENAR ("Double-Quantum-based Dipolar Re-coupling effects Nuclear Alignment Reduction"). The method is analyzed mathematically, and on the basis of detailed simulations, with respect to the order and the geometry of the spin system, the dipolar truncation phenomenon, and the influence of the chemical shift anisotropy on experimental curves. Within the range of (S0 - S')?S0 ?0.3-0.5 such DRENAR curves can be approximated by simple parabolae, yielding effective squared dipole-dipole coupling constants summed over all the pairwise interactions present. The method has been successfully validated for (31)P-(31)P distance determinations of numerous crystalline model compounds representing a wide range of dipolar coupling strengths. PMID:23635131

Ren, Jinjun; Eckert, Hellmut

2013-04-28

43

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

SciTech Connect

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

Li Wenhui; Tanner, Paul J.; Gallagher, T. F. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904 (United States)

2005-05-06

44

Dipole-dipole-coupled double-Rydberg molecules  

NASA Astrophysics Data System (ADS)

We show that the dipole-dipole interaction between two Rydberg atoms can give rise to long-range molecules. The binding potential arises from two states that converge to different separated-atom asymptotes. These states interact weakly at large distances, but start to repel each other strongly as the van der Waals interaction turns into a resonant dipole-dipole interaction with decreasing separation between the atoms. This mechanism leads to the formation of an attractive well for one of the potentials. If the two separated-atom asymptotes come from the small Stark splitting of an atomic Rydberg level, which lifts the Zeeman degeneracy, the depth of the well and the location of its minimum are controlled by the external electric field. We discuss two different geometries that result in a localized and a donut-shaped potential, respectively.

Kiffner, Martin; Park, Hyunwook; Li, Wenhui; Gallagher, T. F.

2012-09-01

45

A basic program to transform continuous polar dipole-dipole resistivity soundings to half-Schlumberger soundings  

USGS Publications Warehouse

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.

Zerilli, A.; Bisdorf, R. J.

1990-01-01

46

Helping Students Assess the Relative Importance of Different Intermolecular Interactions  

ERIC Educational Resources Information Center

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…

Jasien, Paul G.

2008-01-01

47

Helping Students Assess the Relative Importance of Different Intermolecular Interactions  

ERIC Educational Resources Information Center

|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…

Jasien, Paul G.

2008-01-01

48

Perturbation analyses of intermolecular interactions.  

PubMed

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the ? state and PPII (polyproline II) + ? states) for larger cutoff length, the separation between the PPII state and the ? state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information. PMID:21929141

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-12

49

Weak intermolecular interaction  

Microsoft Academic Search

The SCF interaction energy (?ESCF) between two hydrogen molecules was separated into (Coulomb + exchange) and (induction + charge-transfer) components. The effect of the basis set and orientation of the two molecules on the ?ESCF energy and its components are discussed.

Miroslav Urban; Pavel Hobza

1975-01-01

50

Manifestation of resonance dipole-dipole interaction in spectra of low-temperature molecular mixtures of C2F6 in CF4 and CF4 in C2F6  

NASA Astrophysics Data System (ADS)

We have measured IR absorption spectra of solutions C2F6 in CF4 ( T = 178 K) and CF4 in C2F6 ( T = 173 K) in the overtone range of the spectrum. We have studied how the resonance dipole-dipole interaction affects the formation of contours of bands that correspond to transitions to states involving the vibrations ?10(C2F6) and ?3(CF4), which are strong in the dipole absorption. For the system C2F6 in liquid CF4, the state ?2 + ?10(C2F6) resonantly interacts with the state ?2(C2F6) + ?3(CF4), and, for the system CF4 in liquid C2F6, the state ?1 + ?3(CF4) resonantly interacts with the state ?1(CF4) + ?10(C2F6). The contours of the bands ?2 + ?10 (C2F6) in the spectrum of the mixture with CF4 and of the bands ?1 + ?3(CF4) in the spectrum of the mixture with C2F6 have been calculated.

Golubkova, O. S.; Bocharov, V. N.; Kolomiitsova, T. D.; Shchepkin, D. N.

2013-05-01

51

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

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.

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

2012-01-01

52

Dipole-Dipole Induced Forces in the Reaction of Alkali Metal Atoms with Polar Molecules,  

National Technical Information Service (NTIS)

The title reaction is shown to be dominated by a relatively large dipole-dipole induced interaction at distances of 4-5 Angstroms. The cone of nonreaction and orientation dependence of the reactive scattering cross section are estimated from this potentia...

Y. R. Luo S. W. Benson

1988-01-01

53

Intermolecular interaction in water hexamer.  

PubMed

The origin of the intermolecular interaction, especially the many-body interaction, in eight low-lying water hexamer structures (prism, cage, book-1, book-2, cyclic-chair, bag, cyclic-boat-1, and cyclic-boat-2) is unraveled using the localized molecular orbital energy decomposition analysis (LMO-EDA) method at the second-order Møller-Plesset perturbation (MP2) level of theory with a large basis set. It is found that the relative stabilities of these hexamer structures are determined by delicate balances between different types of interaction. According to LMO-EDA, electrostatic and exchange interactions are strictly pairwise additive. Dispersion interaction in these water hexamer structures is almost pairwise additive, with many-body effects varying from -0.13 to +0.05 kcal/mol. Repulsion interaction is roughly pairwise additive, with many-body effects varying from -0.84 to -0.62 kcal/mol. Polarization interaction is not pairwise additive, with many-body effects varying from -13.10 to -8.85 kcal/mol. PMID:20932059

Chen, Yiming; Li, Hui

2010-11-01

54

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

Microsoft Academic Search

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

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

2008-01-01

55

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

NASA Astrophysics Data System (ADS)

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

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

2013-08-01

56

Dipole-dipole broadening of Rb ns-np microwave transitions  

SciTech Connect

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

Park, Hyunwook; Tanner, P. J.; Claessens, B. J.; Shuman, E. S.; Gallagher, T. F. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904-0714 (United States)

2011-08-15

57

Morphological changes from silica tubules to hollow spheres controlled by the intermolecular interactions within block copolymer micelle templates.  

PubMed

The morphological changes from tubules to large hollow spheres to (micelle-sized) small hollow-spherical silica were realized by polystyrene-block-poly(vinylpyridine) (PS-b-PVP) block copolymer micelle templates by controlling the intermolecular interactions with the corona chains. PS-b-PVP with weak intermolecular interactions among PVP corona chains yields the coexistence of tubules, large hollow spheres, and small hollow spheres. The coexistence of the three phases arises from the direct aggregation of block copolymer micelles during hydrolytic condensation of a silica precursor (tetraethylorthosilicate), as evidenced by transmission electron microscopy. When the degree of intermolecular interactions within the PVP corona blocks is increased by a change in either the degree of quaternization of the PVP blocks or the dielectric constant of the medium, small hollow spherical silica, with size equivalent to the block copolymer micelles, were solely obtained. We believe that this morphological change is due to the fact that the dipole-dipole interactions among quaternized PVP blocks physically cross-link the PVP coronas in micelles resisting the curvature change during the silica condensation. PMID:20356017

Lee, Hyemin; Char, Kookheon

2009-04-01

58

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

SciTech Connect

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

Salam, A. [Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486 (United States)

2006-01-07

59

IRIS: Intermolecular RNA Interaction Search  

Microsoft Academic Search

Here we present IRIS, a method for prediction of RNA-RNA interactions that is based on dy- namic programming and extends current RNA secondary structure prediction approaches. Using this method we have found a number of interesting reflnements to the structures of RNA-RNA complexes that have been studied previously and predicted novel targets for several known reg- ulatory RNAs in E.

Dmitri D. Pervouchine

2004-01-01

60

Visualizing Intermolecular Interactions in T Cells  

PubMed Central

The use of appropriate fluorescent proteins has allowed the use of FRET microscopy for investigation of intermolecular interactions in living cells. This method has the advantage of both being dynamic and of working at the subcellular level, so that the time and place where proteins interact can be visualized. We have used FRET microscopy to analyze the interactions between the T cell antigen receptor and the coreceptors CD4 and CD8. This chapter reviews data on how these coreceptors are recruited to the immunological synapse, and how they interact when the T cell is stimulated by different ligands.

Gascoigne, Nicholas R.J.; Ampudia, Jeanette; Clamme, Jean-Pierre; Fu, Guo; Lotz, Carina; Mallaun, Michel; Niederberger, Nathalie; Palmer, Ed; Rybakin, Vasily; Yachi, Pia P.; Zal, Tomasz

2011-01-01

61

QCD saturation equations including dipole-dipole correlations  

SciTech Connect

We derive two coupled nonlinear evolution equations corresponding to the truncation of the Balitsky infinite hierarchy of saturation equations after inclusion of dipole-dipole correlations, i.e., one step beyond the Balitsky-Kovchegov (BK) equation. We exhibit an exact solution for maximal correlation which still satisfies the same asymptotic geometric scaling as BK but with the S matrix going to 1/2 (instead of zero) in the full saturation region.

Janik, Romuald A.; Peschanski, R. [Institute of Physics, Jagellonian University, Reymonta 4, 30-059 Cracow (Poland); Service de Physique Theorique, CEA/Saclay, 91191 Gif-sur-Yvette cedex (France)

2004-11-01

62

Intermolecular Forces (Netorials)  

NSDL National Science Digital Library

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

63

Intermolecular interactions in the presence of an intense radiation field  

Microsoft Academic Search

It is well known that the R-6 dependence of the dispersion interaction is modified to R-7 at large intermolecular separations where retardation effects play an important role. In this paper, the theory of intermolecular interactions between two non-polar molecules in the presence of an external radiation field is given and a general expression for the interaction energy is obtained. The

T. Thirunamachandran

1980-01-01

64

Nuclear spin relaxation and intermolecular interactions  

Microsoft Academic Search

In order to specify what kind of information about intermolecular interactio~ls can be obtained by nuclear spin relaxation, we consider a suitable microscopic representation of a liquid. For reasons which will become clear below, this article is entirely confined to the treatment of the liquid phase. The molecular or microscopic picture of a liquid may be considered to be a

H G Hertz; A Kratochwill; H Weingärtner

1985-01-01

65

The influence of intermolecular interactions in n-pentane-alkane-1-ol systems on their physicochemical properties  

Microsoft Academic Search

The Helmholtz energy of dipole-dipole interaction (SigmaDeltad F) and its long-range (Deltad F°) and short-range (Deltad F*) components were calculated for n-pentane-alkane-1-ol (from methanol to dodecane-1-ol) systems at 298.15 K using the Winkelmann statistical model theory of liquid dielectrics. It was shown that the longer the alkane-1-ol hydrocarbon radical, the greater the extent to which the properties of the systems

E. D. Totchasov; G. A. Al'Per

2008-01-01

66

Quantum discord in spin systems with dipole-dipole interaction  

NASA Astrophysics Data System (ADS)

The behavior of total quantum correlations (discord) in dimers consisting of dipolar-coupled spins 1/2 are studied. We found that the discord Q=0 at absolute zero temperature. As the temperature T increases, the quantum correlations in the system increase at first from zero to its maximum and then decrease to zero according to the asymptotic law T^{-2}. It is also shown that in absence of external magnetic field B, the classical correlations C at T?0 are, vice versa, maximal. Our calculations predict that in crystalline gypsum {CaSO}4\\cdot {2H}2{{O}} the value of natural (B=0) quantum discord between nuclear spins of hydrogen atoms is maximal at the temperature of 0.644 \\upmu ClC-{CH}2{{Cl}} the discord achieves the largest value at T=0.517 \\upmu K. In both cases, the discord equals Q? 0.083 bit/dimer what is 8.3 % of its upper limit in two-qubit systems. We estimate also that for gypsum at room temperature Q˜ 10^{-18} bit/dimer, and for 1,2-dichloroethane at T=90 K the discord is Q˜ 10^{-17} bit per a dimer.

Kuznetsova, E. I.; Yurischev, M. A.

2013-08-01

67

Solute-solvent interactions probed by intermolecular NOEs.  

PubMed

Nuclear Overhauser effects arising from the interactions of spins of solvent molecules with spins of a solute should reveal the "exposure" of solute spins to collisions with solvent. Such intermolecular NOEs could, therefore, provide information regarding conformation or structure of the solute. Determinations of solute-solvent NOEs of 1,3-di-tert-butylbenzene in solvents composed of perfluoro-tert-butyl alcohol, tetramethylsilane, and carbon tetrachloride have been carried out. A crude, but apparently reliable, method for prediction of intermolecular solvent-solute NOEs based on hard (noninteracting) spheres was developed. Comparison of experimental to predicted NOEs indicates that tetramethylsilane interacts with the solute according to the model. By contrast, intermolecular NOE data indicate attractive interactions between the solute and perfluoro-tert-butyl alcohol. All NOE results and the corresponding predictions confirm that proton H2 of the solute is protected by the flanking tert-butyl groups from interactions with solvent molecules. PMID:12816484

Gerig, J T

2003-06-27

68

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

NASA Astrophysics Data System (ADS)

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.

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

1998-07-01

69

Learning about Intermolecular Interactions from the Cambridge Structural Database  

ERIC Educational Resources Information Center

|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…

Battle, Gary M.; Allen, Frank H.

2012-01-01

70

Qualitative change of character of dispersive interaction with intermolecular distance.  

PubMed

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

Haslmayr, Johannes; Renger, Thomas

2013-07-28

71

Qualitative change of character of dispersive interaction with intermolecular distance  

NASA Astrophysics Data System (ADS)

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

Haslmayr, Johannes; Renger, Thomas

2013-07-01

72

Interpretation of the dipole-dipole electrical-resistivity survey, Tuscarora Geothermal Area, Elko County, Nevada  

SciTech Connect

Interpretation of Tuscarora geothermal area model results has suggested that low resistivity zones on two dipole-dipole lines and possibly a third are related to thermal fluids. These two-dimensional models have delineated what appear to be aquifers within the valley sediments and the Tertiary volcanics. Structural breaks noted at the surface by geologic mapping are also evident in the interpretive models. The area southeast of the hot springs in Hot Creek is poorly delineated by the current dipole-dipole coverage, yet this appears to be the most promising prospect area based upon the available data coverage. Exploratory drilling is currently moving in this direction. Perhaps additional dipole-dipole lines could aid in the selection of future drill sites.

Mackelprang, C.E.

1982-02-01

73

The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues  

SciTech Connect

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

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

2002-05-01

74

Tuning intermolecular non-covalent interactions for nanowires of organic semiconductors  

NASA Astrophysics Data System (ADS)

Anthracene and its derivatives are used to demonstrate a simple way to cast assemble nanowires of organic semiconductors with tuning of intermolecular non-covalent interactions by molecular design. The tuning of intermolecular interactions could be achieved by (i) decreasing intermolecular hydrophobic interactions by linking hydrophilic side chains to anthracene rings, (ii) increasing intermolecular interaction for self-assembly with the assistance of hydrogen bonds, and (iii) enhancing molecular ?-? interaction by increasing the conjugated dimension of the compounds.

Jiang, Lang; Gao, Jianhua; Fu, Yanyan; Dong, Huanli; Zhao, Huaping; Li, Hongxiang; Tang, Qingxin; Chen, Keqiu; Hu, Wenping

2010-12-01

75

Strong intermolecular interactions shaping a small piano-stool complex.  

PubMed

The smallest piano stool [CpNa(NH3 )3 ] is not a stand-alone unit in the solid state but is largely shaped by strong intermolecular N?H???? interactions. Small but important structural features, such as the bending of the C?H bonds inwards to the sodium atom that was confirmed by experimental charge density investigations, could only be reproduced by quantum mechanical calculations that included a lattice of more than 300 units. PMID:23929586

Hey, Jakob; Andrada, Diego M; Michel, Reent; Mata, Ricardo A; Stalke, Dietmar

2013-08-08

76

Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment  

PubMed Central

Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing 15N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity.

Liu, Yizhou; Prestegard, James H.

2008-01-01

77

The influence of intermolecular interactions in n -pentane-alkane-1-ol systems on their physicochemical properties  

Microsoft Academic Search

The Helmholtz energy of dipole-dipole interaction (??d\\u000a F) and its long-range (?d\\u000a F°) and short-range (?d\\u000a F*) components were calculated for n-pentane-alkane-1-ol (from methanol to dodecane-1-ol) systems at 298.15 K using the Winkelmann statistical model theory of\\u000a liquid dielectrics. It was shown that the longer the alkane-1-ol hydrocarbon radical, the greater the extent to which the\\u000a properties of the systems

E. D. Totchasov; G. A. Al’per

2008-01-01

78

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

SciTech Connect

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

Park, Hyunwook; Shuman, E. S.; Gallagher, T. F. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904-0714 (United States)

2011-11-15

79

Intermolecular interactions and the thermodynamic properties of supercritical fluids  

NASA Astrophysics Data System (ADS)

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.

Yigzawe, Tesfaye M.; Sadus, Richard J.

2013-05-01

80

Intermolecular interactions and the thermodynamic properties of supercritical fluids.  

PubMed

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

Yigzawe, Tesfaye M; Sadus, Richard J

2013-05-21

81

Weak intermolecular interactions in gas-phase nuclear magnetic resonance.  

PubMed

Gas-phase nuclear magnetic resonance (NMR) spectra demonstrating the effect of weak intermolecular forces on the NMR shielding constants of the interacting species are reported. We analyse the interaction of the molecular hydrogen isotopomers with He, Ne, and Ar, and the interaction in the He-CO(2) dimer. The same effects are studied for all these systems in the ab initio calculations. The comparison of the experimental and computed shielding constants is shown to depend strongly on the treatment of the bulk susceptibility effects, which determine in practice the pressure dependence of the experimental values. Best agreement of the results is obtained when the bulk susceptibility correction in rare gas solvents is evaluated from the analysis of the He-rare gas interactions, and when the shielding of deuterium in D(2)-rare gas systems is considered. PMID:21895188

Garbacz, Piotr; Piszczatowski, Konrad; Jackowski, Karol; Moszynski, Robert; Jaszu?ski, Micha?

2011-08-28

82

Characterizing intermolecular interactions that initiate native-like protein aggregation.  

PubMed

Folded proteins can access aggregation-prone states without the need for transitions that cross the energy barriers for unfolding. In this study we characterized the initial steps of aggregation from a native-like state of the acylphosphatase from Sulfolobus solfataricus (Sso AcP). Using computer simulations restrained by experimental hydrogen/deuterium (H/D) exchange data, we provide direct evidence that under aggregation-promoting conditions Sso AcP populates a conformational ensemble in which native-like structure is retained throughout the sequence in the absence of local unfolding (N?), although the protein exhibits an increase in hydrodynamic radius and dynamics. This transition leads an edge strand to experience an increased affinity for a specific unfolded segment of the protein. Direct measurements by means of H/D exchange rates, isothermal titration calorimetry, and intermolecular relaxation enhancements show that after formation of N?, an intermolecular interaction with an antiparallel arrangement is established between the edge strand and the unfolded segment of the protein. However, under conditions that favor the fully native state of Sso AcP, such an interaction is not established. Thus, these results reveal a novel (to our knowledge) self-assembly mechanism for a folded protein that is based on the increased flexibility of highly aggregation-prone segments in the absence of local unfolding. PMID:22713575

Bemporad, Francesco; De Simone, Alfonso; Chiti, Fabrizio; Dobson, Christopher M

2012-06-05

83

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

ERIC Educational Resources Information Center

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…

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

2008-01-01

84

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

PubMed Central

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.

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

2002-01-01

85

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

SciTech Connect

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

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

1984-04-01

86

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

PubMed

We reveal quite small but different intermolecular valence band dispersions of sub-100-meV scale in crystalline films of Zn and Mn phthalocyanine (ZnPc and MnPc) and fluorinated ZnPc (F_{16}ZnPc). The intermolecular transfer integrals are found to be reasonably dependent on the intermolecular distance with the 75±5??meV/Å relation. Furthermore, the angle-resolved photoemission spectra show anomalous dispersive behaviors such as phase flips and local-dimerization-derived periodicities, which originate from the site-specific intermolecular interaction induced by substituents. PMID:24010459

Yamane, Hiroyuki; Kosugi, Nobuhiro

2013-08-21

87

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

NASA Astrophysics Data System (ADS)

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

Yamane, Hiroyuki; Kosugi, Nobuhiro

2013-08-01

88

Determining the parameters of the potential of intermolecular interaction by the Zeno line  

NASA Astrophysics Data System (ADS)

The method of determination of intermolecular interaction potential parameters by the Zeno line is proposed. The intermolecular interaction of ethane, propane, ethylene, and propylene is described using a model of site-site interactions and Karr-Konowalow potential. It is shown that the parameters of intermolecular interaction for this potential can be determined from a small number of experimental data in the single-phase area. It is noted that the final parameters allow us to describe the thermodynamic properties over a broad range of gas and liquid states with precision acceptable for practical use.

Anashkin, I. P.; Klinov, A. V.

2013-11-01

89

Interpretation of dipole-dipole resistivity monitoring data at Cerro Prieto  

SciTech Connect

Repetitive dipole-dipole resistivity data have been taken on a yearly basis at Cerro Prieto since 1978. Stations along a single profile line extending from the Cucapa Mountains to the center of the Mexicali Valley and passing over the present production zone have been remeasured with sufficient accuracy to detect subsurface changes in resistivity, some of which are probably related to fluid production. The precision of the most recent measurements (November 1981) averages about 1%. Results from two and one-half years of monitoring indicate a 5% annual increase in apparent resistivity over the present production area and decreases in apparent resistivity of the same magnitude in the regions immediately eastward and westward from the production zone.

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

1982-10-01

90

Measurement of dipole-dipole cross-correlated relaxation in fast rotating CH2D groups  

NASA Astrophysics Data System (ADS)

Studies of protein dynamics are key to understanding their biological function. NMR relaxation studies of proteins to date have focused primarily on characterizing backbone dynamics. In this paper, we focus on the aliphatic side-chains (Ala, Thr, Val, Leu, and Ile) with the goal of deriving dynamical information on the motion of terminal methyl groups. Dipole-dipole cross-correlated cross-relaxation is analyzed in a fast rotating CH2D group, as found in partially deuteriated proteins. In comparison with previous studies on AMX spin systems (methylene C?H2 groups), the fast rotation of the methyl group makes a number of relaxation pathways efficient, through the coherence C+H1+H2-+C+H1-H 2+. Several pulse schemes were designed to evaluate these relaxation rates: the measured values are small and well predicted by taking into account the complete relaxation network, but they remain strongly influenced by 1H-1H relaxation with all protons in the neighborhood of the CH2D moiety. The prospects and limitations of this method are discussed in comparison with 2H relaxation measurements. Part of this work was carried out at the Departments of Medical Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ont., Canada M5S 1A8.

Marion, Dominique

2004-02-01

91

Electron Dipole-Dipole ESEEM in Field-Step ELDOR of Nitroxide Biradicals  

NASA Astrophysics Data System (ADS)

The use of a rapid stepping of the magnetic field for investigation of electron dipole-dipole ESEEM in pulsed X-band ELDOR is described. The magnetic field jump, synchronized with a microwave pumping pulse, is positioned between the second and the third pulses of the stimulated echo pulse sequence. This echo is measured as a function of the delay between the first and the second pulses. The data are analyzed for a Fourier transform resulting in a Pake resonance pattern. To remove the electron-nuclear contributions to ESEEM, time traces with pumping were divided by those without. This resulted in complete elimination of electron-nuclear contributions, which is seen from the absence of peaks at nuclear frequencies and the similarity of results for protonated and deuterated solvents. For increasing the electron-electron modulation depth, a scanning of the magnetic field during the microwave pumping is proposed. The interspin distances and their distribution are determined for two long-chained (ca. 2 nm) nitroxide biradicals in glassy toluene and in frozen nematic liquid crystal 4-cyano-4'-pentyl-biphenyl. For the latter solvent, the alignment of the axis connecting two nitroxides in biradicals is quantitatively analyzed.

Kulik, L. V.; Grishin, Yu. A.; Dzuba, S. A.; Grigoryev, I. A.; Klyatskaya, S. V.; Vasilevsky, S. F.; Tsvetkov, Yu. D.

2002-07-01

92

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

SciTech Connect

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

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

2008-10-01

93

Problem-Based Learning in 9th Grade Chemistry Class: ‘Intermolecular Forces’  

Microsoft Academic Search

This research study aims to examine the effectiveness of a problem-based learning (PBL) on 9th grade students’ understanding\\u000a of intermolecular forces (dipole–dipole forces, London dispersion forces and hydrogen bonding). The student’s alternate conceptions\\u000a about intermolecular bonding and their beliefs about PBL were also measured. Seventy-eight 9th grade students were stratified\\u000a by cognitive levels and then randomly assigned to experimental (PBL,

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

2008-01-01

94

Combined Electrostatics and Hydrogen Bonding Determine PIP2 Intermolecular Interactions  

PubMed Central

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

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

2010-01-01

95

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

SciTech Connect

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

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

2012-04-28

96

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

PubMed Central

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

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

2013-01-01

97

Intermolecular interactions of the malate synthase of Paracoccidioides spp  

PubMed Central

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.

2013-01-01

98

Laser induced phonons: A probe of intermolecular interactions in molecular solids  

Microsoft Academic Search

A new type of density dependent spectroscopy is developed and applied to the study of acoustics phonons and excited state–phonon interactions in molecular crystals. It is shown that intermolecular separations in solids can be varied in a controlled manner along a selected crystalline direction and that the consequences of the molecular displacements can be observed optically in time-resolved transient grating,

Keith A. Nelson; M. D. Fayersl

1980-01-01

99

Laser induced phonons: A probe of intermolecular interactions in molecular solids  

Microsoft Academic Search

A new type of density dependent spectroscopy is developed and applied to the study of acoustics phonons and excited state-phonon interactions in molecular crystals. It is shown that intermolecular separations in solids can be varied in a controlled manner along a selected crystalline direction and that the consequences of the molecular displacements can be observed optically in time-resolved transient grating,

Keith A. Nelson; M. D. Fayer

1980-01-01

100

Influence of intermolecular interaction on kinetics of conformational transitions in poly-m-phenyleneisophthalamide  

Microsoft Academic Search

UDC 535.33 It is known that the character and energy of intermolecular interaction (IMI) can appreciably influence the physicomechanical characteristics~ the phase transition temperature, and other properties of the polymers. The role of IMI is especially marked in the solid or in the blocklike state of the polymer. All the polymers can be conditionally divided into three groups according to

P. M. Pakhomov; I. I. Novak; Mo V. Shablygin; V. E. Korsukov

1985-01-01

101

Studies on the Intermolecular Potential and its Anisotropy.  

NASA Astrophysics Data System (ADS)

Nuclear spin-lattice relaxation times (T _1) have been measured for ^ {19}F in the SeF_6 and TeF_6 molecules. These measurements have been made in the pure gases SeF_6 and TeF_6 and with each of these pure gases in various buffer gases. Buffer gases include Xe, Kr, Ar, CH_4, CF_4 , N_2, CO, CO_2 , HCl, SF_6, and O _2. It has been found that except for SeF _6 in O_2 and TeF_6 in O_2 , all of the probe-buffer systems (probe = SeF _6 or TeF_6) studied relax via the spin rotation relaxation mechanism. Relaxation times were measured as a function of temperature and density. In the case of oxygen gas as a buffer, there were two dominant mechanisms for spin relaxation: spin rotation (intramolecular) and nuclear spin electron spin dipole-dipole interaction (intermolecular). The semiclassical and classical theories of nuclear spin relaxation by Gordon related these results to cross sections for the transfer of rotational angular momentum. These cross sections include both changes in molecular reorientation as well as the effects of rotational inelasticity (changes in the magnitude of the J vector) and have been determined for all of the collision pairs mentioned above. The intermolecular interactions which cause these changes in the rotational angular momentum are due to the anisotropy of intermolecular forces which depend on the relative orientation of the colliding pair. Collision efficiencies obtained from these cross sections increase with increasing polarizability of the buffer gas, indicating sensitivity to dispersion forces. The temperature dependence of the relaxation times (T_1) have been determined by this study and hence, the temperature dependence of the cross sections for each collision pair. The cross sections obtained from the spin relaxation studies are given as experimental data which may be used with other observables to construct potential energy surfaces for the collisional pairs studied.

Terry, Ronald Julius

102

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

SciTech Connect

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

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

1981-01-01

103

Probing Intermolecular Interaction through Thermal-Lens Spectroscopy  

PubMed Central

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

Bhattacharyya, Indrajit; Kumar, Pardeep; Goswami, Debabrata

2013-01-01

104

Robust NMR approaches for the determination of homonuclear dipole-dipole coupling constants in studies of solid materials and biomolecules.  

PubMed

This review addresses the NMR spectroscopy study of molecular structure and dynamics by way of homonuclear dipole-dipole couplings by relying on their orientation and direct distance dependence. The study of homonuclear couplings as opposed to heteronuclear couplings poses specific challenges. On the one hand, two like spins cannot be independently manipulated easily, which means that simple shift-refocusing concepts by using hard ? pulses cannot be used to cope with potentially large chemical-shift dispersions at the high fields used today. On the other hand, the noncommutativity of the different pair Hamiltonians in a multispin system leads to complications associated with the isolation of specific pair couplings while minimizing the influence of the other spins. In particular, the so-called dipolar-truncation effect challenges the observation of weak couplings of interest in the presence of stronger ones. Recent advances in determining homonuclear dipole-dipole coupling constants are reviewed, stressing the use of double-quantum spectroscopy approaches and their similarity to the popular heteronuclear rotational-echo double-resonance experiment. Particular emphasis is put on corrections for the influence of transverse relaxation effects on the measured data, and the handling of distribution effects as well as potential dynamic heterogeneities in complex substances. PMID:23754803

Saalwächter, Kay

2013-06-10

105

Avoiding bias effects in NMR experiments for heteronuclear dipole-dipole coupling determinations: principles and application to organic semiconductor materials.  

PubMed

Carbon-proton dipole-dipole couplings between bonded atoms represent a popular probe of molecular dynamics in soft materials or biomolecules. Their site-resolved determination, for example, by using the popular DIPSHIFT experiment, can be challenged by spectral overlap with nonbonded carbon atoms. The problem can be solved by using very short cross-polarization (CP) contact times, however, the measured modulation curves then deviate strongly from the theoretically predicted shape, which is caused by the dependence of the CP efficiency on the orientation of the CH vector, leading to an anisotropic magnetization distribution even for isotropic samples. Herein, we present a detailed demonstration and explanation of this problem, as well as providing a solution. We combine DIPSHIFT experiments with the rotor-directed exchange of orientations (RODEO) method, and modifications of it, to redistribute the magnetization and obtain undistorted modulation curves. Our strategy is general in that it can also be applied to other types of experiments for heteronuclear dipole-dipole coupling determinations that rely on dipolar polarization transfer. It is demonstrated with perylene-bisimide-based organic semiconductor materials, as an example, in which measurements of dynamic order parameters reveal correlations of the molecular dynamics with the phase structure and functional properties. PMID:23780575

Kurz, Ricardo; Cobo, Marcio Fernando; Ribeiro de Azevedo, Eduardo; Sommer, Michael; Wicklein, André; Thelakkat, Mukundan; Hempel, Günter; Saalwächter, Kay

2013-06-18

106

Statistical Analysis of Cluster Structures Formed by Dipole-Dipole Interactions  

NASA Astrophysics Data System (ADS)

We developed a statistical model of the cluster formation of ferromagnetic particles and analysed the cluster structures. We investigated the effect of the control parameter ?, that is, the ratio of magnetic dipole moment energy to thermal energy, and external magnetic fields on the fractal dimensions of three-dimensional ferromagnetic clusters. We found that the fractal dimension of clusters, D, changes from 5/3 to 2 as ? increases in the absence of a magnetic field. We also found that when clusters are subjected to a magnetic field, the fractal dimension decreases and the transition region from high fractal dimension to D=1 becomes shorter as ? increases.

Morimoto, Hisao; Maekawa, Toru

107

Effect of ``Electronic Shielding'' on the Dipole-Dipole Interaction in Rochelle Salt  

Microsoft Academic Search

The various parameters appearing in Mitui's theory should be mutually related or confined in certain ranges in order to make the theory agree with the experimental result for Rochelle salt. A trial was made to examine whether these relations or limitations are actually satisfied for the real crystal structure of Rochelle salt. The examination shows that the Mitui's conditions could

Ryuji Abe; Michiko Matsuda

1973-01-01

108

Confinement effects on dipole-dipole interactions in nanofluids: The role of equilibrium fluctuations  

NASA Astrophysics Data System (ADS)

When spin bearing molecules are enclosed in an elongated nanovoid, and each molecule diffuses across the whole volume in times much shorter than the characteristic times of NMR spin dynamics, a time independent average dipolar Hamiltonian emerges which couples the spins in each molecule equally with the spins in any other molecule. Baugh et al. [Science, 134, 1505 (2001)] have observed the remarkable orientation dependent linewidth in such a situation, and offered a convincing interpretation using the techniques of solid state NMR. In the present paper I show that, contrary to previous expectations, the same linewidth can be predicted with liquid NMR techniques, provided that one takes into account equilibrium fluctuations in the estimation of the dipolar field.

Jeener, J.

2011-03-01

109

Extraordinary superatom containing double shell nucleus: Li(HF)3Li connected mainly by intermolecular interactions  

Microsoft Academic Search

The structure and properties of the Li(HF)3Li cluster with C3h symmetry are investigated using ab initio calculations. This Li(HF)3Li is a metal-nonmetal-metal sandwich-like cluster connected mainly by the intermolecular interactions. In the special cluster, the (HF)3 containing the triangular F ring with the negative charges is sandwiched between two Li atom. It is interesting that under the action of the

Xiao-Ying Sun; Zhi-Ru Li; Di Wu; Chia-Chung Sun

2007-01-01

110

Experimental Charge Densities and Intermolecular Interactions:  Electrostatic and Topological Analysis of dl Histidine  

Microsoft Academic Search

A high-resolution, low-temperature X-ray diffraction data set on DL-histidine, collected with a CCD detector, is used in the analysis of molecular bonding and intermolecular interactions. The molecular dipole moment in the crystal is enhanced relative to that from HF and DFT calculations. Topological properties of the molecular electron density differ from theory for the polar bonds but generally agree well

Philip Coppens; Yuriy Abramov; Michael Carducci; Boris Korjov; Irina Novozhilova; Cristobal Alhambra; Mark R. Pressprich

1999-01-01

111

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

NASA Astrophysics Data System (ADS)

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.

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

2005-01-01

112

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

PubMed

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. PMID:15638652

Cybulski, S?awomir M; Seversen, Christopher E

2005-01-01

113

The formation of strong intermolecular interactions in immiscible blends of poly(vinyl alcohol) (PVA) and lignin.  

PubMed

The intermolecular interactions of lignin with a hydrophilic polymer, poly(vinyl alcohol) (PVA), were studied using thermal analyses and FT-IR spectroscopy of a series of PVA/hardwood kraft lignin blend fibers prepared by thermal extrusion. Although two phases are observed in this blend system, some of the lignin was closely associated with the PVA in the PVA-rich phase. The crystallinity of the PVA fraction was reduced with increasing lignin content. An interaction energy density of -9.34 cal cm(-1), calculated from melting point depression data, suggests that strong intermolecular interactions exist between PVA and lignin. FT-IR analysis indicates the formation of strong intermolecular hydrogen bonds between the hydroxyl groups of PVA and lignin. Although the PVA/lignin blend system is immiscible in the bulk, the results herein show the existence of some specific intermolecular interaction between PVA and lignin. PMID:12741770

Kubo, Satoshi; Kadla, John F

114

Phase transition in GeF2 driven by change of type of intermolecular interaction  

NASA Astrophysics Data System (ADS)

A first-order phase transition from the low-temperature P212121 (?) phase to the high-temperature Pnma (?) phase of the GeF2 crystal is studied experimentally and theoretically. GeF2 consists of covalently bonded chains, which arrange to the three-dimensional crystal due to noncovalent intermolecular forces. In addition to relatively strong electrostatic and van der Waals interactions, the ? phase features anisotropic “electrostatic bonds” (reminiscent of hydrogen bonds). During the phase transition these electrostatic bonds melt, which causes expansion of the lattice, driven by excess exchange repulsion, until compensated by the remaining interchain interactions.

Usvyat, Denis; Yin, Congling; Wälz, Gero; Mühle, Claus; Schütz, Martin; Jansen, Martin

2012-08-01

115

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

SciTech Connect

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.

Chou, Chiate.

1990-01-01

116

Long-range interactions between polar alkali-metal diatoms in external electric fields  

NASA Astrophysics Data System (ADS)

We computed the long-range interactions between two identical polar bialkali molecules in their rovibronic ground level for all ten species involving Li, Na, K, Rb, and Cs, using accurate quantum chemistry results combined with available spectroscopic data. A huge van der Waals interaction is found for eight species in free space. The competition of the van der Waals interaction with the dipole-dipole interaction induced by an external electric field parallel or perpendicular to the intermolecular axis is investigated by varying the electric-field magnitude and the intermolecular distance. Our calculations predict a regime with the mutual orientation of the two molecules but with no preferential direction in the laboratory frame. A mechanism for the stimulated one-photon radiative association of a pair of ultracold polar molecules into ultracold tetramers is proposed, which would open the way towards the optical manipulation of ultracold polyatomic molecules.

Lepers, M.; Vexiau, R.; Aymar, M.; Bouloufa-Maafa, N.; Dulieu, O.

2013-09-01

117

Drug-polymer intermolecular interactions in hot-melt extruded solid dispersions.  

PubMed

The purpose of the study was to investigate and identify the interactions within solid dispersions of cationic drugs and anionic polymers processed by hot-melt extrusion (HME) technique. Propranolol HCl (PRP) and diphenhydramine HCl (DPD) were used as model cationic active substances while pH sensitive anionic methacrylic acid based methyl methacrylate copolymers Eudragit L100 (L100) and ethyl acrylate copolymer Eudragit L100-55 (Acryl EZE) (L100-55) were used as polymeric carriers. The extrudates were further characterised using various physicochemical characterisation techniques to determine the morphology, the drug state within the polymer matrices and the type of drug-polymer interactions. Molecular modelling predicted the existence of two possible H-bonding types while the X-ray photon spectroscopy (XPS) advanced surface analysis of the extrudates revealed intermolecular ionic interactions between the API amino functional groups and the polymer carboxylic groups through the formation of hydrogen bonding. The magnitude of the intermolecular interactions varied according to the drug-polymer miscibility. PMID:23262428

Maniruzzaman, Mohammed; Morgan, David J; Mendham, Andrew P; Pang, Jiayun; Snowden, Martin J; Douroumis, Dennis

2012-12-20

118

Intermolecular interactions in staphylokinase-plasmin(ogen) bimolecular complex: function of His43 and Tyr44.  

PubMed

Staphylokinase (SAK) forms a 1:1 stoichiometric complex with human plasmin (Pm) and switches its substrate specificity to generate a plasminogen (Pg) activator complex. Site-directed mutagenesis of SAKHis43 and SAKTyr44 demonstrated the crucial requirement of a positively charged and an aromatic residue, respectively, at these positions for optimal functioning of SAK-Pm activator complex. Molecular modeling studies further revealed the role of these residues in making cation-pi and pi-pi interactions with Trp215 of Pm and thus establishing the crucial intermolecular contacts within the active site cleft of the activator complex for the cofactor activity of SAK. PMID:21510941

Dahiya, Monika; Singh, Satish; Rajamohan, Govindan; Sethi, Deepti; Ashish; Dikshit, Kanak L

2011-04-16

119

Laser induced phonons: A probe of intermolecular interactions in molecular solids  

NASA Astrophysics Data System (ADS)

A new type of density dependent spectroscopy is developed and applied to the study of acoustics phonons and excited state-phonon interactions in molecular crystals. It is shown that intermolecular separations in solids can be varied in a controlled manner along a selected crystalline direction and that the consequences of the molecular displacements can be observed optically in time-resolved transient grating, absorption, and fluorescence experiments. The technique involves the generation of specific acoustic waves (phonon modes of definite wave vector) by transient grating optical excitation of the sample. The resulting time-dependent density changes cause time-varying spectral shifts, the magnitude of which are dependent on the detailed nature of the anisotropic intermolecular interactions in the crystal, e.g., anisotropic van der Waals interactions in molecular crystals can be directly investigated. First a formalism is presented which permits the determination of the nature of the phonons produced (longitudinal, quasilongitudinal, or quasitransverse) by transient grating excitation in anisotropic crystals. Next, the effect of the transient grating generated phonons on experimental observables (absorption, fluorescence, and transient grating) due to anisotropic spectral shifts is obtained. Model calculations illustrate the results. Finally experimental data for the perylene pure crystal excimer system and the pentacene in p-terphenyl mixed system are presented. In the perylene system, the various types of phonons predicted by theory are observed and phonon dispersions are obtained for several crystal directions. In pentacene in p-terphenyl, the theoretically predicted phonon-induced spectral shifts are clearly observed.

Nelson, Keith A.; Fayer, M. D.

1980-05-01

120

Quantitative characterization of intermolecular dipolar interactions of two-component systems in solution nuclear magnetic resonance  

NASA Astrophysics Data System (ADS)

Liquid nuclear magnetic resonance behaviors related to intermolecular dipolar interactions were investigated theoretically and experimentally in highly polarized two-component spin systems. A modified CRAZED pulse sequence was designed to investigate relative signal intensities with considerations of spin transverse relaxation, longitudinal relaxation, molecular diffusion, and optimal radio-frequency flip angles. The dissipation of the demagnetizing field due to relaxation and diffusion processes during the detection period was taken into account as well. For the first time, vigorous analytical expressions of the spin dynamics, including all the effects mentioned above, were derived from the combination of the demagnetizing field model and product operator formalism. In the regime where the linear approximation (??0M0t<<1) is valid, these explicit analytical expressions can quantitatively describe the signal behaviors related to intermolecular dipolar interactions. All the theoretical predictions based on the analytical expressions for the directly excited component are in excellent agreement with experimental observations reported previously. Several valuable insights for the indirectly excited component were gained from the analytical expressions and verified by experimental measurements, including optimal radio-frequency flip angles, unusual relative signal intensities for n=-2 and n=2, and unconventional diffusion and multi-exponential longitudinal relaxation processes, where n is the ratio of the coherence-selection gradient areas in the CRAZED pulse sequence. In addition, n-order diffusion coefficients of the directly and indirectly excited spins during the evolution period predicted by the demagnetizing field picture are found to be the same as those obtained with the combination of the intermolecular multiple-quantum picture and Gaussian phase distribution approximation which is valid in the case of unrestricted isotropic diffusion. These results suggest that a combination of the demagnetizing field model and product operator formalism provides excellent predictive power and computational convenience for diffusion and relaxation behaviors in two-component systems. These quantitative studies may also provide an opportunity to probe specific sources of new contrast for medical MR imaging.

Chen, Zhong; Chen, Zhiwei; Zhong, Jianhui

2001-12-01

121

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

PubMed

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

Archambault, Fabien; Chipot, Christophe; Soteras, Ignacio; Luque, F Javier; Schulten, Klaus; Dehez, François

2009-01-01

122

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

PubMed Central

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

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

2010-01-01

123

Regions of the herpes simplex virus scaffolding protein that are important for intermolecular self-interaction.  

PubMed

The herpes simplex virus type 1 (HSV-1) scaffolding protein encoded by gene UL26.5 promotes the formation of the icosahedral capsid shell through its association with the major capsid protein VP5 and through intermolecular interactions with itself. Inside the capsid shell, the UL26.5 product together with the maturational protease, a minor protein, form a spherical structure which is broken down and released from the capsid during packaging of the viral genome. Selected residues from four internal regions of the HSV-1 scaffolding protein that have significant conservation of amino acids within the scaffolding proteins of alphaherpesviruses were mutated, and the properties of the proteins were examined. Only the HSV-1 scaffolding protein with mutations in the conserved N-terminal domain showed reduced interaction with the varicella-zoster virus homologue in a cell-based immunofluorescence assay, providing the first evidence that this domain in the HSV-1 protein is likely to be involved in intermolecular self-interaction. Scaffolding protein with mutations in this domain or in either of two other domains failed to assemble into scaffold-like particles but retained the ability to self-interact, although the aggregates were significant smaller than most of the aggregates formed by the wild-type protein. These results suggest that there are multiple domains involved in the intermolecular self-association of the HSV-1 scaffolding protein that can act independently of one another. This conclusion was supported by the observation that none of the mutant proteins with lesions in an individual domain, including a protein with mutations in a central region previously implicated in self-interaction (A. Pelletier, F. Dô, J. J. Brisebois, L. Lagacé, and M. G. Cordingley, J. Virol. 71:5197-5208, 1997), interfered with capsid assembly in a baculovirus expression system. A protein mutated in the central region and another conserved domain, both of which had been predicted to form coiled coils, was impaired for capsid formation but still retained the capacity to interact with VP5. PMID:11752158

Preston, Valerie G; McDougall, Iris M

2002-01-01

124

Structural and functional investigation of the intermolecular interaction between NRPS adenylation and carrier protein domains  

PubMed Central

Summary Non-ribosomal peptide synthetases (NRPSs) are modular proteins that produce peptide antibiotics and siderophores. These enzymes act as catalytic assembly lines where substrates, covalently bound to integrated carrier domains, are delivered to adjacent catalytic domains. The carrier domains are initially loaded by adenylation domains, which use two distinct conformations to catalyze sequentially the adenylation of the substrate and the thioesterification of the pantetheine cofactor. We have used a mechanism-based inhibitor to determine the crystal structure of an engineered adenylation-carrier domain protein illustrating the intermolecular interaction between the adenylation and carrier domains. This structure enabled directed mutations to improve the interaction between non-native partner proteins. Comparison with prior NRPS adenylation domain structures provides insights into the assembly line dynamics of these modular enzymes.

Sundlov, Jesse A.; Shi, Ce; Wilson, Daniel J.; Aldrich, Courtney C.; Gulick, Andrew M.

2012-01-01

125

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

SciTech Connect

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

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

1999-07-01

126

Nanomechanics of Cartilage : Investigation of Biomacromolecular Intermolecular Interactions via High-Resolution Force Spectroscopy  

NASA Astrophysics Data System (ADS)

It is thought that the negatively charged, disaccharide macromolecules, glycosaminoglycans (GAGs), are the major determinant of the outstanding biomechanical properties of cartilage; i.e. its ability to resist compressive loading in vivo, responsible for 50-75 percent of the equilibrium compressive elastic modulus, as well as directly related to disease (i.e. osteoarthritis). The underlying molecular mechanism responsible for the outstanding compressive properties of cartilage arises from the unique nanomechanical properties of the constituent GAGs. In particular, intermolecular electrostatic repulsion due to the counterion electrical double layer of the charged polymers, as well as steric repulsion originating from configurational entropy. The technique of high-resolution force spectroscopy was employed to directly quanitfy these intermolecular interactions between biomimetic model end-grafted GAG "brush" surfaces with packing density 6nmx6nm-area per chain and probe tips of well-defined surface chemistry (e.g. sulfate-, methyl-, and GAG-functionalized).The effect of pH, ionic strength, grafting and charge density has been investigated.

Ortiz, Christine; Seog, Joonil; Dean, Delphine; Grodzinsky, Alan; Plaas, Anna; Wong-Palms, Shirley

2001-03-01

127

Quantum phase transitions for two coupled cavities with dipole-interaction atoms  

SciTech Connect

We investigate the quantum phase transitions for two weakly coupled atom-cavity sites. The interatomic dipole-dipole interaction is considered. Our numerical results show that the dipole-dipole interaction is a crucial parameter for the quantum phase transition. For small atom-cavity detuning, the ''superfluid'' becomes more and more obvious with the increase of the dipole-dipole interaction. In addition, the strong dipole-dipole interaction can lead the atomic excitation to be suppressed completely, and only the photonic excitation exists for the ground states. When the atom-cavity detuning is comparable with the dipole-dipole interaction, the dipole-dipole interaction enlarges the positive detunings, which is in favor of exhibiting superfluid photonic states. While for the negative detuning, the dipole-dipole interaction will reduce it, and contribute to the formation of the polaritonic insulator states. The cases for extended models have also been briefly analyzed. We also discuss how to find these novel phenomena in future experiments.

Tan Lei [Institute of Theoretical Physics, Lanzhou University, Lanzhou 730000 (China); Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Zhang Yuqing [Institute of Theoretical Physics, Lanzhou University, Lanzhou 730000 (China); Liu Wuming [Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

2011-12-15

128

The extracellular calcium-sensing receptor dimerizes through multiple types of intermolecular interactions.  

PubMed

Recent studies have shown that the G protein-coupled, extracellular calcium ([Ca(2+)](o))-sensing receptor (CaR) forms disulfide-linked dimers through cysteine residues within its extracellular domain and that dimerization of the CaR has functional implications. In this study, we have investigated which of these disulfide linkages are essential for dimerization of the CaR and whether they are required for these functional interactions. Our results confirm the key roles of Cys(129) and Cys(131) in CaR dimerization. However, utilizing cross-linking of the CaR or immunoprecipitation of a non-FLAG-tagged CaR with a FLAG-tagged CaR using anti-FLAG antibody, we demonstrate that CaRs with or without these two cysteines form dimers on the cell surface to a similar extent. In addition, reconstitution of CaR-mediated signaling by cotransfection of two individually inactive mutant CaRs is nearly identical in the presence or absence of both Cys(129) and Cys(131), showing that covalent linkage of CaR dimers is not needed for functional interactions between CaR monomers. These findings suggest that the CaR has at least two distinct types of motifs mediating dimerization and functional interactions, i.e. covalent interactions involving intermolecular disulfide bonds and noncovalent, possibly hydrophobic, interactions. PMID:11069904

Zhang, Z; Sun, S; Quinn, S J; Brown, E M; Bai, M

2000-11-07

129

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

PubMed

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

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

2012-12-01

130

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

NASA Astrophysics Data System (ADS)

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

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

2012-12-01

131

Molecular oxygen tetramer (O2)4: Intermolecular interactions and implications for the ? solid phase  

NASA Astrophysics Data System (ADS)

Recent data have determined that the structure of the high-pressure ? phase of solid oxygen consists of clusters composed of four O2 molecules. This finding has opened the question about the nature of the intermolecular interactions within the molecular oxygen tetramer. We use multiconfigurational ab initio calculations to obtain an adequate characterization of the ground singlet state of (O2)4, which is compatible with the nonmagnetic character of the ? phase. In contrast to previous suggestions implying covalent bonding, we show that (O2)4 is a van der Waals-like cluster where exchange interactions preferentially stabilize the singlet state. Nevertheless, as the cluster shrinks, there is an extra stabilization due to many-body interactions, i.e., an incipient chemical bonding that just yields a softening of the repulsive wall. We show that these findings can be used to model the intra- and intercluster distances of ?-O2 observed in the lower-pressure range and are consistent with inelastic x-ray measurements of O2 K-edge excitations.

Bartolomei, Massimiliano; Carmona-Novillo, Estela; Hernández, Marta I.; Pérez-Ríos, Jesús; Campos-Martínez, José; Hernández-Lamoneda, Ramón

2011-09-01

132

On the resource evaluation of marine gas hydrate deposits using sea-floor transient electric dipole-dipole methods  

SciTech Connect

Methane hydrates are solid, nonstoichiometric mixtures of water and the gas methane. The depth extent and stability of the hydrate zone is governed by the phase diagram for mixtures of methane and hydrate and determined by ambient pressures and temperatures. The base of the hydrate zone is a phase boundary between solid hydrate and free gas and water. It stands out on seismic sections as a bright reflection. The diffuse upper boundary is not as well marked so that the total mass of hydrate is not determined easily by seismic alone. The addition of electrical data, collected with a seafloor transient electric dipole-dipole system, can aid in the evaluation of the resource. Two exploration scenarios are investigated through numerical modeling. In the first, a very simple example illustrating some of the fundamental characteristics of the electrical response, most of the properties of the section including the probable, regional thickness of the hydrate zone (200 m) are assumed known from seismic and spot drilling. In the second example, less information is assumed available a priori and the complementary electrical survey is required to find both the thickness and the hydrate content in a hydrate zone about 200 m thick beneath the sea floor containing 20 and 40% hydrate in the available pore space, respectively. A linear eigenfunction analysis reveals that for these two models, the total mass of hydrate, the product of hydrate content and thickness, may be estimated to an accuracy of about 3{epsilon}% given measurements of traveltime to an accuracy of {epsilon}% over a range of separations from 100 to 1300 m. Based on these data, the author suggests that the value of {epsilon} may be of the order of 3%.

Edwards, R.N. [Univ. of Toronto, Ontario (Canada). Dept. of Physics

1997-01-01

133

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

NASA Astrophysics Data System (ADS)

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

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

2013-09-01

134

Pentacene on ag(111): correlation of bonding distance with intermolecular interaction and order.  

PubMed

We report coverage and temperature dependent bonding distances of vacuum-sublimed pentacene (PEN) submonolayers on Ag(111) obtained by the X-ray standing wave technique. The average vertical bonding distance of 2.98 Å at room temperature for 0.50 monolayer (ML) coverage increases to 3.12 Å for 0.75 ML due to competing intermolecular and adsorbate-substrate interactions. In contrast, decreasing the temperature from 295 to 145 K does not impact the bonding distance despite the concomitant transition from a "liquidlike" to an ordered molecular arrangement. In combination with X-ray photoelectron spectroscopy results, we could identify "soft chemisorption" with a subtle balance of molecule-molecule and substrate-molecule interactions as being responsible for this special adsorption behavior. Thus our study sheds light not only on the interface between PEN and Ag(111), but also on fundamental adsorption processes of organic adsorbates on metals in the context of chemi- and physisorption. PMID:24016756

Duhm, Steffen; Bürker, Christoph; Niederhausen, Jens; Salzmann, Ingo; Hosokai, Takuya; Duvernay, Julien; Kera, Satoshi; Schreiber, Frank; Koch, Norbert; Ueno, Nobuo; Gerlach, Alexander

2013-09-24

135

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

PubMed Central

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.

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

2010-01-01

136

Intermolecular Interactions within the Abundant DEAD-box Protein Dhh1 Regulate Its Activity in Vivo*  

PubMed Central

Dhh1 is a highly conserved DEAD-box protein that has been implicated in many processes involved in mRNA regulation. At least some functions of Dhh1 may be carried out in cytoplasmic foci called processing bodies (P-bodies). Dhh1 was identified initially as a putative RNA helicase based solely on the presence of conserved helicase motifs found in the superfamily 2 (Sf2) of DEXD/H-box proteins. Although initial mutagenesis studies revealed that the signature DEAD-box motif is required for Dhh1 function in vivo, enzymatic (ATPase or helicase) or ATP binding activities of Dhh1 or those of any its many higher eukaryotic orthologues have not been described. Here we provide the first characterization of the biochemical activities of Dhh1. Dhh1 has weaker RNA-dependent ATPase activity than other well characterized DEAD-box helicases. We provide evidence that intermolecular interactions between the N- and C-terminal RecA-like helicase domains restrict its ATPase activity; mutation of residues mediating these interactions enhanced ATP hydrolysis. Interestingly, the interdomain interaction mutant displayed enhanced mRNA turnover, RNA binding, and recruitment into cytoplasmic foci in vivo compared with wild type Dhh1. Also, we demonstrate that the ATPase activity of Dhh1 is not required for it to be recruited into cytoplasmic foci, but it regulates its association with RNA in vivo. We hypothesize that the activity of Dhh1 is restricted by interdomain interactions, which can be regulated by cellular factors to impart stringent control over this very abundant RNA helicase.

Dutta, Arnob; Zheng, Suting; Jain, Deepti; Cameron, Craig E.; Reese, Joseph C.

2011-01-01

137

Probing intermolecular interactions in water/ionic liquid mixtures by far-infrared spectroscopy.  

PubMed

Far-infrared spectra in the range from 600 to 20 cm-1 of two hydrophilic (1-ethyl-3-methylimidazolium tetrafluoroborate and 1-butyl-3-methylimidazolium tetrafluoroborate) and one hydrophobic (1-butyl-3-methylimidazolium hexafluorophosphate) ionic liquids and their mixtures with water at different concentrations are reported. Shifts of the librational water bands depending on the nature of the anion are found to be related to the strength of the interaction between the water molecules and the anions. For both hydrophilic ionic liquids, the librational band is centered around 460 cm-1, whereas for the hydrophobic ionic liquid, it is shifted to 388 cm-1, indicating less hindered rotation of single water molecules. Multivariate curve resolution, paying special attention to the spectral range from 50 to 350 cm-1, was used to investigate the presence of different species with increasing water concentration. For both hydrophilic ionic liquids, a band located at 153 cm-1 was resolved into two different contributions. A small contribution at 202 cm-1 can be attributed to intermolecular interactions between water molecules forming dimers. The major contribution (centered at 148 cm-1) corresponds to water molecules that do not bond to each other via H-bonding. It is therefore assigned to a hindered translation arising from the stretching of the hydrogen bond between BF4- anions and water molecules. Formation of water dimers in the hydrophobic ionic liquid does not occur. Furthermore, the spectral contribution of the stretching of H-bonds between water molecules and PF6- cannot be unambiguously detected, which indicates an extremely weak interaction between water molecules and this anion. PMID:17408256

Dominguez-Vidal, Ana; Kaun, Nina; Ayora-Cañada, Maria Jose; Lendl, Bernhard

2007-04-05

138

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

NASA Astrophysics Data System (ADS)

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

Gu, Zhiyong

139

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

SciTech Connect

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.

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

2012-02-07

140

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

PubMed

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

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

2011-08-03

141

The Interaction of Paramagnetic Relaxation Reagents with Intra- and Intermolecular Hydrogen Bonded Phenols.  

National Technical Information Service (NTIS)

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) ...

T. A. Holak G. C. Levy

1978-01-01

142

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...

143

Thermodynamics of saturated and unsaturated ketones C13 and C18 and the energy of specific intermolecular interactions  

NASA Astrophysics Data System (ADS)

P- T dependences of the saturated vapor of pseudoionone, hexahydropseudoionone, and saturated and unsaturated ketones C18 were studied using the statistical approach, and the enthalpies and entropies of its vaporization were calculated. The presence of monomer forms of the molecules of these compounds was established by studying the unsaturated vapor pressure. It was demonstrated that the role of isostructural methyl group in ketones is not related to the all-explaining steric effect concealing the real nature of the specific interaction. The energies of specific intermolecular interactions were determined in liquid symmetrical and unsymmetrical ketones.

Baev, A. A.; Baev, A. K.

2011-05-01

144

Effect of the character of homo- and heteronuclear chemical bond on the intermolecular interaction energy and properties of halogens and hydrogen halides  

Microsoft Academic Search

The effect of the chemical bond character (the degrees of covalence C\\u000a c, metallicity C\\u000a m, and ionicity C\\u000a i) on the bond rigidity and the components of the van der Waals intermolecular interaction have been shown for halogens and\\u000a hydrogen halides as an example. The force constant is determined by the chemical bond character. The intermolecular interaction\\u000a energy of

O. S. Sirotkin; R. O. Sirotkin; P. B. Shibaev

2011-01-01

145

Direction-dependent intermolecular interactions: catechol on TiO2(110)-1×1  

Microsoft Academic Search

The adsorption of a submonolayer of catechol (C6H6O2) on the rutile TiO2(110)-1×1 surface has been investigated by Scanning Tunneling Microscopy (STM). The catechol molecules are preferentially adsorbed on the surface 5-fold coordinated Ti4+ sites, and occupy two neighboring lattice Ti sites. No preference for adsorption at surface step edges is observed at room temperature. A statistical analysis of intermolecular distances

Shao-Chun Li; Ulrike Diebold

2009-01-01

146

Adsorption induced surface-stress sensing signal originating from both vertical interface effects and intermolecular lateral interactions.  

PubMed

This research investigates the origin of specific molecule-adsorption induced surface-stress for micro/nano-cantilever bio/chemical sensors. Systematic discussion is presented on the contribution from types of molecule interactions to the generated surface-stress sensing signal. With the main arguments verified by our micro-cantilever sensing experiments, the origin of the adsorption induced surface-stress is, for the first time, clearly categorized into interface vertical effects and lateral interactions, which helps to comprehensively understand the surface-stress generation and overall to optimize the sensing performance of micro-cantilever chemo-mechanical sensors. The key findings of this research are that, vertically at the molecule adsorption surface, interfacial energy change and charge redistribution are the main origins of the generated surface-stress. More importantly, intermolecular lateral interactions may make a more significant contribution to the nano-mechanical surface-stress response. Compared with other lateral interactions like van der Waals force and the electrostatic coulombic effect, intermolecular hydrogen-bond intensity and steric factor easily cause much greater disparity in surface-stress. PMID:22010113

Yang, Tiantian; Li, Xinxin; Chen, Ying; Lee, Dong-Weon; Zuo, Guomin

2011-10-19

147

Proton transfer reaction and intermolecular interactions in associates of 2,5-dihydroxy-1,8-naphthyridine  

Microsoft Academic Search

Tautomerism in monomers\\/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended\\u000a for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates\\u000a the intermolecular proton transfer may take place. Transition state related to the double proton transfer reactions were calculated\\u000a and discussed in terms of energetics, changes in atomic charges

Borys O?mia?owski

148

First-order intermolecular interaction energies from coupled-cluster Brueckner orbitals  

NASA Astrophysics Data System (ADS)

It is investigated to which extent the effect of intramolecular electron correlation on intermolecular first-order Coulomb and exchange energies can be accounted for when solely the reference determinant of the Brueckner coupled-cluster-doubles scheme is used to construct the charge density and the density matrices of the monomers. Considering the dimers He2, Ne2, Ar2, NeAr, NeHF, ArHF, (H2)2, (HF)2, and (H2O)2 the Brueckner orbital approximation in general is found to improve considerably upon the results of the Hartree-Fock determinant.

Heßelmann, Andreas; Jansen, Georg

2000-04-01

149

Analysis of intermolecular interaction of poly(N-isopropylacrylamide) solution with attenuated total reflectance terahertz spectroscopy  

NASA Astrophysics Data System (ADS)

The terahertz attenuated total reflectance spectra of Poly(N-isopropylacrylamide) (P-NIPAAm) solutions were measured in the range of 26.5-47.3 °C. The phase-change in P-NIPAAm was observed via the temperature dependence of the spectra. The collapse of hydrogen bonds in solution was confirmed by the decrease in the signal intensities around 62 cm-1, which corresponds to fast dielectric relaxation by rotation and collision of molecules, and around 166 cm-1, which corresponds to the stretching mode of the intermolecular vibration of water molecules.

Naito, H.; Ogawa, Y.; Hoshina, H.; Sultana, S.; Kondo, N.

2012-05-01

150

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

PubMed Central

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

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

2011-01-01

151

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

PubMed Central

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.

Scott, H L; Pearce, P A

1989-01-01

152

First-order exchange energy of intermolecular interactions from coupled cluster density matrices and their cumulants.  

PubMed

A new method for the calculation of the first-order intermolecular exchange energy is proposed. It is based on the partition of two-particle density matrices of monomers into the antisymmetrized product of one-particle density matrices and the remaining cumulant part. This partition is used to modify the formula for the first-order exchange energy developed by Moszynski et al. [J. Chem. Phys. 100, 5080 (1994)]. The new expression has been applied for the case of monomer density matrices derived from the expectation value expression for the coupled cluster singles and doubles wave function. In this way an accurate method of calculation of the first-order exchange energy for many-electron systems has been obtained, where both monomers are described on the coupled cluster level. Numerical results are presented for several benchmark van der Waals systems to illustrate the performance of the new approach. PMID:18554003

Korona, Tatiana

2008-06-14

153

Structure and intermolecular interactions in selected binary solutions studied by X-ray methods  

NASA Astrophysics Data System (ADS)

The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2? varying from 6° to 120°. Averaged scattered X-ray angular distributions I¯(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4?r?j,knK[?k(r)??0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied.

Drozdowski, Henryk; Romaniuk, Anna; B?aszczak, Zdzis?aw

2013-12-01

154

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

PubMed

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

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

2013-08-09

155

Magnetic Dipole-Dipole Coupled Cu(II) Pairs in Nitric Oxide-Treated Tyrosinase: A Structural Relationship Between the Active Sites of Tyrosinase and Hemocyanin  

PubMed Central

The Tr and T[unk] states of tyrosinase were treated with NO. EPR spectra of the products observed at 14°K and at 113°K showed mixtures of two signals. One had components in the region of g = 2, about 1200 G wide, and in the region of g = 4, showing hyperfine splitting. The other signal was similar to that arising from isolated Cu(II) ions in an axially symmetric environment. The first signal was indicative of ?m = 1 and ?m = 2 transitions arising from magnetic dipole-dipole coupled Cu(II) ion pairs. It closely resembled previously reported EPR spectra obtained from NO-treated hemocyanin, which were confirmed in this study. The normal Curie behavior of the signals between 230°K and 14°K ruled out significant exchange coupling between the ion pairs. The ?m = 2 signals were not saturable up to 350 mW at 14°K. The broad ?m = 1 signals could be separated from accompanying signals by the saturation characteristics of the latter at about 10 mW at 14°K. The results establish the presence of a pair of copper ions at the active site of tyrosinase, and a clsoe structural relationship between this active site and that of hemocyanin.

Uiterkamp, A. J. M. Schoot; Mason, H. S.

1973-01-01

156

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

NASA Astrophysics Data System (ADS)

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.

Renner, Christian; Holak, Tad A.

2000-08-01

157

Proton transfer reaction and intermolecular interactions in associates of 2,5-dihydroxy-1,8-naphthyridine.  

PubMed

Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transition state related to the double proton transfer reactions were calculated and discussed in terms of energetics, changes in atomic charges upon association, aromaticity (HOMA), properties of hydrogen bond critical point (QTAIM methodology) and geometry change during this reaction. It was found that double proton transfer is supported by third hydrogen bond or by weak secondary interaction. Some protons in transition states are shared between two basic atoms, while other are covalently bound only to one of them. The said process leads to replacement of secondary interactions of attractive character to repulsive and vice versa. Overall, results suggest that in subjected compound the triple hydrogen-bonded associate may be in equilibrium with double hydrogen-bonded dimer. PMID:21805130

O?mia?owski, Borys

2011-07-30

158

plasma desorption mass spectrometry of quinolinium salts and method of estimation of their intermolecular interactions with phospholipids  

NASA Astrophysics Data System (ADS)

Using plasma desorption mass spectrometry, the fragmentation of 1-phenyl-2(p-aminostyryl)quinolinium and 1-phenyl-2(p-aminostyryl)benzo(f)quinolinium derivatives, with various substituents at the amino nitrogen, was studied. With plasma desorption ionization, the fragmentation features of the compounds studied are mainly determined by the nature of the N',N'' substituents. The behaviour of some quinolinium derivatives in the presence of lecithin, a basic component of the phospholipid fraction of cell membranes, was investigated. For the benzo(f)quinolinium derivative, the analysis of changes in the mass spectra indicates a strong interaction between these substances, leading to the formation of a molecular complex stabilized by the interactions of the negatively charged phosphate group of lecithin with the quinolinium quaternary nitrogen and the lecithin quaternary nitrogen with the benzene part of the aminophenyl fragment. The effect of the third aromatic ring of the benzoquinolinium system on complex stabilization is discussed. For the benzoquinolinium derivative with lecithin, the changes in the mass spectrometric fragmentation pattern of the molecule can be used as a sensitive and informative method for the characterization of intermolecular interactions which may result in molecular complex formation.

Andrievsky, Grigory V.; Lisnyak, Yury V.; Klochkov, Vladimir K.; Volyansky, Yury L.; Malaya, Lubov T.

1997-06-01

159

Attenuated T2 Relaxation by Mutual Cancellation of Dipole-Dipole Coupling and Chemical Shift Anisotropy Indicates an Avenue to NMR Structures of Very Large Biological Macromolecules in Solution  

Microsoft Academic Search

Fast transverse relaxation of 1H, 15N, and 13C by dipole-dipole coupling (DD) and chemical shift anisotropy (CSA) modulated by rotational molecular motions has a dominant impact on the size limit for biomacromolecular structures that can be studied by NMR spectroscopy in solution. Transverse relaxation-optimized spectroscopy (TROSY) is an approach for suppression of transverse relaxation in multidimensional NMR experiments, which is

Konstantin Pervushin; Roland Riek; Gerhard Wider; Kurt Wuthrich

1997-01-01

160

An IR diode laser spectroscopic study of adsorption and intermolecular interactions on stepped metal surfaces: CO on vicinal Cu(100). [IR (infrared)  

SciTech Connect

The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique. Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority step-CO species accounting for a disporportionate fraction of the spectral intensity. A model has been elaborated which successfully accounts for, and simulates, the observed spectra. This enables site specific concentrations to be determined, even in the presence of strong dynamic-dipole coupling. These methods allow the spectroscopy, kinetics and intermolecular interactions of CO on a stepped Cu(100) surface to be probed. In particular, it has been possible to observe a dynamic equilibrium between CO adsorbed at step and terrace sites and to investigate the kinetics of site exchanges on this surface. The IR spectra also reveal the nature and range of the intermolecular interactions and the local order which results. The CO/Cu(100) system is characterized by repulsive first and second nearest neighbor interactions. As a consequence, the adsorbates adopt a configuration which maximizes the intermolecular distance. Additionally, a non-resonant, broadband, adsorbate induced change in surface reflectivity is observed both in the IR and visible. This linear dependence of this signal with coverage provides a simple method of determining total absorbed CO concentration.

Borguet, E.R.

1993-01-01

161

An IR diode laser spectroscopic study of adsorption and intermolecular interactions on stepped metal surfaces: CO on vicinal Cu(100). [IR (infrared)  

Microsoft Academic Search

The kinetics of elementary surface processes, intermolecular interactions and stepped surfaces are intrinsic scientific interest, as well as being important to industrially relevant processes such as catalysis. A novel time-resolved surface sensitive technique. Transient Diode Laser Infrared Reflection-Absorption Spectroscopy, has been developed to investigate adsorption on stepped metal surfaces. The IR spectra display anomalous intensity behavior resulting in a minority

Borguet

1993-01-01

162

Polymer materials for electro-optic and optoelectronic applications: maximizing device performances by creating desirable intermolecular electrostatic interactions  

NASA Astrophysics Data System (ADS)

In EO polymer materials, the second-order nonlinear optic chromophores must be oriented in one direction in order to be electro-optically active. Interchromophore electrostatic interactions, which encourages the formation of non-active and light-scattering crystalline domains through the antiparallel stacking of dipoles, have long been an obstacle to the translation of large molecular optical nonlinearity into corresponding bulk nonlinearity. Great progresses have been made in the design and synthesis of chormophores with reduced electrostatic interactions. New effort toward the complete elimination of the destructive effect of the electrostatic forces is on the way. On the contrary, strong intermolecular electrostatic interaction (e.g. the force responsible for ?-? stacking of conjugated systems) is often desired in LED, transistor and photovoltaic (PV) devices since high mobilities of the charge carriers are the key to their high performances and often come from ordered stacking of pi-conjugated systems. For PV applications, bi-continuous "bulk heterojunction" of electron donor (D) and acceptor (A) is ideal for efficient charge carrier generation, transport and collection. Differential electrostatic interactions between D and A is the key to the formation of such morphology. We have synthesized a novel type of block copolymer having a basic unit of D-B-A (B is a non-conjugate bridge) for solar cell application. D and A can be designed in such a way that D-D and A-A interactions are stronger than the D-A interaction, and therefore, have a strong tendency to phase separate.

Zhang, Cheng; Sun, Sam-Shajing; Bonner, Carl E.; Kim, Songku; Fetterman, Harold R.; Dalton, Larry R.

2005-12-01

163

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

ERIC Educational Resources Information Center

|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.|

Pullman, David; Peterson, Karen I.

2004-01-01

164

Weak carbonyl-methyl intermolecular interactions in acetone clusters explored by IR plus VUV spectroscopy  

NASA Astrophysics Data System (ADS)

Size-selected IR-VUV spectroscopy is employed to detect vibrational characteristics in the region 2850 ˜ 3550 cm-1 of neutral acetone and its clusters (CH3COCH3)n (n = 1-4). Features around 3440 cm-1 in the spectra of acetone monomer and its clusters are assigned to the carbonyl stretch (CO) overtone. These features red-shift from 3455 to 3433 cm-1 as the size of the clusters increases from the monomer to the tetramer. Based on calculations, the experimental IR spectra in the CO overtone region suggest that the dominant structures for the acetone trimer and tetramer should be cyclic in the supersonic expansion sample. This study also suggests that the carbonyl groups interact with the methyl groups in the acetone clusters. These weak interactions are further confirmed by the use of deuterium substitution.

Guan, Jiwen; Hu, Yongjun; Xie, Min; Bernstein, Elliot R.

2012-09-01

165

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

PubMed Central

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.

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

2007-01-01

166

The molecular structure and intermolecular interactions of 1,3:2,4-dibenzylidene-D-sorbitol  

NASA Astrophysics Data System (ADS)

The 1,3(R):2,4(S)-dibenzylidene-D-sorbitol (DBS) molecule is a low molar mass organic gelator (LMOG) that is capable of hydrogen-bonding with itself. As a consequence, DBS molecules self-organize into nanofibrillar networks at relatively low concentrations in a wide variety of organic solvents and polymers. In this work, molecular mechanics and molecular dynamics simulations were conducted to elucidate the equilibrium structure of DBS and the molecular interactions that govern DBS self-assembly. Molecular mechanics calculations performed on single DBS molecules with Cerius2 and InsightII software reveal that the phenyl rings tend to adopt an equatorial position and that the pendant hydroxyl group prefers to form an intramolecular hydrogen bond with an acetal oxygen, in contrast to the terminal hydroxyl group. Molecular mechanics and molecular dynamics on DBS dimers reveal that they are capable of forming hydrogen bonds and participating in ? interactions, suggesting that the mechanism of nanofibrillar network formation may be complex, involving more than one type of physical interaction.

Wilder, Elizabeth A.; Spontak, Richard J.; Hall, Carol K.

167

Macrocyclic ?-Sheet Peptides that Mimic Protein Quaternary Structure through Intermolecular ?-Sheet Interactions  

PubMed Central

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

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

2008-01-01

168

Potential Intra- and Intermolecular Interactions involving the Unique-5? Region of the HIV-1 5?-UTR  

PubMed Central

The 5?-untranslated region (5?-UTR) of the human immunodeficiency virus type-1 (HIV-1) genome regulates multiple RNA-dependent functions during viral replication and has been proposed to adopt multiple secondary structures. Recent phylogenetic studies identified base pair complementarity between residues of the unique 5? element and those near the gag start codon (gagAUG) that is conserved among evolutionarily distant retroviruses, suggesting a potential long-range RNA-RNA interaction. However, nucleotide accessibility studies led to conflicting conclusions about the presence of such interactions in virions and in infected cells. Here we show that an 11-nucleotide oligo-RNA spanning residues 105-115 of the 5?-UTR (U5) readily binds to oligoribonucleotides containing the gag start codon (AUG), disrupting a pre-existing stem loop and forming a heteroduplex stabilized by 11 Watson Crick base pairs (Kd = 0.47 ± 0.16 ?M). Addition of the HIV-1 nucleocapsid protein (NC), the transacting viral factor required for genome packaging, disrupts the heteroduplex by binding tightly to U5 (Kd = 122 ± 10 nM). The structure of the NC:U5 complex, determined by NMR, exhibits features similar to those observed in NC complexes with HIV-1 stem loop RNAs, including the insertion of guanosine nucleobases to hydrophobic clefts on the surface of the zinc fingers and a 3?-to-5? orientation of the RNA relative to protein. Our findings indicate that the previously proposed long-range U5-gagAUG interaction is feasible, and suggest a potential NC-dependent mechanism for modulating the structure of the 5?-UTR.

Spriggs, Shardell; Garyu, Lianko; Connor, Ryan; Summers, Michael F.

2009-01-01

169

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

SciTech Connect

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.

Leszczynski, Jerzy [Computational Center for Molecular Structure and Interactions, Jackson, MS; Sponer, Judit [Academy of Sciences of the Czech Republic; Sponer, Jiri [Academy of Sciences of the Czech Republic; Sumpter, Bobby G [ORNL; Fuentes-Cabrera, Miguel A [ORNL; Vazquez-Mayagoitia, Alvaro [ORNL

2010-01-01

170

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

NASA Astrophysics Data System (ADS)

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.

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

2013-01-01

171

Acoustic and volumetric studies of intermolecular interactions in dilute solutions of methanol in aromatic amines  

NASA Astrophysics Data System (ADS)

Limiting partial compressibilities and volumes of methanol in pyridine, 2-methylpyridine, 3-methylpyridine, 4-methylpyridine and 2,6-dimethylpyridine were calculated from the experimental speeds of sounds and densities of dilute solutions at 298.15 K. The limiting functions were found to be linearly correlated with the association energies of isolated 1:1 complexes of the pyridine derivatives with water. Those association energies are close to the energies for similar complexes with methanol. The results evidence that ortho effect enhances the ability of pyridines to hydrogen bonding with methanol in the same way as with water. The effect consist in changes of hydrogen bond energy, unspecific interactions with a steric hindrance, e.g. between hydrocarbon tail of the alcohol molecule and the methyl group in the ring, and changes in resonance interactions. Stronger hydrogen bonds cause smaller partial molar compressibilities and volumes of the solute, as well as greater negative enthalpies of solution. Importantly, single molecule of water or methanol forms one hydrogen bond with the proton-accepting solvent.

Marczak, W.; Chowanska, A.; Piwowarska, B.

2005-10-01

172

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

PubMed Central

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.

Gingell, D; Fornes, J A

1976-01-01

173

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

PubMed Central

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

Edwin, Francis; Anderson, Kimberly; Ying, Chunyi

2009-01-01

174

Intermolecular interactions between the neurotensin and the third extracellular loop of human neurotensin 1 receptor.  

PubMed

Neurotensin (NT) is a tridecapeptide hormone in the periphery and neurotransmitter in the brain that principally activates three receptor subtypes, named NTS1, NTS2, and NTS3. Since little is known about its structure in the presence of its principal receptor NTS1, we determined it using the key domain of the receptor, i.e. the third extracellular loop. We conclude the following: (i) for the receptor fragment, NT binding modifies its central part, underlying the great flexibility and adaptability of this region; (ii) for bound NT, the extended conformation of its C-terminus is confirmed for the first time in experimental conditions and in the presence of a part of the receptor; and (iii) despite some substitutions, the human receptor residues that are involved in the interaction with NT could be similar to those of the rat receptor which play an important role in NT binding. PMID:23140271

Da Costa, Grégory; Bondon, Arnaud; Coutant, Jérome; Curmi, Patrick; Monti, Jean-Pierre

2012-11-12

175

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

PubMed

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

Albertí, M; Pirani, F; Laganà, A

2013-05-16

176

A CSOV study of the difference between HF and DFT intermolecular interaction energy values: the importance of the charge transfer contribution.  

PubMed

Intermolecular interaction energy decompositions using the Constrained Space Orbital Variation (CSOV) method are carried out at the Hartree-Fock level on the one hand and using DFT with usual GGA functionals on the other for a number of model complexes to analyze the role of electron correlation in the intermolecular stabilization energy. In addition to the overall stabilization, the results provide information on the variation, with respect to the computational level, of the different contributions to the interaction energy. The complexes studied are the water linear dimer, the N-methylformamide dimer, the nucleic acid base pairs, the benzene-methane and benzene-N2 van der Waals complexes, [Cu+ -(ImH)3]2, where "ImH" stands for the Imidazole ligand, and ImH-Zn++. The variation of the frozen core energy (the sum of the intermolecular electrostatic energy and the Pauli repulsion energy) calculated from the unperturbed orbitals of the interacting entities indicates that the intramolecular correlation contributions can be stabilizing as well as destabilizing, and that general trends can be derived from the results obtained using usual density functionals. The most important difference between the values obtained from HF and DFT computations concerns the charge transfer contribution, which, in most cases, undergoes the largest increase. The physical meaning of these results is discussed. The present work gives reference calculations that might be used to parametrize new correlated molecular mechanics potentials. PMID:15898112

Piquemal, Jean-Philip; Marquez, Antonio; Parisel, Olivier; Giessner-Prettre, Claude

2005-07-30

177

Molecular-beam study of the ammonia-noble gas systems: Characterization of the isotropic interaction and insights into the nature of the intermolecular potential  

NASA Astrophysics Data System (ADS)

We report new high resolution molecular beam experiments aimed at characterizing the intermolecular interaction in the NH3-Ng (Ng = He, Ne, Ar, Kr, Xe) weakly bound complexes. Integral cross section data are obtained over a sufficiently wide velocity range and with rotationally hot NH3 molecules to produce (except for the NH3-He case) a well resolved ``glory'' quantum interference pattern. Data analysis, carried out by employing a recently proposed potential model, allows unique information on the absolute scale of the intermolecular interaction to be obtained both at long range and at the equilibrium distance. An extensive and internally consistent comparison with the behavior of the corresponding Kr-Ng systems is exploited in order to identify those cases where an interaction component due to charge transfer effects provides an appreciable intermolecular bond stabilization that is clearly distinct from and must be added to the standard van der Waals plus induction picture. The results of the present investigation extend the phenomenology of perturbative charge transfer effects in gas phase complexes involving hydrogenated molecules.

Pirani, Fernando; Roncaratti, Luiz F.; Belpassi, Leonardo; Tarantelli, Francesco; Cappelletti, D.

2011-11-01

178

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

PubMed

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

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

2011-09-30

179

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

NASA Astrophysics Data System (ADS)

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

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

2013-02-01

180

Pro42 and Val45 of staphylokinase modulate intermolecular interactions of His43-Tyr44 pair and specificity of staphylokinase-plasmin activator complex.  

PubMed

Staphylokinase (SAK) forms a 1:1 stoichiometric complex with plasmin (Pm) and changes its substrate specificity to create a plasminogen (Pg) activator complex. The His(43)-Tyr(44) pair of SAK resides within the active site cleft of the partner Pm and generates intermolecular contacts to confer Pg activator ability to the SAK-Pm bimolecular complex. Site-directed mutagenesis and molecular modeling studies unravelled that mutation at 42nd or 45th positions of SAK specifically disrupts cation-pi interaction of His(43) with Trp(215) of partner Pm within the active site, whereas pi-pi interaction of Tyr(44) with Trp(215) remain energetically favoured. PMID:22321644

Singh, Satish; Ashish; Dikshit, Kanak L

2012-02-02

181

Dipole interactions in electrofusion. Contributions of membrane potential and effective dipole interaction pressures.  

PubMed Central

The contributions of pulse-induced dipole-dipole interaction to the total pressure acting normal to the membranes of closely positioned pronase treated human erythrocytes during electrofusion was calculated. The total pressure was modeled as the sum of pressures arising from membrane potential and dipole-dipole attraction opposed by interbilayer repulsion. The dipole-dipole interaction was derived from the experimentally obtained cell polarizability. The threshold electric field amplitude necessary for fusion of pronase-treated human erythrocytes was experimentally obtained at various combinations of pulse duration, frequency, and the conductivity of the external medium. The theoretical values of the critical electric field amplitude compared favorably to the experimentally obtained threshold field amplitudes. Fusion by dc pulses may be primarily attributed to attainment of sufficiently high membrane potentials. However, with decreasing external conductivity and increasing sinusoidal pulse frequency (100 kHz-2.5 MHz), the induced dipole-dipole interactions provide the principal driving force for membrane failure leading to fusion. Images FIGURE 5

Stenger, D A; Kaler, K V; Hui, S W

1991-01-01

182

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

SciTech Connect

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.}

Dang, L.X. [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

1999-05-01

183

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

SciTech Connect

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.

Hyeon-Deuk, K.; Tanimura, Yoshitaka [Department of Chemistry, Kyoto University, Kyoto 606-8502 (Japan)

2005-12-08

184

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

PubMed

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. PMID:16375479

Hyeon-Deuk, Kim; Hyeon-Deuk, K; Tanimura, Yoshitaka

2005-12-01

185

Solvent interactions with the Trp-cage peptide in 35% ethanol-water.  

PubMed

Intermolecular NOE experiments have been used to explore interactions of water and ethanol molecules in 35% ethanol/65% water (v/v) with the peptide Trp-cage at temperatures from 5 to 25 degrees C. Magnetic dipole-dipole cross-relaxation terms sigma(HH) (NOE) and sigma(HH) (ROE) for interaction of solvent components with spins of the peptide suggest that ethanol molecules associate with backbone atoms for times of the order of nanoseconds at 5 degrees C. Formation of peptide-ethanol complexes can also account for the larger-than-expected values of cross-relaxation terms at higher temperatures. Hydrocarbon side chains of the peptide do not appear to experience such interactions with ethanol. Cross relaxation resulting from water-peptide interactions are consistent with long-lived water interactions with the backbone atoms. Water cross relaxation with nonpolar side chains of the peptide (Leu2, Ile4, Leu7, and proline residues) are only those expected for bulk solvent. However, long-lived association of both water and ethanol with the polar side chains of Tyr3 and Trp6 is indicated by the data. PMID:18506810

Neuman, Robert C; Gerig, John T

2008-10-01

186

Microscopic theory of the interaction of ultracold dense Bose and Fermi gases with electromagnetic field  

Microsoft Academic Search

We present the rigorous microscopic quantum theory of the interaction of ultracold Bose and Fermi gases with the electromagnetic field of vacuum and laser photons. The main attention has been paid to the consistent consideration of dynamical dipole-dipole interactions. The theory developed is shown to be consistent with the general principles of the canonical quantization of electromagnetic field in a

K. V. Krutitsky; F. Burgbacher; J. Audretsch

1999-01-01

187

Observation of Excitonic Quenching by Long-Range Dipole-Dipole Interaction in Sequentially Doped Organic Phosphorescent Host-Guest System  

Microsoft Academic Search

We studied the quenching mechanisms responsible for the low efficiency of thin film phosphorescence by a specially designed organic light-emitting diode with an emission layer consisting of a few repeating cells made of a sequentially evaporated host and guest. Variation of the thickness of the guest layer in each cell enables the study of the effect of molecule aggregation on

Y. Divayana; X. W. Sun

2007-01-01

188

Self-assembled monolayers of aromatic thiols stabilized by parallel-displaced pi-pi stacking interactions.  

PubMed

Parallel-displaced pi-pi stacking interactions have been known to be the dominant force in stabilizing the double helical structure of DNA and the tertiary structure of proteins. However, little is known about their roles in self-assembled monolayers of other large pi molecules such as aromatic thiols. Here we report on a systematic study of the self-assembled monolayers of four kinds of anthracene-based thiols, 9-mercaptoanthracene (MA), (4-mercaptophenyl) (9-anthryl) acetylene (MPAA), (4-mercaptophenyl) (10-nitro-9-anthryl) acetylene (MPNAA), and (4-mercaptophenyl) (10-carboxyl-9-anthryl) acetylene (MPCAA) on Au(111), in which a spacer and different functional groups (NO2 and COOH) are intentionally designed to introduce and thus allow the investigation of various intermolecular interactions, in addition to pi-pi interactions in the base molecules. We find that all molecules form long-range-ordered monolayers and, more interestingly, that these assembled monolayers exhibit essentially the same fundamental packing structure. On the basis of high-resolution scanning tunneling microscopy observations, we propose the space-filling models for the observed superstructures and demonstrate that all superstructures can be understood in terms of the parallel-displaced pi-pi stacking interactions, despite the presence of competing dipole-dipole and H-bonding interactions associated with these specially designed functional groups. PMID:16548556

Dou, Rui-Fen; Ma, Xu-Cun; Xi, Luan; Yip, Hin Lap; Wong, King Young; Lau, Woon Ming; Jia, Jin-Feng; Xue, Qi-Kun; Yang, Wei-Sheng; Ma, Hong; Jen, Alex K-Y

2006-03-28

189

Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus  

PubMed Central

The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a Ka of 5.3 × 104 M–1. Ka determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function.

Guenther, Richard H.; Sit, Tim L.; Gracz, Hanna S.; Dolan, Michael A.; Townsend, Hannah L.; Liu, Guihua; Newman, Winnell H.; Agris, Paul F.; Lommel, Steven A.

2004-01-01

190

Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus.  

PubMed

The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenomic RNA synthesis. Short synthetic oligoribonucleotide mimics of the RNA-1 TABS and the RNA-2 TA form a weak 1:1 bimolecular complex in vitro with a K(a) of 5.3 x 10(4) M(-1). K(a) determination for a series of RNA-1 and RNA-2 mimic variants indicated optimum stability is obtained with seven-base complementarity. Thermal denaturation and NMR show that the RNA-1 TABS 8mers are weakly ordered in solution while RNA-2 TA oligomers form the predicted hairpin. NMR diffusion studies confirmed RNA-1 and RNA-2 oligomer complex formation in vitro. MC-Sym generated structural models suggest that the bimolecular complex is composed of two stacked helices, one being the stem of the RNA-2 TA hairpin and the other formed by the intermolecular base pairing between RNA-1 and RNA-2. The RCNMV TA structural model is similar to those for the Simian retrovirus frameshifting element and the Human immunodeficiency virus-1 dimerization kissing hairpins, suggesting a conservation of form and function. PMID:15155850

Guenther, Richard H; Sit, Tim L; Gracz, Hanna S; Dolan, Michael A; Townsend, Hannah L; Liu, Guihua; Newman, Winnell H; Agris, Paul F; Lommel, Steven A

2004-05-20

191

Studies on tolfenamic acid-chitosan intermolecular interactions: effect of pH, polymer concentration and molecular weight.  

PubMed

Solid-state properties of tolfenamic acid (TA) and its complexes with chitosan (CT) have been studied. Effect of medium pH, molecular weight of polymer and its different concentrations on these TA-CT complexes were studied in detail. Low and medium molecular weight CT have been used in different ratios at pH ranging from 4 to 6 and freeze-drying technique has been employed to modify the appearance of crystalline TA. Physical properties of the formed complexes have been studied by employing X-ray diffraction, differential scanning calorimetry and scanning electron microscopy; chemical structure has been studied using Fourier transform infrared spectroscopy. The results showed that both forms of the polymer exhibited complete conversion in 1:8 ratio at pH 4, 1:4 at pH 5 and 1:1 at pH 6 indicating a marked effect of pH on drug-polymer complexation. The percent crystallinity calculations indicated low molecular weight CT slightly more effective than the other form. No changes in the complexes have been observed during the 12 week storage under controlled conditions. Both forms of CT at different pH values indicated retardation of recrystallization in TA during cooling of the melt from 1:1 ratios exhibiting formation of strong intermolecular hydrogen bonding between the drug and the polymer. PMID:23620261

Ahmed, Sofia; Sheraz, Muhammad Ali; Rehman, Ihtesham Ur

2013-04-27

192

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

PubMed

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

Kuchenbecker, Dennis; Jansen, Georg

2012-06-13

193

Interactions determining phospholipid domain growth in monolayers: experimental results and computer simulations  

Microsoft Academic Search

Results are presented from a quantitative analysis of liquid condensed (LC) domain shapes in monolayers of the phospholipid dipalmitoylphosphatidylcholine (DPPC). Comparison with existing theory shows that the dominant dependence of LC domain shape factor on in-plane density is described well by electric dipole-dipole interactions; however, the detailed chirality of the LC domains remains unexplained. Also unaccounted for is the noncompact

Suzanne Amador; Madison Compton; Lyle Roelofs; Nicholas Wilder

1998-01-01

194

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

PubMed Central

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.

da Silva, Julio Cesar; Sforca, Mauricio Luis; 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, Jorg

2013-01-01

195

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

PubMed

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

Alborghetti, Marcos Rodrigo; Furlan, Ariane da Silva; da Silva, Júlio César; Sforça, Maurício Luís; 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, Jörg

2013-10-07

196

FT-IR study on interactions between medroxyprogesterone acetate and solvent in CHCl?/cyclo-C6H?? and CCl?/cyclo-C6H?? binary solvent systems.  

PubMed

The intermolecular interactions between medroxyprogesterone acetate (MPA) and CHCl(3) and CCl(4) solvent in CHCl(3)/cyclo-C(6)H(12) and CCl(4)/cyclo-C(6)H(12) binary solvent systems have been studied by Fourier transform infrared spectroscopy (FT-IR). The experimental results showed that there are hydrogen bonding interactions between oxygen atoms of all carbonyl groups in MPA and hydrogen atom of CHCl(3) so as to form 1:3 complex of MPA with CHCl(3) and produce three new absorption bands at 1728.9-1736.1, 1712.7-1717.4 and 1661.9-1673.8 cm(-1), respectively. And, 1:1 complex of MPA with CCl(4) is formed in CCl(4)/cyclo-C(6)H(12) binary solvent as a result of hydrogen bonding interaction between C3 carbonyl group and empty d-orbital in chlorine atom of CCl(4) leading to producing new absorption band at 1673.2-1674.2 cm(-1). However, all free carbonyl and associated carbonyl stretching vibrations of MPA in CHCl(3)/cyclo-C(6)H(12) and CCl(4)/cyclo-C(6)H(12) binary solvent systems shift to lower wavenumbers with the increasing of volume fraction of CHCl(3) and CCl(4) in binary solvent systems owing to the dipole-dipole interaction and the dipole-induced dipole interaction between MPA and solvents. PMID:22634415

Shi, Jie-hua; Fan, Chun-hui

2012-05-09

197

Insight into intra- and inter-molecular interactions of PKC: design of specific modulators of kinase function  

PubMed Central

Protein kinase C (PKC) is a family of kinases that are critical in many cellular events. These enzymes are activated by lipid-derived second messengers, are dependent on binding to negatively charged phospholipids and some members also require calcium to attain full activation. The interaction with lipids and calcium activators is mediated by binding to the regulatory domains C1 and C2. In addition, many protein-protein interactions between PKC and other proteins have been described. These include interactions with adaptor proteins, substrates and cytoskeletal elements. Regulation of the interactions between PKC, small molecules and other proteins is essential for signal transduction to occur. Finally, a number of auto-inhibitory intramolecular protein-protein interactions have also been identified in PKC. This chapter focuses on mapping the sites for many of these inter and intramolecular interactions and how this information may be used to generate selective inhibitors and activators of PKC signaling.

Kheifets, Viktoria; Mochly-Rosen, Daria

2007-01-01

198

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

PubMed

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

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

2012-12-26

199

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

NASA Astrophysics Data System (ADS)

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??.

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

2012-12-01

200

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

Microsoft Academic Search

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

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

2006-01-01

201

Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS  

Microsoft Academic Search

Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine

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

2012-01-01

202

Regulation of protein kinase C-related protein kinase 2 (PRK2) by an intermolecular PRK2-PRK2 interaction mediated by Its N-terminal domain.  

PubMed

Protein kinase C-related protein kinases (PRKs) are effectors of the Rho family of small GTPases and play a role in the development of diseases such as prostate cancer and hepatitis C. Here we examined the mechanism underlying the regulation of PRK2 by its N-terminal region. We show that the N-terminal region of PRK2 prevents the interaction with its upstream kinase, the 3-phosphoinositide-dependent kinase 1 (PDK1), which phosphorylates the activation loop of PRK2. We confirm that the N-terminal region directly inhibits the kinase activity of PRK2. However, in contrast to previous models, our data indicate that this inhibition is mediated in trans through an intermolecular PRK2-PRK2 interaction. Our results also suggest that amino acids 487-501, located in the linker region between the N-terminal domains and the catalytic domain, contribute to the PRK2-PRK2 dimer formation. This dimerization is further supported by other N-terminal domains. Additionally, we provide evidence that the region C-terminal to the catalytic domain intramolecularly activates PRK2. Finally, we discovered that the catalytic domain mediates a cross-talk between the inhibitory N-terminal region and the activating C-terminal region. The results presented here describe a novel mechanism of regulation among AGC kinases and offer new insights into potential approaches to pharmacologically regulate PRK2. PMID:22511787

Bauer, Angelika F; Sonzogni, Silvina; Meyer, Lucas; Zeuzem, Stefan; Piiper, Albrecht; Biondi, Ricardo M; Neimanis, Sonja

2012-04-16

203

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)

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.

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

2013-02-01

204

Intermolecular interactions in albumin-sulfoxide-water systems at low temperatures, investigated by means of fluorescence quenching  

NASA Astrophysics Data System (ADS)

The effect of low temperatures on the interaction in human serum albumin (HSA)-diethyl sulfoxife (DESO)-dipropyl sulfoxide (DPSO)-water systems is investigated by means of fluorescence spectroscopy (intrinsic protein fluorescence, three-dimensional excitation/emission matrix (3D EEM)). The Stern-Volmer constants of HSA quenching are calculated for these systems. The structural changes occurring in these systems are characterized using 3D EEM profiles of HSA. It is shown that the HSA structural changes depend not only on the direct interaction of protein with sulfoxides but on structural changes in the solvent as well.

Grigoryan, K. R.; Shilajyan, H. A.

2013-05-01

205

Effect of water activity and solvent-ordering on intermolecular interaction of high-methoxyl pectins in various sugar solutions  

Microsoft Academic Search

Inter-macromolecular interaction of high-methoxyl pectins from citrus and apple in various sugar solutions (ribose, mannose, glucose, sucrose, trehalose, and maltose) was investigated through the analysis of the specific viscosity, ?sp, excluding the background effect of sugar solutions. With an increase in the sugar concentration, the water activity, AW, decreased and ?sp increased linearly with a decrease in AW for all

Yukinori Sato; Shima Kawabuchi; Yoshinobu Irimoto; Osato Miyawaki

2004-01-01

206

Pair interaction of disperse particles in electric field. 3. Hydrodynamic interaction of ideally polarizable metal particles and dead biological cells  

SciTech Connect

A theory has been developed for the interaction of ideally polarizable particles and biological cells in a steady (dc) electric field. The proposed approach differs from the classical dipole-dipole theory in that the carrier of the interaction is not the electric field, but rather the hydrodynamic field. For this reason, the indicated interaction decreases with increasing distance between particles at a considerably lower rate, similar to Coulomb interaction.

Dukhin, A.S.

1986-11-01

207

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

PubMed

Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5'GGGGTTGGGG3') designated as d(T(2)G(8)), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T(2)G(8)) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T(2)G(8))(2) and d(T(2)G(8))(4) forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T(2)G(8)) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex. PMID:22558271

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

2012-04-27

208

Interaction of Pyrrolobenzodiazepine (PBD) Ligands with Parallel Intermolecular G-Quadruplex Complex Using Spectroscopy and ESI-MS  

PubMed Central

Studies on ligand interaction with quadruplex DNA, and their role in stabilizing the complex at concentration prevailing under physiological condition, has attained high interest. Electrospray ionization mass spectrometry (ESI-MS) and spectroscopic studies in solution were used to evaluate the interaction of PBD and TMPyP4 ligands, stoichiometry and selectivity to G-quadruplex DNA. Two synthetic ligands from PBD family, namely pyrene-linked pyrrolo[2,1-c][1,4]benzodiazepine hybrid (PBD1), mixed imine-amide pyrrolobenzodiazepine dimer (PBD2) and 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) were studied. G-rich single-stranded oligonucleotide d(5?GGGGTTGGGG3?) designated as d(T2G8), from the telomeric region of Tetrahymena Glaucoma, was considered for the interaction with ligands. ESI-MS and spectroscopic methods viz., circular dichroism (CD), UV-Visible, and fluorescence were employed to investigate the G-quadruplex structures formed by d(T2G8) sequence and its interaction with PBD and TMPyP4 ligands. From ESI-MS spectra, it is evident that the majority of quadruplexes exist as d(T2G8)2 and d(T2G8)4 forms possessing two to ten cations in the centre, thereby stabilizing the complex. CD band of PBD1 and PBD2 showed hypo and hyperchromicity, on interaction with quadruplex DNA, indicating unfolding and stabilization of quadruplex DNA complex, respectively. UV-Visible and fluorescence experiments suggest that PBD1 bind externally where as PBD2 intercalate moderately and bind externally to G-quadruplex DNA. Further, melting experiments using SYBR Green indicate that PBD1 unfolds and PBD2 stabilizes the G-quadruplex complex. ITC experiments using d(T2G8) quadruplex with PBD ligands reveal that PBD1 and PBD2 prefer external/loop binding and external/intercalative binding to quadruplex DNA, respectively. From experimental results it is clear that the interaction of PBD2 and TMPyP4 impart higher stability to the quadruplex complex.

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

2012-01-01

209

All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System  

NASA Astrophysics Data System (ADS)

N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA-water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H...O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

Zhang, Rong; Tan, Zai-you; Luo, San-lai

2008-06-01

210

Competition between cation-pi interactions and intermolecular hydrogen bonds in alkali metal ion-phenol clusters. I. Phenol dimer  

Microsoft Academic Search

The competition between ion-molecule and molecule-molecule interactions was investigated in M+(phenol)2 cluster ions for M=Li, Na, K, and Cs. Infrared predissociation spectroscopy in the O-H stretch region was used to characterize the structure of the cluster ions. By adjusting the experimental conditions, it was possible to generate species where argon was additionally bound in order to investigate cold cluster ions.

Timothy D. Vaden; James M. Lisy

2005-01-01

211

Competition between cation-? interactions and intermolecular hydrogen bonds in alkali metal ion-phenol clusters. I. Phenol dimer  

Microsoft Academic Search

The competition between ion-molecule and molecule-molecule interactions was investigated in M+(phenol)2 cluster ions for M=Li, Na, K, and Cs. Infrared predissociation spectroscopy in the O–H stretch region was used to characterize the structure of the cluster ions. By adjusting the experimental conditions, it was possible to generate species where argon was additionally bound in order to investigate cold cluster ions.

Timothy D. Vaden; James M. Lisy

2005-01-01

212

Competition between cation-pi interactions and intermolecular hydrogen bonds in alkali metal ion-phenol clusters. II. Phenol trimer  

Microsoft Academic Search

The competition between ion-molecule and molecule-molecule interactions was investigated in M+(phenol)3 cluster ions for M=Li, Na, K, and Cs. Infrared predissociation spectroscopy in the O-H stretch region was used to characterize the structure of the cluster ions. By adjusting the experimental conditions, it was possible to generate species where argon was additionally bound in order to investigate cold cluster ions.

Timothy D. Vaden; James M. Lisy

2006-01-01

213

Competition between cation-? interactions and intermolecular hydrogen bonds in alkali metal ion-phenol clusters. II. Phenol trimer  

Microsoft Academic Search

The competition between ion-molecule and molecule-molecule interactions was investigated in M+(phenol)3 cluster ions for M=Li, Na, K, and Cs. Infrared predissociation spectroscopy in the O–H stretch region was used to characterize the structure of the cluster ions. By adjusting the experimental conditions, it was possible to generate species where argon was additionally bound in order to investigate cold cluster ions.

Timothy D. Vaden; James M. Lisy

2006-01-01

214

Accurate Intermolecular Interactions at Dramatically Reduced Cost and a Many-Body Energy Decomposition Scheme for XPol+SAPT  

NASA Astrophysics Data System (ADS)

An efficient, monomer-based electronic structure method is introduced for computing non-covalent interactions in molecular and ionic clusters. It builds upon our ``explicit polarization" (XPol) with pairwise-additive symmetry-adapted perturbation theory (SAPT) using the Kohn-Sham (KS) version of SAPT, but replaces the problematic and expensive sum-over-states dispersion terms with empirical potentials. This modification reduces the scaling from {O}(N^5) to {O}(N^3) and also facilitates the use of Kohn-Sham density functional theory (KS-DFT) as a low-cost means to capture intramolecular electron correlation. Accurate binding energies are obtained for benchmark databases of dimer binding energies, and potential energy curves are also captured accurately, for a variety of challenging systems. As compared to traditional DFT-SAPT or SAPT(DFT) methods, it removes the limitation to dimers and extends SAPT-based methodology to many-body systems. For many-body systems such as water clusters and halide-water cluster anions, the new method is superior to established density-functional methods for non-covalent interactions. We suggest that using different asymptotic corrections for different monomers is necessary to get good binding energies in general, as DFT-SAPT or SAPT(DFT), especially for hydrogen-bonded complexes. We also introduce a decomposition scheme for the interaction energy that extends traditional SAPT energy decomposition analysis to systems containing more than two monomers, and we find that the various energy components (electrostatic, exchange, induction, and dispersion) are in very good agreement with high-level SAPT benchmarks for dimers. For (H_2O)_6, the many-body contribution to the interaction energy agrees well with that obtained from traditional Kitaura-Morokuma energy decomposition analysis.

Lao, Ka Un; Herbert, John M.

2013-06-01

215

Intermolecular interaction energies by topologically partitioned electric properties II. Dispersion energies in one-centre and multicentre multipole expansions  

NASA Astrophysics Data System (ADS)

Multicentre multipole expansions in principle should allow one to solve the 'shape' convergence problem arising in the calculation of long-range interaction energies between large non-spherical molecules via point-multipole expansions. In part I of this series (1996, Molec. Phys., 88, 69) it was shown that this indeed is the case for first-order electrostatic and secondorder induction energies when employing distributed multipole moments and static polarizabilities generated from the topological partitioning of the molecular volume as provided by Bader's 'atoms-in-molecules' theory. Their topologically partitioned polarizabilities is used in the present contribution to compare the convergence behaviour of one-centre and multicentre multipole expansions of the secondorder dispersion energy for homomolecular dimers of the water, carbon monoxide, cyanogen and urea molecules. The findings are similar to those for the induction energy; the radial 'extension' convergence problem, which already exists for point-multipole expanded interaction energies between atoms, necessarily persists, but the angular convergence problems linked to the shape of the interacting molecules can successfully be treated by multicentre multipole expansions of the dispersion energy. generalization to frequency-dependent,

Hattig, Christof; Jansen, Georg; Hess, Bernd A.; Angyan, Janos G.

216

Intermolecular Interaction Between CO or CO{_2} and Ether or Thioether or Propylene Oxide in a Complex, Investigated by Fourier Transform Microwave Spectroscopy and AB Initio Calculations  

NASA Astrophysics Data System (ADS)

In sharp contrast with the hydrogen bond, which has beenwell established to be one of the strongest interactions between two atomic and/or molecular species, weak interactions between two closed-shell molecules have not been understood in detail. We have thus carried out a systematic study on complexes shown in the title; examples include the CO-ethylene oxide (EO), CO-ethylene sulfide (ES), CO-dimethyl ether (DME), CO-dimehtyl sulfide (DMS), CO{_2}-EO, CO{_2}-ES, CO{_2}-DME, and CO{_2}-propylene oxide (PO) complexes. From their Fourier transform microwave spectra, we determined the {RS} structure, the force constant of the van der Waals stretching mode, and the dissociation energy by analyzing the observed rotational and centrifugal distortion constants. We have also carried out ab initio molecular orbital calculations at the level of MP2 with basis sets 6-311++G(d, p) and aug-cc-pVDZ using the Gaussian 09 package. In most cases, the MP2/6-311++G(d, p) calculations yield rotational constants in better agreement with the experimental values, than the other basis set, in other word, the molecular structures calculated using this basis set are close to those experimentally found for the ground state. The estimated bond dissociation energies including the zero-point vibrational energy corrections ?ZPV and the basis set superposition errors (BSSE) calculated with the counterpoise correction (CP) are in good agreement with the observed binding energies {E_B}. We have applied an NBO analysis to the complexes to calculate the stabilization energy CT (= ?E{??*}), which we found are closely correlated with the binding energies {E_B}. We have thus achieved a consistent overview on the intermolecular interaction in the complexes under consideration.

Kawashima, Yoshiyuki; Orita, Yukari; Sato, Akinori; Hirota, Eizi

2011-06-01

217

Vibrational absorption, vibrational circular dichroism, and theoretical studies of methyl lactate self-aggregation and methyl lactate-methanol intermolecular interactions  

NASA Astrophysics Data System (ADS)

The infrared vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of methyl lactate in carbon tetrachloride and methanol have been measured in the 1000-1800 cm-1 region. Noticeable changes due to the solute self-aggregation and solvent-solute intermolecular hydrogen-bonding interactions have been detected in the reported spectra of the 2M methyl lactate solution in CCl4 and in methanol, respectively. Molecular dynamics simulations and a series of density functional theory (DFT) B3LYP/6-311++G**) and single point MP2/6-311++G** energy calculations have been performed to identify and to model the explicit hydrogen-bonding interactions between the methanol solvent and the methyl lactate solute and among the methyl lactate molecules. Geometry search and optimization have been performed for the most stable conformers of the methyl lactate dimer and the methyl lactate-(methanol)N clusters, with N=1, 2, and 3. The relative single point MP2 energies among conformers are noticeably different from those obtained with DFT for the larger methyl lactate-methanol complexes. The VA and VCD spectra of these complexes have been simulated and compared to the corresponding experimental spectra. From the combined experimental and theoretical VA and VCD studies, it has been identified that both the methyl lactate monomer and dimer are the main species in the 2M CCl4 solution with 65% and 35% relative abundances, respectively, while the binary (55%) and quaternary (30%) methyl lactate-methanol clusters dominate in the 2M methanol solution, together with a smaller amount (15%) of the methyl lactate monomer. The effects of solute self-aggregation and solute-solvent interactions have been investigated in detail.

Liu, Yang; Yang, Guochun; Losada, Martin; Xu, Yunjie

2010-06-01

218

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

PubMed

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

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

2013-08-13

219

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

NASA Astrophysics Data System (ADS)

We report on the crystal structures of three polymorphs of 9-aminoacridinium 2,4-dinitrobenzoate ? 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 ?-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 ? 2,4-dinitrobenzoic acid is the first in which the appearance of monoanionic dimers of 2,4-dinitrobenzoic acid has been documented.

Sikorski, Artur; Trzybi?ski, Damian

2013-10-01

220

Extended intermolecular interactions in a serine protease-canonical inhibitor complex account for strong and highly specific inhibition.  

PubMed

We have previously shown that a trypsin inhibitor from desert locust Schistocerca gregaria (SGTI) is a taxon-specific inhibitor that inhibits arthropod trypsins, such as crayfish trypsin, five orders of magnitude more effectively than mammalian trypsins. Thermal denaturation experiments, presented here, confirm the inhibition kinetics studies; upon addition of SGTI the melting temperatures of crayfish and bovine trypsins increased 27 degrees C and 4.5 degrees C, respectively. To explore the structural features responsible for this taxon specificity we crystallized natural crayfish trypsin in complex with chemically synthesized SGTI. This is the first X-ray structure of an arthropod trypsin and also the highest resolution (1.2A) structure of a trypsin-protein inhibitor complex reported so far. Structural data show that in addition to the primary binding loop, residues P3-P3' of SGTI, the interactions between SGTI and the crayfish enzyme are also extended over the P12-P4 and P4'-P5' regions. This is partly due to a structural change of region P10-P4 in the SGTI structure induced by binding of the inhibitor to crayfish trypsin. The comparison of SGTI-crayfish trypsin and SGTI-bovine trypsin complexes by structure-based calculations revealed a significant interaction energy surplus for the SGTI-crayfish trypsin complex distributed over the entire binding region. The new regions that account for stronger and more specific binding of SGTI to crayfish than to bovine trypsin offer new inhibitor sites to engineer in order to develop efficient and specific protease inhibitors for practical use. PMID:15922357

Fodor, Krisztián; Harmat, Veronika; Hetényi, Csaba; Kardos, József; Antal, József; Perczel, András; Patthy, András; Katona, Gergely; Gráf, László

2005-07-01

221

Anisotropy in the interaction of ultracold dysprosium.  

PubMed

The nature of the interaction between ultracold atoms with a large orbital and spin angular momentum has attracted considerable attention. It was suggested that such interactions can lead to the realization of exotic states of highly correlated matter. Here, we report on a theoretical study of the competing anisotropic dispersion, magnetic dipole-dipole, and electric quadrupole-quadrupole forces between two dysprosium atoms. Each dysprosium atom has an orbital angular momentum of L = 6 and a magnetic moment of ? = 10 ?(B). We show that the dispersion coefficients of the ground state adiabatic potentials lie between 1865 a.u. and 1890 a.u., creating a non-negligible anisotropy with a spread of 25 a.u. and that the electric quadrupole-quadrupole interaction is weak compared to the other interactions. We also find that for interatomic separations R < 50a(0) both the anisotropic dispersion and magnetic dipole-dipole potential are larger than the atomic Zeeman splittings for external magnetic fields of order 10 G to 100 G. At these separations the atomic angular momentum can be reoriented. We finish by describing two scattering models for these inelastic m-changing collisions. A universal scattering theory is used to model loss due to the anisotropy in the dispersion and a Born approximation is used to model losses from the magnetic dipole-dipole interaction for the (164)Dy isotope. These models find loss rates that are of the same order of magnitude as the experimental value. PMID:21804964

Kotochigova, Svetlana; Petrov, Alexander

2011-08-01

222

13C/15N-19F Intermolecular REDOR NMR Study of the Interaction of TAR RNA with Tat Peptides  

PubMed Central

The complex of the HIV TAR RNA with the viral regulatory protein Tat is of considerable interest, but the plasticity of this interaction has made it impossible so far to establish the structure of that complex. In order to explore a new approach to obtain structural information on protein-RNA complexes, we performed 13C/15N-19F REDOR NMR experiments in the solid state on TAR bound to a peptide comprising the RNA-binding section of Tat. A critical arginine in the peptide was uniformly 13C and 15N labeled and 5-fluorouridine was incorporated at the U23 position of TAR. REDOR irradiation resulted in dephasing of the 13C and 15N resonances, indicating proximity of the U23(5F)-C and U23(5F)-N spin pairs. Best fits to the REDOR data shows the U23(5F)-C distances and the U23(5F)-N distances are in good agreement with the distances obtained from solution NMR structures of partial complexes of Tat with TAR. These results demonstrate that it is possible to study protein-RNA complexes using solid-state REDOR NMR measurements, adding to a growing list of solid state techniques for studying protein-nucleic acid complexes.

Huang, Wei; Varani, Gabriele; Drobny, Gary P.

2010-01-01

223

Structures and Intermolecular Interactions in Dimethyl Sulfoxide-Water System Studied by All-atom Molecular Simulations  

NASA Astrophysics Data System (ADS)

An all-atom dimethyl sulfoxide (DMSO) and water model have been used for molecular dynamics simulation. The NMR and IR spectra are also performed to study the structures and interactions in the DMSO-water system. And there are traditional strong hydrogen bonds and weak C-H ··· O contacts existing in the mixtures according to the analysis of the radial distribution functions. The insight structures in the DMSO-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Interestingly, the molar fraction of DMSO 0.35 is found to be a special concentration by the network. It is the transitional region which is from the water rich region to the DMSO rich region. The stable aggregates of (DMSO)m·S=O···HW-OW·(H2O)n might play a key role in this region. Moreover, the simulation is compared with the chemical shifts in NMR and wavenumbers in IR with concentration dependence. And the statistical results of the average number hydrogen bonds in the MD simulations are in agreement with the experiment data in NMR and IR spectra.

Zhang, Rong; Wu, Wen-juan

2010-10-01

224

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

NASA Astrophysics Data System (ADS)

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.

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

2012-03-01

225

Rydberg Atom - Atom Interactions and Collisions  

NASA Astrophysics Data System (ADS)

The interaction between highly excited Rydberg atoms exerts a crucial role in such modern issues as ultracold Rydberg plasmas, Rydberg matter, dipole blockade and quantum computing. For two-electron states in a Rydberg-Rydberg dimer Rg_2, the dipole-dipole interaction ( ˜ 1/R^3) between the Rydberg atoms Rg with internuclear distance R can be both attractive or repulsive, depending on electronic state. For the two-electron states with maximum dipole-dipole attraction, the next term in the potential energy originates from the quadrupole-quadrupole interaction which is repulsive. Since the attraction prevails at larger internuclear separations R and repulsion dominates at smaller R, the related potential curve exhibits a minimum at separation R = (10 ?5/3?2) n^2. For such large R, the autoionization width is small and long-living vibrational states are possible. In the simplest case of H(n=2)-H(n=2) pair, the potential well supports several tens of vibrational bound states. Estimates for higher n are provided. A theory of ?-mixing intrashell transitions in Rydberg-Rydberg collisions induced by the dipole-dipole interaction will also be presented. Research supported by AFOSR, Grant 49620-02-1-0338 and NSF Grant 01-00890.

Flannery, Raymond; Ostrovsky, Valentin; Prudov, N.; Vrinceanu, Daniel

2003-05-01

226

C-NOT gate based on ultracold Rydberg atom interactions  

NASA Astrophysics Data System (ADS)

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

Rashid, Muhammad; Maarten, Hoogerland; Yasir, Jamil

2013-09-01

227

Two body and multibody interaction in a cold Rydberg gas  

NASA Astrophysics Data System (ADS)

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).

Han, Jianing; Gallagher, Tom

2009-05-01

228

Electron and nuclear spin interactions in the optical spectra of single GaAs quantum dots.  

PubMed

Fine and hyperfine splittings arising from electron, hole, and nuclear spin interactions in the magneto-optical spectra of individual localized excitons are studied. We explain the magnetic field dependence of the energy splitting through competition between Zeeman, exchange, and hyperfine interactions. An unexpectedly small hyperfine contribution to the splitting close to zero applied field is described well by the interplay between fluctuations of the hyperfine field experienced by the nuclear spin and nuclear dipole/dipole interactions. PMID:11384450

Gammon, D; Efros, A L; Kennedy, T A; Rosen, M; Katzer, D S; Park, D; Brown, S W; Korenev, V L; Merkulov, I A

2001-05-28

229

Controlled many-body interactions in a frozen Rydberg gas  

SciTech Connect

Previous resonant dipole-dipole energy-transfer experiments of cold Rydberg gases [Anderson et al., Phys. Rev. Lett. 80, 249 (1998); Mourachko et al., Phys. Rev. Lett. 80, 253 (1998)] have been interpreted as providing evidence of many-body, as opposed to purely binary, effects. Here we separate two-body and many-body interactions by introducing an additional Rydberg state, which does not participate directly in the energy-transfer process, but is strongly coupled to one of the final states. We observe broadening of the energy-transfer resonances due to this added Rydberg state, which clearly demonstrates the many-body nature of the dipole-dipole interactions in such a system.

Mourachko, I.; Li Wenhui; Gallagher, T.F. [Department of Physics, University of Virginia, Charlottesville, Virginia 22904 (United States)

2004-09-01

230

Intermolecular Interactions in the Mechanism of Skeletal Muscle Sarcoplasmic Reticulum Ca2+-ATPase (SERCA1): Evidence for a Tri-protomer*  

PubMed Central

Native membrane sarcoplasmic reticulum (SR) Ca2+-ATPase isolated from skeletal muscle (SERCA1) exhibits oligomeric kinetic behavior (Mahaney, J.E., Thomas, D.D., and Froehlich, J.P. (2004) Biochemistry 43:4400–4416). In the present study we used quenched-flow mixing, electron paramagnetic resonance (EPR) and chemical cross-linking to probe for intermolecular interactions at physiological (0.1M) and high (0.4 M) KCl. Exposure SR membranes to water- and lipid-soluble cross-linking reagents revealed a mixture of SERCA1 oligomeric species consisting mainly of dimers and trimers. Titration of iodoacetamide spin labeled-SERCA1 with AMPPCP in the presence of 10 µM Ca2+ and 0.1 M KCl revealed high (KD = 45 µM) and low affinity (KD = 315 µM) nucleotide binding sites in a 2:1 ratio, respectively. Raising the [KCl] to 0.4 M increased the fraction of weak binding sites and lowered the KD of the high affinity component (20 µM). Phosphorylation by 10 µM ATP at 21°C and 0.1 M KCl produced an early burst of Pi production without a corresponding decline in the steady state phosphoenzyme (EP) level. The steady state EP level was twice as large as the Pi burst and received equal contributions from E1P and E2P. Chasing the phosphoenzyme at 0.4 M KCl and 2°C with ADP revealed a biphasic time course of E1P formation with a slow phase that matched the kinetics of the transient EPR signal from the spin-labeled Ca2+-ATPase. The absence of a fast component in the EPR signal excludes E1P as its source. Instead, it arises from the slow, KCl-dependent transformation at the start of the cycle which controls the formation of downstream intermediates with an increased mole fraction of rotationally restricted probes. We modeled this behavior with a SERCA1 trimer in which the formation of E1P/E2/E2P from E1ATP/E2P/E1P results from concerted transformations in the subunits coupling phosphorylation (E1ATP ? E1P + ADP) to dephosphorylation (E2P ? E2 + Pi) and the conversion of E1P to E2P.

Mahaney, James E.; Thomas, David D.; Farrance, Iain K.; Froehlich, Jeffrey P.

2013-01-01

231

Intermolecular interactions of benzene and carbon tetrachloride with selected free radicals in solution as studied by 13C and 1H dynamic nuclear polarization  

Microsoft Academic Search

Intermolecular hyperfine coupling between 13C nuclei and free-radical unpaired electron spins has been examined for six combinations of three free radicals and two solvent molecules. From magnetic field and temperature-dependent dynamic nuclear polarization measurements, scalar and dipolar coupling contributions have been separated. Interpretation of these results in terms of a modified diffusion model revealed scalar spectral density functions with two

W. Müller-Warmuth; Reynir Vilhjalmsson; P. A. M. Gerlof; J. Smidt; J. Trommel

1976-01-01

232

Effect of Solution Conditions on the Nanoscale Intermolecular Interactions Between Human Serum Albumin and Low Grafting Density Surfaces of Poly(ethylene oxide)  

Microsoft Academic Search

The first step in the biological rejection response to an implanted blood-contacting biomaterial is the non-covalent adsorption of proteins onto the surface, which triggers a cascade reaction ultimately resulting in thrombus formation. Using the technique of high resolution force spectroscopy, we have quantified the nonspecific intermolecular forces between fatty acid-complexed human serum albumin (HSA) covalently attached to a cantilever probe

Monica Rixman; Celia Macias; Delphine Dean; Christine Ortiz

2003-01-01

233

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

SciTech Connect

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

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

2011-08-15

234

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

SciTech Connect

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

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

1991-12-31

235

Interaction-Induced Chiral Quantum States of the Ultracold Polar Molecules  

NASA Astrophysics Data System (ADS)

The ultracold polar molecules with the tunable dipole-dipole interaction, not only would enable explorations of a large class of exotic many-body physics phenomena, but also could be used for quantum information processing. In the present paper we demonstrate that this dipole-dipole interaction can generate the degenerate chiral quantum states acting as a qubit robust against noise when the ultracold polar molecules are confined by a triangular lattice. Moreover, we also find two first-order quantum phase transitions by controlling an external driving field. One is the transition with the change of the different degenerate chiral quantum states. The other is the transition with the breaking of the degenerate quantum chiral states to the nondegenerate state. In experiment, these first-order quantum phase transitions can be detected by measuring the collective molecular population.

Wang, Ming-Hao; Liang, Jiu-Qing; Ma, Jie; Chen, Gang; Jia, Suo-Tang

2012-11-01

236

Contribution of dipolar interactions to third-order nonlinear dielectric susceptibility of nanocomposites.  

PubMed

We consider an ensemble of identical semiconductor nanoparticles randomly embedded into dielectric matrix. The nanoparticles are polarized by the laser irradiation having linear polarization. The contribution of dipole-dipole interactions to third-order dielectric susceptibility is calculated by using mean random field method. It is shown that this contribution always has a negative sign, and it can be comparable with the values of optical nonlinearity observed experimentally. PMID:20517431

Panov, Andrey V

2010-06-01

237

Effect of Solution Conditions on the Nanoscale Intermolecular Interactions Between Human Serum Albumin and Low Grafting Density Surfaces of Poly(ethylene oxide)  

NASA Astrophysics Data System (ADS)

The first step in the biological rejection response to an implanted blood-contacting biomaterial is the non-covalent adsorption of proteins onto the surface, which triggers a cascade reaction ultimately resulting in thrombus formation. Using the technique of high resolution force spectroscopy, we have quantified the nonspecific intermolecular forces between fatty acid-complexed human serum albumin (HSA) covalently attached to a cantilever probe tip and individual end-grafted poly(ethylene oxide) mushrooms. In order to help elucidate the molecular origins of the constituent forces (e.g. steric, electrostatic, van der Waals), experiments were performed varying both the solution environmental conditions (e.g. ionic strength, removal of the bound fatty acids, and the addition of the antihydrophobic agent isopropanol), and the probe deflection rate.

Rixman, Monica; Macias, Celia; Dean, Delphine; Ortiz, Christine

2003-03-01

238

Intermolecular electrostatic energies using density fitting  

PubMed Central

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.

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

2009-01-01

239

Dynamics of a magnetic dimer with exchange, dipolar, and Dzyalozhinski-Moriya interaction  

NASA Astrophysics Data System (ADS)

We investigate the dynamics of a magnetic system consisting of two magnetic moments coupled by either the exchange, dipole-dipole, or Dzyalozhinski-Moriya interaction. We compare the switching mechanisms and switching rates as induced by the three couplings. For each coupling and each configuration of the two anisotropy axes, we describe the switching modes and, using the kinetic theory of Langer, we provide (semi-)analytical expressions for the switching rate. We then compare the three interactions with regard to their efficiency in the reversal of the net magnetic moment of the dimer. We also investigate how the energy barriers vary with the coupling. For the dipole-dipole interaction we find that the energy barrier may either increase or decrease with the coupling depending on whether the latter is weak or strong. Finally, upon comparing the various switching rates, we find that the dipole-dipole coupling leads to the slowest magnetic dimer, as far as the switching of its net magnetic moment is concerned.

Franco, A. F.; Martinez, J. M.; Déjardin, J. L.; Kachkachi, H.

2011-10-01

240

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

NASA Astrophysics Data System (ADS)

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.

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

2012-01-01

241

Long-Range Metal-Mediated Interactions Between S and CO on Cu(100)  

SciTech Connect

The infrared study of carbon monoxide (CO) on presulfided Cu(100), combined with Auger electron spectroscopy and thermal desorption mass spectrometry, reveals that sulfur (S) introduces a long-range modification (Friedel oscillations) to the local density of states, which affects the bond strength of CO adsorbates. A local minimum of the LDOS is induced at the second nearest neighbor adsorption sites, suppressing CO adsorption, but a local maximum at the third nearest neighbor adsorption sites enhances the C-metal bond strength. For a low S coverage, where dipole-dipole coupling is still dominant, a coherent potential approximation treatment of dipole-dipole coupling by Persson and Ryberg is used to estimate the spatial extent (r{sub effective}) of S and CO metal-mediated interactions. r{sub effective} is found to be between 6-7 Angstroms.

Hu,X.; Hirschmugl, C.

2005-01-01

242

Influence of the magnetic dipole interaction on the properties of magnetic vortices in particles of small size  

Microsoft Academic Search

Two type of plaquette systems are proposed for modeling a vortex in an easy-plane two-dimensional Heisenberg ferromagnet with the dipole–dipole interaction of the magnetic moments of the lattice taken into account. The first plaquette describes a system with the boundary spins fixed in the easy plane perpendicular to the “surface” of the magnet, while in the second plaquette the boundary

A. S. Kovalev; J. E. Prilepsky

2004-01-01

243

Mutagenesis of the bovSERPINA3-3 demonstrates the requirement of aspartate-371 for intermolecular interaction and formation of dimers.  

PubMed

The family of serpins is known to fold into a metastable state that is required for the proteinase inhibition mechanism. One of the consequences of this conformational flexibility is the tendency of some mutated serpins to form polymers, which occur through the insertion of the reactive center loop of one serpin molecule into the A-sheet of another. This "A-sheet polymerization" has remained an attractive explanation for the molecular mechanism of serpinopathies. Polymerization of serpins can also take place in vitro under certain conditions (e.g., pH or temperature). Surprisingly, on sodium dodecyl sulfate/polyacrylamide gel electrophoresis, bovSERPINA3-3 extracted from skeletal muscle or expressed in Escherichia coli was mainly observed as a homodimer. Here, in this report, by site-directed mutagenesis of recombinant bovSERPINA3-3, with substitution D371A, we demonstrate the importance of D371 for the intermolecular linkage observed in denaturing and reducing conditions. This residue influences the electrophoretic and conformational properties of bovSERPINA3-3. By structural modeling of mature bovSERPINA3-3, we propose a new "non-A-sheet swap" model of serpin homodimer in which D371 is involved at the molecular interface. PMID:22505318

Blanchet, X; Péré-Brissaud, A; Duprat, N; Pinault, E; Delourme, D; Ouali, A; Combet, C; Maftah, A; Pélissier, P; Brémaud, L

2012-05-18

244

Critical Temperature of Weakly Interacting Dipolar Condensates  

SciTech Connect

We calculate perturbatively the effect of a dipolar interaction upon the Bose-Einstein condensation temperature. This dipolar shift depends on the angle between the symmetry axes of the trap and the aligned atomic dipole moments, and is extremal for parallel or orthogonal orientations, respectively. The difference of both critical temperatures exhibits most clearly the dipole-dipole interaction and can be enhanced by increasing both the number of atoms and the anisotropy of the trap. Applying our results to chromium atoms, which have a large magnetic dipole moment, shows that this dipolar shift of the critical temperature could be measured in the ongoing Stuttgart experiment.

Glaum, Konstantin; Kleinert, Hagen [Fachbereich Physik, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin (Germany); Pelster, Axel [Fachbereich Physik, Universitaet Duisburg-Essen, Lotharstrasse 1, 47048 Duisburg (Germany); Pfau, Tilman [5. Physikalisches Institut, Universitaet Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart (Germany)

2007-02-23

245

Collective Many-Body Interaction in Rydberg Dressed Atoms  

SciTech Connect

We present a method to control the shape and character of the interaction potential between cold atomic gases by weakly dressing the atomic ground state with a Rydberg level. For increasing particle densities, a crossover takes place from a two-particle interaction into a collective many-body interaction, where the dipole-dipole or van der Waals blockade phenomenon between the Rydberg levels plays a dominant role. We study the influence of these collective interaction potentials on a Bose-Einstein condensate and present the optimal parameters for its experimental detection.

Honer, Jens; Weimer, Hendrik; Buechler, Hans Peter [Institute for Theoretical Physics III, University of Stuttgart, Stuttgart (Germany); Pfau, Tilman [5. Physikalische Institut, University of Stuttgart, Stuttgart (Germany)

2010-10-15

246

The effect of dipolar interaction on the magnetic isotope effect  

NASA Astrophysics Data System (ADS)

A multi-channel kinetic description is used to study the magnetic isotope effect (MIE) in zero magnetic field. The maximal isotope effect is equal to the number of channels, two for the hyperfine interaction but four for the electron spin dipole-dipole interaction of the intermediate radical pair. Quantum mechanical calculations agree with these conclusion and show that large MIE may be obtained even in the presence of a strong exchange interaction. The observed magnesium isotope effect on the rate of enzymatic synthesis of adenosine triphosphate (ATP) is approximately 3 implying that the dipolar interaction is responsible for the effect. Our calculations provide support for the proposed mechanism.

Pedersen, J. Boiden; Mojaza, Matin; Lukzen, Nikita N.

2010-08-01

247

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

PubMed

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

Takayama, Yuki; Clore, G Marius

2012-06-20

248

2-Acylamino-6-pyridones: breaking of an intramolecular hydrogen bond by self-association and complexation with double and triple hydrogen bonding counterparts. Uncommon steric effect on intermolecular interactions.  

PubMed

2-Acylamino-6-pyridones (acyl = RCO, where R = Me, Et, i-Pr, t-Bu, and 1-adamantyl) were previously characterized by X-ray diffractometry and solid-state NMR techniques by us. One of these compounds was used recently in organocatalysis. The series is now studied in solution and by computational methods recommended for noncovalent interactions (DFT/M05). These compounds showed interesting behavior during dilution and titration experiments monitored by (1)H NMR. 2-Acylamino-6-pyridones change their conformation at higher concentrations, forming double hydrogen-bonded dimers and trimers in which an uncommon steric effect is observed. To the best of our knowledge, this is the first example of such behavior of hydrogen-bonded molecules. Heterocomplexation of the studied compounds happens via double or triple hydrogen bonding, depending on the properties of the counterpart. The computation data support and explain the effects observed experimentally, including the tautomeric, closed/open form equilibrium and intermolecular interaction preferences. PMID:22263658

O?mia?owski, Borys; Kolehmainen, Erkki; Kowalska, Magdalena

2012-02-02

249

Intermolecular Forces: Solids and Liquids  

NSDL National Science Digital Library

General chemistry WebCT exam/quiz questions. The Intermolecular Forces: Solids and Liquids topic covers the forces that exist between atoms and molecules in solids and liquids, and how these affect properties such as boiling point, conductivity, and lattice energy.

2007-09-07

250

Single-molecule force spectroscopic studies on intra- and intermolecular interactions of G-quadruplex aptamer with target Shp2 protein.  

PubMed

With widespread applications in biosensors, diagnostics, and therapeutics, much investigation has been made in the structure of the G-quadruplexes and mechanism of their interactions with protein targets. However, in view of AFM based single-molecule force spectroscopic (SMFS) studies of G-quadruplex systems, only bimolecular approaches have been employed. In this article, we present an improved dual-labeling approach for surface immobilization of G-quadruplex DNA apatmers for investigation of intramolecular interaction from an integral unimolecular G-quadruplex system. The melting force of HJ24 G-quadruplex aptamer in the presence of K(+) has been successfully measured. It has been found that dynamic equilibrium exists between unfolding and folding structures of the HJ24 aptamer even in pure water. We also investigated the interactions between the HJ24 aptamer and its target protein (Shp2) under the same solution condition. The HJ24/Shp2 unbinding force in the absence of K(+), 42.0 pN, is about 50% smaller than that in the presence of K(+), 61.7 pN. The great reduction in force in the absence of K(+) suggests that the stability of G-quadruplex secondary structure is important for a stable HJ24/Shp2 binding. The methodology developed and demonstrated in this work is applicable for studying the stability of secondary structures of other unimolecular G-quadruplex aptamers and their interactions with target proteins. PMID:22924632

Zhao, Xue-Qin; Wu, Jie; Liang, Jing-Hong; Yan, Jia-Wei; Zhu, Zhi; Yang, Chaoyong James; Mao, Bing-Wei

2012-09-10

251

An evaluation of the thermal properties of H2 and O2 on the basis of ab initio calculations for their intermolecular interactions  

Microsoft Academic Search

We have calculated the potential energy surfaces for the singlet state of H2–H2 and for the quintet state of using the coupled-cluster theory with singles, doubles and perturbative triple excitations [CCSD(T)] and an aug-cc-pVQZ basis set. Resulting interaction potentials were expanded in spherical harmonics, separating the radial and the angular dependencies to obtain analytical expressions. Monte-Carlo simulations for the NVT

Mitsuo Koshi; Shin-ichi Tsuda; Kazuya Shimizu

2011-01-01

252

An evaluation of the thermal properties of H2 and O2 on the basis of ab initio calculations for their intermolecular interactions  

Microsoft Academic Search

We have calculated the potential energy surfaces for the singlet state of H2–H2 and for the quintet state of using the coupled-cluster theory with singles, doubles and perturbative triple excitations [CCSD(T)] and an aug-cc-pVQZ basis set. Resulting interaction potentials were expanded in spherical harmonics, separating the radial and the angular dependencies to obtain analytical expressions. Monte-Carlo simulations for the NVT

Mitsuo Koshi; Shin-ichi Tsuda; Kazuya Shimizu

2012-01-01

253

The Different Biological Effects of Telomestatin and TMPyP4 Can Be Attributed to Their Selectivity for Interaction with Intramolecular or Intermolecular G-Quadruplex Structures  

Microsoft Academic Search

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

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

2003-01-01

254

Failure of lamin A/C to functionally assemble in R482L mutated familial partial lipodystrophy fibroblasts: altered intermolecular interaction with emerin and implications for gene transcription.  

PubMed

Familial partial lipodystrophy is an autosomal dominant disease caused by mutations of the LMNA gene encoding alternatively spliced lamins A and C. Abnormal distribution of body fat and insulin resistance characterize the clinical phenotype. In this study, we analyzed primary fibroblast cultures from a patient carrying an R482L lamin A/C mutation by a morphological and biochemical approach. Abnormalities were observed consisting of nuclear lamin A/C aggregates mostly localized close to the nuclear lamina. These aggregates were not bound to either DNA-containing structures or RNA splicing intranuclear compartments. In addition, emerin did not colocalize with nuclear lamin A/C aggregates. Interestingly, emerin failed to interact with lamin A in R482L mutated fibroblasts in vivo, while the interaction with lamin C was preserved in vitro, as determined by coimmunoprecipitation experiments. The presence of lamin A/C nuclear aggregates was restricted to actively transcribing cells, and it was increased in insulin-treated fibroblasts. In fibroblasts carrying lamin A/C nuclear aggregates, a reduced incorporation of bromouridine was observed, demonstrating that mutated lamin A/C in FPLD cells interferes with RNA transcription. PMID:14597414

Capanni, Cristina; Cenni, Vittoria; Mattioli, Elisabetta; Sabatelli, Patrizia; Ognibene, Andrea; Columbaro, Marta; Parnaik, Veena K; Wehnert, Manfred; Maraldi, Nadir M; Squarzoni, Stefano; Lattanzi, Giovanna

2003-11-15

255

Theoretical study of properties of H bonds and intermolecular interactions in linear cis-, trans-cyclotriazane clusters (n=2-8)  

NASA Astrophysics Data System (ADS)

Our calculations based upon Becke's three-parameter functional of density-functional theory (DFT) with the correlation of Lee, Yang, and Parr (B3LYP), natural bond orbital, and atoms in molecule indicate that in drastic contrast to most H-bonded systems, the anticooperative and cooperative effects coexist in the linear H-bonded cis-,trans (c,t)-cyclotriazane clusters (n=2-8). As cluster size increases, the properties along the H-bonded chains at trans-positions take on the unexpectedly anticooperative changes which are reflected in elongation of the N...H hydrogen bonds, frequency blueshift in the N-H stretching vibrations, decay in the n(N)-->?*(N-H) charge transfers, and weakening of strengths of the N...H bonds. And the cooperative changes in the corresponding properties for the cis- H-bonded chains are observed to be concurrent with the anticooperativities. The rise and fall in the n(N)-->?*(N-H) interactions cause increment and decrement in capacities of the clusters to concentrate electrons at the bond critical points of the N...H bonds, and thereby leading to the cooperative and the anticooperative changes especially in the N...H lengths and the N-H stretching frequencies. In terms of three-body symmetry-adapted perturbation theory (three-body SAPT), the first exchange nonadditivity plays a more important role in stabilizing trimer than the nonadditive induction. However, the dominance of the first exchange nonadditivity in three-body interaction unexpectedly triggers the anticooperative effect that counteracts the concurrent cooperative effect. According to the SAPT(DFT), which is a combination of SAPT with asymptotically corrected DFT, DFT/B3LYP is able to succeed in describing the electrostatic, exchange, and induction components, but fails to yield satisfactory interaction energies due to the fact that about 40% of short-range dispersion energy is neglected by the DFT, which is different from many H-bonded described well by the DFT. A quantum cluster equilibrium model illustrates that the c,t-cyclotriazane liquid phase exhibits a weak cooperative effect.

Song, Hua-Jie; Xiao, He-Ming; Dong, Hai-Shan

2006-02-01

256

The Role of Proton-Proton Interaction in NH4H2PO4-Type Crystals  

NASA Astrophysics Data System (ADS)

The interaction between the protons on the nearby hydrogen bonds in NH4H2PO4 (ADP)-type crystals, called the Ishibashi interaction, was analyzed to derive theoretically, i.e., not in an ad hoc way, the effective dipole-dipole interaction between PO4 radicals, which plays a substantial role in phase transitions. It turns out that at low temperatures the ADP-type antiferroelectric phase is stabilized if the Ishibashi interaction is repulsive, while the monoclinic ferroelectric phase is stabilized otherwise.

Ishibashi, Yoshihiro; Iwata, Makoto

2009-01-01

257

Direct determination of intermolecular potentials from gaseous transport coefficients alone  

Microsoft Academic Search

Intermolecular pair-potential energy functions are given for all the unlike interactions of the monatomic gases. The potentials are obtained by direct inversion of experimental measurements of low density binary mixture viscosity and diffusion coefficients. In those cases where these data extend to sufficiently low temperatures to enable the potential well depth ?\\/k to be determined, the values obtained for this

G. C. Maitland; W. A. Wakeham

1978-01-01

258

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

SciTech Connect

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.

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

2010-11-15

259

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

NASA Astrophysics Data System (ADS)

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.

Han, Jianing

2010-11-01

260

Librational echo: Subpicosecond intermolecular interactions in liquid  

SciTech Connect

The ultrafast optical Kerr effect observed in liquids upon two-pulse laser excitation is studied theoretically. It is shown that a Raman echo on librational frequencies (librational echo) can be excited in liquid. The librational echo has the following features: its shape and amplitude strongly depend on the local inhomogeneity of a medium and the form of local potentials; and the echo signal can be separated into the contributions of the phase and irreversible relaxation of coherent molecular librations. These properties of the librational echo can be used for studying the specific features of the local structure of liquids by the method of selective subpicosecond spectroscopy of molecular librations. (nonlinear optical phenomena)

Nikiforov, V G [E.K.Zavoisky Physical-Technical Institute, Kazan Scientific Center, Russian Academy of Sciences, Kazan (Russian Federation)

2008-02-28

261

Optical investigations of intermolecular electronic interactions and "free" charge carriers in quasi-two-dimensional organic conductors and superconductors of the group ?-(BEDT-TTF)2Cu[N(CN)2]Br x Cl1 - x  

NASA Astrophysics Data System (ADS)

The reflectance spectra and optical conductivity spectra of quasi-two-dimensional organic conductor crystals of the group of compounds ?-(BEDT-TTF)2Cu[N(CN)2]Br x Cl1 - x with x = 0, 0.40, 0.73, 0.85, and 0.90 in the spectral region from 6 meV to 0.74 eV at temperatures T = 90-20 K have been quantitatively analyzed in the framework of a combined semiempirical model including the cluster (tetramer) theory for strongly correlated electrons coupling with intramolecular vibrations and the Drude theory of free electrons with the aim of studying intermolecular electronic interactions and their influence on the formation of the ground state in these crystals. It has been established that the parameters characterizing the charge transfer between molecules in dimers and tetramers and the vibronic coupling constants are almost identical for the compounds under investigation. A large value of the effective Coulomb repulsion ( U/t = 1.3-1.5) indicates that strong electron correlations occur in the compounds both with a metal-insulator phase transition ( x = 0, 0.40) and with a metal-superconductor phase transition ( x = 0.85, 0.90). The conclusion has been drawn that, at x = 0, electron correlations favor an antiferromagnetic spin ordering and a metal-insulator phase transition, whereas for superconductors ( x = 0.85, 0.90), the metal-insulator phase transition is hindered as a result of the structural disorder due to the difference in orientations of the terminal CH2 groups of the BEDT-TTF molecule. It has been shown that quasi-free charge carriers interact with electrons localized on the clusters and do not interact with intramolecular vibrations. It has been noted that the oscillator strength of the observed electronic transitions in the initial metallic band ( N eff = 0.38-0.31 per dimer) is considerably less than the corresponding value for free (noninteracting) charge carriers ( N = 1). This suggests that the Coulomb correlations and vibronic coupling play a decisive role in the kinetic phenomena observed in the molecular conductors and superconductors under investigation.

Vlasova, R. M.; Petrov, B. V.; Semkin, V. N.

2011-09-01

262

Synthesis and structure of an unprecedented supramolecular bridged-hydroxyl manganese(III)-lithium(I) coordination polymer [Mn IIIL(OH) 2Li I] n through both intermolecular hydrogen bonds and ?–? stacking interactions  

Microsoft Academic Search

An unprecedented linear supramolecular manganese(III)-lithium(I) coordination polymer, [MnIIIL(OH)2LiI]n, has been prepared and structurally characterized. The polymer is a one-dimensional infinite Mn(III)–O–Li(I) chain supramolecular structure formed by intermolecular O–H···O and O–H···Cl hydrogen bonds and ?–? stacking of neighboring benzene rings.

Wen-Kui Dong; Chun-Yu Zhao; Yin-Xia Sun; Xiao-Lu Tang; Xue-Ni He

2009-01-01

263

Interaction between two spherical particles in a nematic liquid crystal  

NASA Astrophysics Data System (ADS)

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 .

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

2004-04-01

264

Exciton-exciton interactions in CdWO{sub 4} irradiated by intense femtosecond vacuum ultraviolet pulses  

SciTech Connect

Exciton-exciton interaction is experimentally revealed and quantitatively analyzed in a wide band-gap scintillator material CdWO{sub 4}. Under high-intensity femtosecond vacuum ultraviolet excitation, the CdWO{sub 4} luminescence is quenched, while its decay becomes essentially nonexponential. We propose an analytical model, which successfully reproduces the decay kinetics recorded in a wide range of excitation densities. The dipole-dipole interaction between excitons leading to their nonradiative decay is shown to be the main cause of a nonproportional response common for many scintillators.

Kirm, M.; Nagirnyi, V.; Feldbach, E.; De Grazia, M.; Carre, B.; Merdji, H.; Guizard, S.; Geoffroy, G.; Gaudin, J.; Fedorov, N.; Martin, P.; Vasil'ev, A.; Belsky, A. [Institute of Physics, University of Tartu, Riia 142, 51014 Tartu (Estonia); Service des Photons Atomes et Molecules, CEA/Iramis, 91191 Gif sur Yvette (France); Laboratoire des Solides Irradies, CEA/Iramis, CNRS and Ecole Polytechnique, 91128 Palaiseau (France); European XFEL, Notkestrasse 85, 22607 Hamburg (Germany); Laboratoire CELIA, CNRS, CEA et Universite de Bordeaux I, 33400 Talence (France); Skobeltsyn Institute of Nuclear Physics, Lomonosov Moscow State University, 119991 Moscow (Russian Federation); Laboratoire de Physico-Chimie des Materiaux Luminescents, CNRS, UMR5620, Universite Lyon 1, Villeurbanne F-69622 (France)

2009-06-15

265

Quantum phases of a dipolar Bose-Einstein condensate in an optical lattice with three-body interaction  

SciTech Connect

We investigate the quantum phases of a dipolar Bose-Einstein condensate (BEC) in an optical lattice based on the extended Bose-Hubbard model taking into account the three-body scattering. Accordingly, the phase diagrams from the superfluid state to the Mott-insulator state for such BEC systems are obtained and analyzed, employing both the mean-field approach and the functional-integral method. In particular, we explore the combined effects of three-body interaction and dipole-dipole interaction on the insulating lobes in detail. The experimental scenario is also discussed.

Zhou Kezhao; Liang Zhaoxin; Zhang Zhidong [Shenyang National Laboratory for Materials Science, Institute of Metal Research, and International Centre for Materials Physics, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016 (China)

2010-07-15

266

Theoretical study on the effect of solvent and intermolecular fluctuations in proton transfer reactions: General theory  

SciTech Connect

We present a theory of proton transfer reactions which incorporate the modulation of the proton's potential surface by intermolecular vibrations and the effect of coupling to solvent degree of freedom. The proton tunnels between states corresponding to it being localized in the wells of a double minimum potential. The resulting tunnel splitting depends on the intermolecular separation. The solvent response to the proton's charge is modeled as that of a continuous distribution of harmonic oscillators and the intermolecular stretching mode is also damped because of the interaction with solvent degree of freedom. The transition rate is given by the Fermi Gorlden Rule expression.

Kato, Nobuhiko; Ida, Tomonori; Endo, Kazunaka [Department of Chemistry, Faculty of Science, Kanazawa University, Kakuma, Kanazawa, 920-1192 (Japan)

2004-04-30

267

Electromagnetic interaction of split-ring resonators: The role of separation and relative orientation.  

PubMed

Extinction cross-section spectra of split-ring-resonator dimers have been measured at near-infrared frequencies with a sensitive spatial modulation technique. The resonance frequency of the dimer's coupled mode as well as its extinction cross-section and its quality factor depend on the relative orientation and separation of the two split-ring resonators. The findings can be interpreted in terms of electric and magnetic dipole-dipole interaction. Numerical calculations based on a Discontinuous Galerkin Time-Domain approach are in good agreement with the experiments and support our physical interpretation. PMID:20389678

Feth, Nils; König, Michael; Husnik, Martin; Stannigel, Kai; Niegemann, Jens; Busch, Kurt; Wegener, Martin; Linden, Stefan

2010-03-29

268

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

SciTech Connect

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

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

2007-06-15

269

Interactions in a frozen Rydberg gas  

NASA Astrophysics Data System (ADS)

This thesis is an attempt to discover the properties of interactions between highly excited atoms with very low kinetic energies. A magneto-optical trap is used as the basis for achieving a dense frozen Rydberg gas where the atoms are essentially stationary on the time scale of the experiments. The experiments contained within are at the intersection of atomic, condensed matter, and plasma physics. Dipole-dipole interactions in this frozen Rydberg gas are examined. The low kinetic energies and large dipole moments of the Rydberg atoms make it possible to observe many-body interactions. Specifically, the resonance widths of the dipole-dipole energy transfer process Rb25s1/2+Rb33 s1/2?Rb24p 1/2+Rb34p3/2 1 resonant at fields of 3.0 and 3.4 V/cm are larger than expected considering only the strength of the interaction. A variant of the Ramsey interference method is used to explicitly show the importance of two omnipresent and always resonant dipole-dipole interactions, Rb25s1/2+Rb24 p1/2?Rb24p 1/2+Rb25s1/2 2 and Rb33s1/2+Rb34 p3/2?Rb34p 3/2+Rb33s1/2 .3 The density dependent dephasing of the Ramsey interference fringes is of the same order as the broadening of the resonance line and is attributed to the simultaneous interaction of more than two atoms. The spontaneous evolution of a cold dense gas of Rydberg atoms into an ultra-cold plasma is also observed. The build up of space charge due to many different slow ionization processes is examined and modelled. The avalanche ionization process that ensues once the space charge is large enough to trap electrons of kinetic energies comparable to the binding energy of the Rydberg atoms is studied in detail. The avalanche ionization is examined in terms of the collision rate of the electrons. A model based on a rate equation is put forth that qualitatively reproduces the features in both time and density. The evolution is examined in terms of initial Rydberg state, initial density, and time delay. DC electric fields and radio-frequency fields are used to suppress and enhance the avalanche process, and the slow ionization process is slowed by suppression of hot background Rydberg atoms.

Robinson, Michael Parker

2002-09-01

270

Intermolecular vibrations in hydrophobic amino Acid crystals: experiments and calculations.  

PubMed

Intermolecular vibrations of amino acid crystals occur in the THz, or far-infrared, region of the electromagnetic spectrum. We have measured the THz and Raman spectra of dl-leucine as well as two polymorphs of dl-valine, the spectroscopic properties of which have not previously been compared. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals interactions between molecules are not accounted for in standard density functional theory. Therefore, to calculate the vibrational modes, we used a recently developed approach that includes these nonlocal electron correlation forces. We discuss methods for comparing results from different theoretical models using metrics other than calculated vibrational frequency and intensity, and we also report a new approach enabling concise comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements. PMID:23931283

Williams, Michael R C; Aschaffenburg, Daniel J; Ofori-Okai, Benjamin K; Schmuttenmaer, Charles A

2013-08-28

271

Hyperpolarized carbon - carbon intermolecular multiple quantum coherences  

PubMed Central

Intermolecular multiple quantum coherences (iMQCs) can provide unique contrast with sub-voxel resolution. However, the characteristic growth rate of iMQCs mostly limits these effects to either hydrogen or hydrogen-coupled systems for thermally polarized samples. Hyperpolarization techniques such as dynamic nuclear polarization (DNP) allow for significant increases in the carbon signal (even more signal than that from hydrogen), making carbon iMQCs achievable. We present the first intermolecular multiple quantum signal between two carbon nuclei.

Jenista, Elizabeth R.; Branca, Rosa T.; Warren, Warren S.

2009-01-01

272

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

PubMed

Indium phosphide is investigated using molecular dynamics (MD) simulations and density-functional theory calculations. MD simulations use a proposed effective interaction potential for InP fitted to a selected experimental dataset of properties. The potential consists of two- and three-body terms that represent atomic-size effects, charge-charge, charge-dipole and dipole-dipole interactions as well as covalent bond bending and stretching. Predictions are made for the elastic constants as a function of density and temperature, the generalized stacking fault energy and the low-index surface energies. PMID:21817375

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

2009-01-29

273

Optical properties of strongly interacting supported silver nanocube monolayers  

NASA Astrophysics Data System (ADS)

Plasmonic properties of monolayers of strongly interacting silver nanocubes (AgNC) with controlled interparticle spacing are investigated. Uniform monolayers with controlled particle densities are made using the Langmuir-Blodgett technique with passive phospholipid spacers, such as dioleoyl phosphatidylcholine (DOPC). Both extinction intensity and wavelength of dipole-dipole coupling modes are tuned via particle spacing. The refractive indices of the substrates are used to tune dipolar and interparticle coupling modes via deposition onto thin films of silicon (0 - 25nm). By varying silicon film thickness it is possible to shift and control peak widths and position for both the dipole and interparticle dipole-dipole coupling modes. Control of plasmon shifts and interparticle spacing is applied towards the optimization of SERS substrates. SERS substrates using a Rhodamine B label are tuned at different excitation wavelengths which are in resonance with either the plasmon dipole, fluorescent dye, or interparticle coupling mode. Substrates display reproducible enhancement across multiple sites. This work presents methodology to design and optimize uniform silver nanocube SERS substrates through tuning of plasmon shifts and particle spacing.

Prezgot, Daniel; Ianoul, Anatoli

2013-02-01

274

Effect of intermolecular hydrogen bonding on the fluorescence spectra of three-component indole solutions  

Microsoft Academic Search

As is known, indole and some of its derivatives dissolved in alcohols, ethers, nitriles, and water exhibit an anomalously large (up to 5000 cm -~) Stokes shift [i]. In this case, the actually generally accepted mechanism of intermolecular interactions is the formation of exciplexes, with the anomalous Stokes shift being assigned to universal interactions of the exciplex with the solvent

V. N. Umetskaya; E. L. Trubina; O. M. Artamonova

1984-01-01

275

Intermolecular and intramolecular contributions to the relaxation process in sorbitol and maltitol  

NASA Astrophysics Data System (ADS)

Molecular mobility in sorbitol and maltitol is studied with spectroscopic techniques and molecular dynamics simulations in order to evaluate the relative contributions of the intermolecular and intramolecular interactions involved in the relaxation processes. The results of the molecular dynamics simulations performed on the polyols in the bulk or in vacuum compares well with the results of the analysis of the relaxation diagrams in the framework of the Perez et al . model. They both imply that the difference in the relative contributions of the intermolecular and intramolecular interactions associated with the different chemical architectures of the two polyols must be taken into account. The intermolecular interactions cannot be neglected and they are stronger in sorbitol than in maltitol in relation with the linear structure of this polyol. The intramolecular barrier, higher in the maltitol molecule with a more complex structure, could be at the origin of the higher junction temperature between the ?and ?relaxation processes.

Sixou, B.; Faivre, A.; David, L.; Vigier, G.

276

Limits on Exotic Long-Range Spin-Spin Interactions of Electrons  

NASA Astrophysics Data System (ADS)

We surrounded a rotating torsion pendulum containing 9.8×1022 polarized electrons by 2 or 4 stationary sources, each with a net spin of 6.0×1024 polarized electrons. Multiple source configurations gave sensitivity to hypothetical dipole-dipole, spin-dot-spin, and spin-cross-spin exchange interactions mediated by bosons with masses up to 20?eV. For bosons with masses ?0.1?eV our null results for the dipole-dipole, spin-dot-spin, and spin-cross-spin forces imply 1? upper limits on (gPe)2/(?c), (gAe)2/(?c) and (gVegAe)/(?c) of 2.2×10-16, 3.8×10-40, and 1.2×10-28, respectively. We also constrain, for the first time, any possible linear combination of static spin-spin interactions. In this case our upper limits relax to 5.6×10-16, 9.8×10-40, and 1.2×10-28, respectively.

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

2013-10-01

277

Limits on exotic long-range spin-spin interactions of electrons.  

PubMed

We surrounded a rotating torsion pendulum containing 9.8×10^{22} polarized electrons by 2 or 4 stationary sources, each with a net spin of 6.0×10^{24} polarized electrons. Multiple source configurations gave sensitivity to hypothetical dipole-dipole, spin-dot-spin, and spin-cross-spin exchange interactions mediated by bosons with masses up to 20???eV. For bosons with masses ?0.1???eV our null results for the dipole-dipole, spin-dot-spin, and spin-cross-spin forces imply 1? upper limits on (g_{P}^{e})^{2}/(?c), (g_{A}^{e})^{2}/(?c) and (g_{V}^{e}g_{A}^{e})/(?c) of 2.2×10^{-16}, 3.8×10^{-40}, and 1.2×10^{-28}, respectively. We also constrain, for the first time, any possible linear combination of static spin-spin interactions. In this case our upper limits relax to 5.6×10^{-16}, 9.8×10^{-40}, and 1.2×10^{-28}, respectively. PMID:24160591

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

2013-10-10

278

1H relaxation dispersion in solutions of nitroxide radicals: effects of hyperfine interactions with 14N and 15N nuclei.  

PubMed

(1)H relaxation dispersion of decalin and glycerol solutions of nitroxide radicals, 4-oxo-TEMPO-d(16)-(15)N and 4-oxo-TEMPO-d(16)-(14)N was measured in the frequency range of 10 kHz-20 MHz (for (1)H) using STELAR Field Cycling spectrometer. The purpose of the studies is to reveal how the spin dynamics of the free electron of the nitroxide radical affects the proton spin relaxation of the solvent molecules, depending on dynamical properties of the solvent. Combining the results for both solvents, the range of translational diffusion coefficients, 10(-9)-10(-11) m(2)/s, was covered (these values refer to the relative diffusion of the solvent and solute molecules). The data were analyzed in terms of relaxation formulas including the isotropic part of the electron spin - nitrogen spin hyperfine coupling (for the case of (14)N and (15)N) and therefore valid for an arbitrary magnetic field. The influence of the hyperfine coupling on (1)H relaxation of solvent molecules depending on frequency and time-scale of the translational dynamics was discussed in detail. Special attention was given to the effect of isotope substitution ((14)N/(15)N). In parallel, the influence of rotational dynamics on the inter-molecular (radical - solvent) electron spin - proton spin dipole-dipole coupling (which is the relaxation mechanism of solvent protons) was investigated. The rotational dynamics is of importance as the interacting spins are not placed in the molecular centers. It was demonstrated that the role of the isotropic hyperfine coupling increases for slower dynamics, but it is of importance already in the fast motion range (10(-9)m(2)/s). The isotope effects is small, however clearly visible; the (1)H relaxation rate for the case of (15)N is larger (in the range of lower frequencies) than for (14)N. It was shown that when the diffusion coefficient decreases below 5 × 10(-11) m(2)/s electron spin relaxation becomes of importance and its role becomes progressively more significant when the dynamics slows done. As far as the influence of the rotational dynamics is concerned, it was show that this process is of importance not only in the range of higher frequencies (like for diamagnetic solutions) but also at low and intermediate frequencies. PMID:22852636

Kruk, D; Korpa?a, A; Kowalewski, J; Rössler, E A; Moscicki, J

2012-07-28

279

Photoinduced Intermolecular and Intramolecular Electron Transfer  

Microsoft Academic Search

The finite sink approximation to the Smoluchowski -Collins-Kimball expression is used here to parameterize intermolecular electron transfer fluorescence quenching data. Values are determined for the relative diffusion coefficient, D_{rm FQ} and the effective encounter diameter, R in both diffusion limited and influenced cases. The effective encounter diameter is seen to increase with decreasing oxidation potential of electron donating quenchers of

Carl John Biver III

1993-01-01

280

Polysilicon piezoresistive cantilevers for intermolecular force detection  

Microsoft Academic Search

We describe the development of polycrystalline silicon piezoresistive micro\\/nanocantilevers for the measurement of intermolecular forces in biochemical sensing. The cantilevers have been fabricated both in a dedicated technology and in a commercial CMOS technology with an additional micromachining postprocessing. The sensitivity and resolution required by the application are achieved with cantilevers with submicrometer thickness and width in the micrometer range.

G. Villanueva; J. Bausells; J. Montserrat; F. Perez-Murano

2005-01-01

281

Thermodynamic curvature for attractive and repulsive intermolecular forces  

NASA Astrophysics Data System (ADS)

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.

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

2013-09-01

282

Experimental search for anomalous spin-spin interactions  

SciTech Connect

This paper reports on a Cavendish-type torsion pendulum, having test masses with 2.5 {times} 10{sup 11} polarized electrons and attracting masses with 8 {times} 10{sup 23} polarized electrons, is used to search for an anomalous spin interaction of macroscopic range. Competition from magnetic forces is reduced by using ferrimagnetic Dy-Fe masses which exhibit orbital compensation of the electron spin magnetic moments. Combined with magnetic shielding, the sensitivity is 2 {times} 10{sup {minus}4} of the gravitational force. Fluctuations set the overall experimental limit at about 5 times this level. The authors' results set limits on electron spin interactions and on moments which are not of electromagnetic origin. In terms of a standard dipole-dipole form, the limit is 1.5 {times} 20{sup {minus}12} of the interaction strength between the magnetic moments of the electrons. Compared to previous results, this is a six-fold improvement.

Pan, S.S.; Ni, W.T.; Chen, S.C. (National Tsing Hua Univ., Hsinchu (Taiwan, Province of China). Dept. of Physics)

1992-05-10

283

Quantum phases of strongly interacting Rydberg atoms in triangular lattices  

NASA Astrophysics Data System (ADS)

We present a theoretical study on the system of laser-driven strongly interacting Rydberg atoms trapped in a two-dimensional triangular lattice, in which the dipole-dipole interactions between Rydberg states result in exotic quantum phases. By using the mean-field theory, we investigate the steady state solutions and analyze their dynamical stabilities. We find that in the strong-interaction limit, the dynamics of the system is chaotic and exhibits random oscillations under appropriate laser detunings. The Lyapunov exponent criterion is introduced to confirm the existence of this chaotic behavior. In addition, we present a full quantum calculation based on a six-atom model, and find that the system exhibits some biantiferromagnetic properties in every triangular cell when the one-photon detuning is exactly resonant or blue shifted.

Qian, Jing; Zhou, Lu; Zhang, Weiping

2013-06-01

284

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

NASA Astrophysics Data System (ADS)

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.

Hyeon-Deuk, Kim; Ando, Koji

2012-04-01

285

Intermolecular dimerization with pillared layered clay templates.  

SciTech Connect

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

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

2001-11-19

286

Tannin oxidation: intra- versus intermolecular reactions.  

PubMed

Grape and apple condensed tannin fractions were autoxidized at high concentrations (5 g/L) in aqueous solutions and analyzed by thiolysis (depolymerization followed by HPLC analysis) and small angle X-ray scattering (SAXS). Structural parameters of native (unoxidized) tannin polymers were derived from SAXS according to the wormlike chain model: the length per monomer is 15 A, the length of the statistical segment 17 A, and the cross section of the macromolecule has a radius within the range 3-4.5 A. The rather short length of the statistical segment is an effect of the different location of interflavanol linkages, which cause a loss of orientational correlation between successive monomers. Oxidation created new bonds that were resistant to thiolysis, and, according to thiolysis, some of these new bonds were intramolecular. However, according to SAXS, oxidation at high tannin concentration caused the weight average degree of polymerization to increase, indicating that intermolecular reactions took place as well, creating larger macromolecules. In the case of the smaller grape seed tannins, these intermolecular reactions took place "end to end" leading to the formation of longer linear macromolecules, at least in the earlier stages of oxidation. In the case of the larger apple tannins, the SAXS patterns were characteristic of larger branched macromolecules. Accordingly, the intermolecular reactions were mainly "end to middle". This is in agreement with the higher probabilities of "end to middle" reactions arising from a higher ratio extension unit/terminal unit in the latter case. PMID:20831276

Poncet-Legrand, Céline; Cabane, Bernard; Bautista-Ortín, Ana-Belén; Carrillo, Stéphanie; Fulcrand, Hélène; Pérez, Javier; Vernhet, Aude

2010-09-13

287

Selective intermolecular amination of c?h bonds at tertiary carbon centers.  

PubMed

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

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

2013-09-02

288

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

PubMed Central

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

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

2013-01-01

289

Intra- and intermolecular hydrogen bondings in steroids—a combined experimental and theoretical study  

Microsoft Academic Search

FTIR measurements on the solutions of previously not studied steroids [(20R)[6?(3?,4?[2?H]-dihydropyranyl)]-pregn-5-ene-3?,20-diol 3(2?-tetrahydropyranyl) ether (1) and (20R)[6?(3?,4?[2?H]-dihydropyranyl)]-pregn-5-ene-3?,20-diol 3-acetate (2)] with varying concentrations revealed, that intra- as well as intermolecular interactions existed for both molecules. The former was more important for compound 1 and the latter for compound 2. Only intermolecular hydrogen bonds were found in the crystalline state, however. Molecular modeling

A. Magyar; Z. Szendi; J. T. Kiss; I. Pálinkó

2003-01-01

290

He-, Ne-, and Ar-Phosgene Intermolecular Potential Energy Surfaces.  

PubMed

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

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

2013-04-26

291

Spanin function requires subunit homodimerization through intermolecular disulfide bonds.  

PubMed

The ? Rz and Rz1 proteins are the subunits of the spanin complex, required for the disruption of the outer membrane during host lysis. Rz, the inner membrane or i-spanin, has a largely alpha-helical periplasmic domain, whereas Rz1, the outer membrane or o-spanin, has a 25% proline content with no predicted secondary structure. We report that both Rz and Rz1 accumulate as homodimers covalently linked by intermolecular disulfide bonds involving all three Cys residues, two in Rz and one in Rz1. Moreover, of these three intermolecular disulfides, spanin function requires the presence of at least one of the two linkages nearest the Rz-Rz1 C-terminal interaction domains; i.e. either the Rz1-Rz1 disulfide or the distal Rz-Rz disulfide link. In a dsbC host, but not in dsbA or dsbA dsbC hosts, formation of the covalent homodimers of Rz is severely reduced and outer membrane disruption is significantly delayed, suggesting that the spanin pathway normally proceeds through DsbA-mediated formation of an intramolecular disulfide in Rz. In contrast, efficient formation of the Rz1-Rz1 disulfide requires DsbA. Finally, Dsb-independent formation of the covalent homodimer of either subunit requires the presence of the other, presumably as a template for close apposition of the thiols. PMID:23387988

Berry, Joel D; Rajaure, Manoj; Young, Ry

2013-02-28

292

The water-nitric oxide intermolecular potential-energy surface revisited.  

PubMed

The two lowest energy intermolecular potential-energy surfaces (IPESs) of the water-nitric oxide complex are evaluated using the spin-restricted coupled-cluster R-CCSD(T) model and the augmented correlation-consistent polarized-valence triple-zeta basis set extended with a set of the 3s3p2d1f1g midbond functions. A detailed characterization of the IPESs for both the (2)A(') and (2)A(") electronic states in the C(s)-symmetry configurations of the complex is performed. The global minimum for the (2)A(') state represented by the lowest energy of -461.8 cm(-1) is deeper than the global minimum in the (2)A(") state with an energy of -435.2 cm(-1). To explore the physics of the interaction an open-shell implementation of the symmetry-adapted perturbation theory is employed and the results are analyzed as a function of the intermolecular parameters. The electrostatic term shows the strongest geometric anisotropy, while the exchange, induction, and dispersion contributions mostly depend on the intermolecular distance. The energy separation between the (2)A(') and (2)A(") states is largely dominated by electrostatic contribution for long intermolecular distances. In the region of short intermolecular distances the exchange part is as important as the electrostatic one and the induction and dispersion effects are also substantial. PMID:19292530

Cybulski, Hubert; Zuchowski, Piotr S; Fernández, Berta; Sadlej, Joanna

2009-03-14

293

Evaluation of intermolecular forces in a circulating system.  

PubMed

Intercellular interactions, which are mediated by a variety of complex intercellular molecules through the processes of formation and dissociation of molecular bonds, play a critical role in regulating cellular functions in biological systems. Various approaches are applied to evaluate intercellular or molecular bonding forces. To quantify the intermolecular interaction forces, flow chamber has become a meaningful technique as it can ultimately mimic the cellular microenvironment in vivo under physiological flow conditions. Hydrodynamic forces are usually used to predict the intercellular forces down to the single molecular level. However, results show that only using hydrodynamic force will overestimate up to 30% of the receptor-ligand strength when the non-specific forces such as Derjaguin-Landau-Verway-Overbeek (DLVO) forces become un-neglected. Due to the nature of high ion concentration in the physiological condition, electrostatic force is largely screened which will cause DLVO force unbalanced. In this study, we propose to take account of the DLVO force, including van der Waals (VDW) force and electrostatic force, to predict the intermolecular forces of a cell doublet and cell-substrate model in a circulating system. Results also show that the DLVO force has a nonlinear effect as the cell-cell or cell-substrate distance changes. In addition, we used the framework of high accuracy hydrodynamic theories proved in colloidal systems. It is concluded that DLVO force could not be ignored in quantitative studies of molecular interaction forces in circulating system. More accurate prediction of intercellular forces needs to take account of both hydrodynamic force and DLVO force. PMID:21843592

Guo, Qiuquan; Liu, Mei; Yang, Jun

2011-08-05

294

Interaction between two spherical particles in a nematic liquid crystal.  

PubMed

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 Q(ij) 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 approximately 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 less than or approximately equal 10R0, which is stronger than the dipole-dipole repulsion (approximately D-3 ) expected theoretically as an asymptotic behavior for large D. PMID:15169032

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

2004-04-30

295

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

NASA Astrophysics Data System (ADS)

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.

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

1998-01-01

296

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

SciTech Connect

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

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

2009-01-01

297

Mechanisms of interaction between polycyclic aromatic hydrocarbons and dissolved organic matters.  

PubMed

Binding of phenanthrene and fluorene to a number of humic and fulvic substances isolated from various sources as well as a commercially available humic acid, was investigated using a fluorescence quenching approach. The observed fluorescence quenching indicated by linear Stern-Volmer plots and high bimolecular quenching rate constant was induced by a static interaction process. A significant correlation of binding constants with aromaticity and polarity of dissolved organic matter (DOM) was observed. It is hypothesized that the binding of polycyclic aromatic hydrocarbons (PAHs) by DOM is due to both ?-? interactions and hydrophobic interactions. In addition, energy transfer from PAHs to DOM occurs because of the significant overlap between the absorbance spectra of DOM and emission spectra of PAHs. Thus, dipole-dipole interaction may also play an important role in the binding mechanism between PAHs and DOM. PMID:24117086

Wang, Huan Bo; Zhang, Yu Jun

2014-01-01

298

Intermolecular hybridization governs molecular electrical doping.  

PubMed

Current models for molecular electrical doping of organic semiconductors are found to be at odds with other well-established concepts in that field, like polaron formation. Addressing these inconsistencies for prototypical systems, we present experimental and theoretical evidence for intermolecular hybridization of organic semiconductor and dopant frontier molecular orbitals. Common doping-related observations are attributed to this phenomenon, and controlling the degree of hybridization emerges as a strategy for overcoming the present limitations in the yield of doping-induced charge carriers. PMID:22400758

Salzmann, Ingo; Heimel, Georg; Duhm, Steffen; Oehzelt, Martin; Pingel, Patrick; George, Benjamin M; Schnegg, Alexander; Lips, Klaus; Blum, Ralf-Peter; Vollmer, Antje; Koch, Norbert

2012-01-18

299

Intermolecular electrical conductance in self-assembled monolayers  

NASA Astrophysics Data System (ADS)

Intermolecular interaction was investigated by measuring the properties of self-assembled monolayers (SAMs) in the lateral direction. We formed SAMs of octadecyltrichlorosilane (OTS) and phenethyltrichlorosilane with Ag- or Au-patterned electrodes on mica surfaces and measured the conductance under various bias voltages. Using an atomic force microscope with a conductive cantilever, we could not detect current through the SAMs in the vicinity of the electrodes about 85 nm from the edge. The resistivity of the OTS film measured using the substrates with interdigitated (comb) electrodes was strongly dependent on the humidity. From the result in a dry N2 atmosphere, the resistivity of a SAM of OTS in a lateral direction was estimated to be 9×1010 ?cm.

Inoue, A.; Mizutani, W.; Ishida, T.; Tokumoto, H.

300

Inter-molecular correlations in liquid Se2Br2  

NASA Astrophysics Data System (ADS)

The structure of molecular liquid Se2Br2 was analyzed by means of reverse Monte Carlo structural modeling, using a calculation based on high-energy x-ray diffraction data. It was found that, between the optical isomers of L and D types, the number of L–D neighboring molecular pairs increases, while that of the L–L and D–D pairs decreases with increasing temperature. From this temperature dependence and from the relaxation mode analysis of quasi-elastic neutron scattering spectra, it is reasonable to assume that the presence of L–D pairs relates to genuine inter-molecular interactions while the L–L and D–D pairs appear due to geometrical packing of the gauche-shaped molecules.

Shimakura, Hironori; Kawakita, Yukinobu; Ohara, Koji; Pusztai, László; Wakisaka, Yuiko; Takeda, Shin’ichi

2013-11-01

301

Inter-molecular correlations in liquid Se2Br2.  

PubMed

The structure of molecular liquid Se2Br2 was analyzed by means of reverse Monte Carlo structural modeling, using a calculation based on high-energy x-ray diffraction data. It was found that, between the optical isomers of L and D types, the number of L-D neighboring molecular pairs increases, while that of the L-L and D-D pairs decreases with increasing temperature. From this temperature dependence and from the relaxation mode analysis of quasi-elastic neutron scattering spectra, it is reasonable to assume that the presence of L-D pairs relates to genuine inter-molecular interactions while the L-L and D-D pairs appear due to geometrical packing of the gauche-shaped molecules. PMID:24140925

Shimakura, Hironori; Kawakita, Yukinobu; Ohara, Koji; Pusztai, László; Wakisaka, Yuiko; Takeda, Shin'ichi

2013-10-18

302

Effect of intermolecular hydrogen bonding on the micro-mechanical properties of high performance organic fibers  

NASA Astrophysics Data System (ADS)

Since their introduction in the early 1970s, high performance organic fibers have gained an increasingly significant role in a wide range of weight-sensitive applications. However, the use of organic fibers in structural applications has been restricted by their performance under compression. Organic fibers have a fibrillar structure in which the lack of strong lateral support between fibrils results in failure at low compressive loads. Despite the relevance of lateral interactions on organic fiber mechanical properties, there is not a reliable method to measure and quantify the effect of hydrogen bonding on fiber compressive properties. The mechanisms by which intermolecular hydrogen bonding affects fiber compressive properties have been elucidated by analyzing the state of hydrogen bonding in M5, a poly-pyridobisimidazole experimental fiber developed by Akzo Nobel. An experimental methodology based on FTIR microspectroscopy has been developed in order to detect and quantify the state of hydrogen bonding in M5 fibers with varying degrees of heat treatment. The methodology has shown that in the as-spun material, 72% of the N-H vibration groups are hydrogen-bonded to water, while in the fully heat-treated fiber more than 90% of the N-H vibration groups develop intermolecular hydrogen bonds. Saturation of previously annealed M5 fiber has been shown to result in a reduction of the measured degree of intermolecular hydrogen bonding from 93 to 64%, providing the first direct evidence of partial reversibility of hydrogen bonding in high performance organic fibers. The compressive properties of five high performance organic fibers with varying degrees of lateral molecular interactions have been analyzed. A novel micro-mechanical technique applies an axial compressive load on a segment of free fiber in order to quantify the axial compressive modulus of single filaments. The resulting ratios of axial compressive to tensile modulus show values ranging between 0.3--1.0, depending on the type and degree of intermolecular interactions present in the fiber. The assumption of equal tensile and compressive modulus necessary to determine single fiber axial compressive strength from the elastica loop test has been relaxed by deriving a compressive strength equation based on the analysis of the flexural response of a fiber with different modulus in tension and compression. Using the FTIR methodology to quantify the degree of intermolecular hydrogen bonding in M5 fiber as a function of annealing conditions, and the micro-mechanical techniques suitable for the evaluation of the effect of intermolecular interactions on fiber compressive properties, a direct relationship between the degree of intermolecular hydrogen bonding in the fiber and the measured compressive strength values is established.

Leal Ayala, Angel Andres

303

The p-difluorobenzene-argon S1 excited state intermolecular potential energy surface.  

PubMed

The first excited state (S1) intermolecular potential energy surface for the p-difluorobenzene-Ar van der Waals complex is evaluated using the coupled-cluster method and the augmented correlation consistent polarized valence double-zeta basis set extended with a set of 3s3p2d1f1g midbond functions. In order to calculate the S1 interaction energies we use the ground state surface evaluated with the same basis set and the coupled-cluster singles and doubles [CCSD] including connected triple excitations [CCSD(T)] model, and interaction and excitation energies evaluated at the CCSD level. The surface minima are characterized by the Ar atom located above and below the p-difluorobenzene center of mass at a distance of 3.4736 A. The corresponding interaction energy is -435.233 cm-1. The surface is used in the evaluation of the intermolecular level structure of the complex. PMID:17149844

Fajín, José Luis Cagide; Fernandez, Berta; Felker, Peter M

2006-12-14

304

Intermolecular potential functions from spectroscopic properties of weakly bound complexes  

SciTech Connect

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)

Muenter, J.S.

1992-01-01

305

Diastereoselective intermolecular radical addition to nitrones.  

PubMed

The intermolecular radical addition to chiral nitrones 2, 4, 5, and 16 was studied. The isopropyl radical addition to Oppolzer's camphorsultam derivative 2 of glyoxylic nitrone proceeded with excellent diastereoselectivity to give the desired isopropylated product 3a accompanied by the diisopropylated product 3b. A high degree of stereocontrol in the reaction of cyclic nitrone 4 was achieved. The ethyl radical addition to nitrone 4 with triethylborane afforded the desired ethylated product 9a accompanied by the diethylated product 10a and the ethylated nitrone 11a. To evaluate the utility of cyclic nitrone 4, several alkyl radicals were employed in the addition reaction, which afforded the alkylated products 9b-d with excellent diastereoselectivities. In the presence of Mg(ClO(4))(2), the ethyl radical addition to BIGN 16 afforded selectively syn isomers. In contrast, the alkyl radical addition to 16 took place even in the absence of Lewis acid to give anti isomers. PMID:16095283

Ueda, Masafumi; Miyabe, Hideto; Teramachi, Masako; Miyata, Okiko; Naito, Takeaki

2005-08-19

306

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

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.

Ghazzali, Mohamed [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)], E-mail: mghazz@chalmers.se; Langer, Vratislav; Ohrstroem, Lars [Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)

2008-09-15

307

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

The interactions of Fe(II)Pc and Fe(III)Pc with ?-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 ?-? 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

Balraj, Chellamuthu; Elango, Kuppanagounder P

2011-10-04

308

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

SciTech Connect

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

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

2008-08-14

309

Dielectric spectra broadening as the signature of dipole-matrix interaction. II. Water in ionic solutions  

NASA Astrophysics Data System (ADS)

In this, the second part of our series on the dielectric spectrum symmetrical broadening of water, we consider ionic aqueous solutions. If in Part I, dipole-dipole interaction was the dominant feature, now ion-dipole interplay is shown to be the critical element in the dipole-matrix interaction. We present the results of high-frequency dielectric measurements of different concentrations of NaCl/KCl aqueous solutions. We observed Cole-Cole broadening of the main relaxation peak of the solvent in the both electrolytes. The 3D trajectory approach (described in detail in Part I) is applied in order to highlight the differences between the dynamics and structure of solutions of salts on one hand and dipolar solutes on the other hand.

Levy, Evgeniya; Puzenko, Alexander; Kaatze, Udo; Ishai, Paul Ben; Feldman, Yuri

2012-03-01

310

Protected state enhanced quantum metrology with interacting two-level ensembles.  

PubMed

Ramsey interferometry is routinely used in quantum metrology for the most sensitive measurements of optical clock frequencies. Spontaneous decay to the electromagnetic vacuum ultimately limits the interrogation time and thus sets a lower bound to the optimal frequency sensitivity. In dense ensembles of two-level systems, the presence of collective effects such as superradiance and dipole-dipole interaction tends to decrease the sensitivity even further. We show that by a redesign of the Ramsey-pulse sequence to include different rotations of individual spins that effectively fold the collective state onto a state close to the center of the Bloch sphere, partial protection from collective decoherence is possible. This allows a significant improvement in the sensitivity limit of a clock transition detection scheme over the conventional Ramsey method for interacting systems and even for noninteracting decaying atoms. PMID:24093259

Ostermann, Laurin; Ritsch, Helmut; Genes, Claudiu

2013-09-18

311

Protected State Enhanced Quantum Metrology with Interacting Two-Level Ensembles  

NASA Astrophysics Data System (ADS)

Ramsey interferometry is routinely used in quantum metrology for the most sensitive measurements of optical clock frequencies. Spontaneous decay to the electromagnetic vacuum ultimately limits the interrogation time and thus sets a lower bound to the optimal frequency sensitivity. In dense ensembles of two-level systems, the presence of collective effects such as superradiance and dipole-dipole interaction tends to decrease the sensitivity even further. We show that by a redesign of the Ramsey-pulse sequence to include different rotations of individual spins that effectively fold the collective state onto a state close to the center of the Bloch sphere, partial protection from collective decoherence is possible. This allows a significant improvement in the sensitivity limit of a clock transition detection scheme over the conventional Ramsey method for interacting systems and even for noninteracting decaying atoms.

Ostermann, Laurin; Ritsch, Helmut; Genes, Claudiu

2013-09-01

312

Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum  

NASA Astrophysics Data System (ADS)

We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set extended with a series of 3s3p2d1f1g midbond functions. The potential is characterized by two equivalent global minima where the Ar atom is located above and below the phenylacetylene plane at a distance of 3.5781 A? from the molecular center of mass and at an angle of 9.08° with respect to the axis perpendicular to the phenylacetylene plane and containing the center of mass. The calculated interaction energy is -418.9 cm-1. To check further the potential, we obtain the rovibrational spectrum of the complex and the results are compared to the available experimental data.

Cybulski, Hubert; Fernández, Berta; Henriksen, Christian; Felker, Peter M.

2012-08-01

313

Atom-atom partitioning of intramolecular and intermolecular Coulomb energy  

NASA Astrophysics Data System (ADS)

An atom-atom partitioning of the (super)molecular Coulomb energy is proposed on the basis of the topological partitioning of the electron density. Atom-atom contributions to the molecular intra- and intermolecular Coulomb energy are computed exactly, i.e., via a double integration over atomic basins, and by means of the spherical tensor multipole expansion, up to rank L=lA+lB+1=5. The convergence of the multipole expansion is able to reproduce the exact interaction energy with an accuracy of 0.1-2.3 kJ/mol at L=5 for atom pairs, each atom belonging to a different molecule constituting a van der Waals complex, and for nonbonded atom-atom interactions in single molecules. The atom-atom contributions do not show a significant basis set dependence (3%) provided electron correlation and polarization basis functions are included. The proposed atom-atom Coulomb interaction energy can be used both with post-Hartree-Fock wave functions and experimental charge densities in principle. The Coulomb interaction energy between two molecules in a van der Waals complex can be computed by summing the additive atom-atom contributions between the molecules. Our method is able to extract from the supermolecule wave function an estimate of the molecular interaction energy in a complex, without invoking the reference state of free noninteracting molecules. We provide computational details of this method and apply it to (C2H2)2; (HF)2; (H2O)2; butane; 1,3,5-hexatriene; acrolein and urocanic acid, thereby covering a cross section of hydrogen bonds, and covalent bonds with and without charge transfer.

Popelier, P. L. A.; Kosov, D. S.

2001-04-01

314

Photoinduced intermolecular electron transfer from aromatic amines to coumarin dyes in sodium dodecyl sulphate micellar solutions  

Microsoft Academic Search

Photoinduced intermolecular electron transfer interaction between coumarin dyes and aromatic amines has been investigated in sodium dodecyl sulphate micellar solutions using steady-state and time-resolved fluorescence quenching measurements. Steady-state fluorescence quenching of the coumarin dyes by the amine quenchers always shows a positive deviation from linear Stern-Volmer relationship, which arises due to the localized high quencher concentrations at the micellar Stern

Manoj Kumbhakar; Sukhendu Nath; Haridas Pal; Avinash V. Sapre; Tulsi Mukherjee

2003-01-01

315

Interpreting the widespread nonlinear force spectra of intermolecular bonds.  

PubMed

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

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

2012-08-06

316

Quantitative tomographic imaging of intermolecular FRET in small animals.  

PubMed

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

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

2012-11-08

317

Statistical thermodynamics of fluids with both dipole and quadrupole moments.  

PubMed

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

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

2011-06-21

318

Dielectric spectra broadening as a signature for dipole-matrix interaction. III. Water in adenosine monophosphate/adenosine-5'-triphosphate solutions  

NASA Astrophysics Data System (ADS)

In this, the third part of our series on the dielectric spectrum symmetrical broadening of water, we consider the nucleotide aqueous solutions. Where in Parts I [E. Levy et al., J. Chem. Phys. 136, 114502 (2012)] and II [E. Levy et al., J. Chem. Phys. 136, 114503 (2012)], the dipole-dipole or ion-dipole interaction had a dominant feature, now the interplay between these two types of dipole-matrix interactions will be considered. We present the results of high frequency dielectric measurements of different concentrations of adenosine monophosphate/adenosine-5'-triphosphate aqueous solutions. We observed the Cole-Cole broadening of the main relaxation peak of the solvent in the solutions. Moreover, depending on the nucleotide concentration, we observed both types of dipole-matrix interaction. The 3D trajectory approach (described in detail in Part I) is applied in order to highlight the differences between the two types of interaction.

Puzenko, Alexander; Levy, Evgeniya; Shendrik, Andrey; Talary, Mark S.; Caduff, Andreas; Feldman, Yuri

2012-11-01

319

Photoinduced Intermolecular and Intramolecular Electron Transfer  

NASA Astrophysics Data System (ADS)

The finite sink approximation to the Smoluchowski -Collins-Kimball expression is used here to parameterize intermolecular electron transfer fluorescence quenching data. Values are determined for the relative diffusion coefficient, D_{rm FQ} and the effective encounter diameter, R in both diffusion limited and influenced cases. The effective encounter diameter is seen to increase with decreasing oxidation potential of electron donating quenchers of similar dimensions; this finding suggests that a long range electron transfer mechanism is present under these conditions which explains the absence of a Marcus inverted region noted by Rehm and Weller in 1970. Values of the intrinsic rate constant for electron transfer, k^circ, recovered for diffusion influenced systems are found to be independent of both solvent and temperature. These results are consistent with electron tunneling as the long range electron transfer mechanism. Intramolecular electron transfer is studied spectroscopically for derivatives of p-terphenyl and bianthranyl. The results obtained lead to a detailed examination of the photophysical behavior of 4-nitro-4^{' '}-amino-p-terphenyl (NATP) for which a state diagram consistent with the observed results are presented.

Biver, Carl John, III

320

Intermolecular Interactions between Retroviral Gag Proteins in the Nucleus  

Microsoft Academic Search

The retroviral Gag polyprotein directs virus particle assembly, resulting in the release of virions from the plasma membranes of infected cells. The earliest steps in assembly, those immediately following Gag synthesis, are very poorly understood. For Rous sarcoma virus (RSV), Gag proteins are synthesized in the cytoplasm and then undergo transient nuclear trafficking before returning to the cytoplasm for transport

Scott P. Kenney; Timothy L. Lochmann; Cullen L. Schmid; Leslie J. Parent

2008-01-01

321

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

Microsoft Academic Search

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

Joshua Jasensky; M. Junaid Farooqi; Paul Urayama

2008-01-01

322

Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins  

PubMed Central

A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and ?-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S2 band of ?-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available.

Renge, I.; van Grondelle, R.; Dekker, J. P.

2007-01-01

323

Magnetization of densely packed interacting magnetic nanoparticles with cubic and uniaxial anisotropies: A Monte Carlo study  

NASA Astrophysics Data System (ADS)

The magnetization curves of densely packed single domain magnetic nanoparticles (MNPs) are investigated by Monte Carlo simulations in the framework of an effective one spin model. The particles whose size polydispersity is taken into account are arranged in spherical clusters, and both dipole dipole interactions (DDI) and magnetic anisotropy energy (MAE) are included in the total energy. Having in mind the special case of spinel ferrites of intrinsic cubic symmetry, combined cubic and uniaxial magnetocrystalline anisotropies are considered with different configurations for the orientations of the cubic and uniaxial axes. It is found that the DDI together with a marked reduction of the linear susceptibility are responsible for a damping of the peculiarities due to the MAE cubic component on the magnetization. As an application, we show that the simulated magnetization curves compare well to experimental results for ?-Fe2O3 MNP for small to moderate values of the field.

Russier, V.; de-Montferrand, C.; Lalatonne, Y.; Motte, L.

2013-10-01

324

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

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

325

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

PubMed

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

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

2012-01-01

326

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

PubMed

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites. PMID:24072819

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-09-26

327

Photochemistry of Intermolecular C-H Bond Activation Reactions.  

National Technical Information Service (NTIS)

The major goal of this project has been to gain photophysical and photochemical insight as to why transition-metal organometallic systems facilitate intermolecular C-H bond activation reactions with various hydrocarbon substrates. The emphasis of the rese...

A. J. Lees

2000-01-01

328

How intermolecular charge transfer influences the air-water interface  

NASA Astrophysics Data System (ADS)

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

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

2012-10-01

329

Investigation of Intermolecular Association in Concentrated Solutions of Cellulose Acetate.  

National Technical Information Service (NTIS)

The role of intermolecular association in concentrated solutions of cellulose triacetate (CTA) is investigated with respect to its importance in controlling the properties of CTA films formed from concentrated solutions for use, for example, as membranes ...

G. C. Berry T. S. Sham M. A. Leech

1979-01-01

330

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

PubMed Central

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.

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

2005-01-01

331

Hyperpolarized carbon-carbon intermolecular multiple quantum coherences  

NASA Astrophysics Data System (ADS)

Intermolecular multiple quantum coherences (iMQCs) can provide unique contrast with sub-voxel resolution. However, the characteristic growth rate of iMQCs mostly limits these effects to either hydrogen or hydrogen-coupled systems for thermally polarized samples. Hyperpolarization techniques such as dynamic nuclear polarization (DNP) allow for significant increases in the carbon signal (even more signal than that from hydrogen), making carbon iMQCs achievable. We present the first intermolecular multiple quantum signal between two carbon nuclei.

Jenista, Elizabeth R.; Branca, Rosa T.; Warren, Warren S.

2009-01-01

332

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

NASA Astrophysics Data System (ADS)

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

Fujisawa, Tomotsumi; Nishikawa, Keiko; Shirota, Hideaki

2009-12-01

333

Intermolecular structure determination of amyloid fibrils with magic-angle spinning and dynamic nuclear polarization NMR  

PubMed Central

We describe magic-angle spinning NMR experiments designed to elucidate the interstrand architecture of amyloid fibrils. Three methods are introduced for this purpose, two being based on the analysis of long-range 13C-13C correlation spectra and a third based on the identification of intermolecular interactions in 13C-15N spectra. We show, in studies of fibrils formed by the 86-residue SH3 domain of PI3 kinase (PI3-SH3), that efficient 13C-13C correlation spectra display a resonance degeneracy that establishes a parallel, in-register alignment of the proteins in the amyloid fibrils. In addition, this degeneracy can be circumvented to yield direct intermolecular constraints. The 13C-13C experiments are corroborated by 15N-13C correlation spectrum obtained from a mixed [15N,12C]/[14N,13C] sample which directly quantifies interstrand distances. Furthermore, when the spectra are recorded with signal enhancement provided by dynamic nuclear polarization (DNP) at 100 K, we demonstrate a dramatic increase (from 23 to 52) in the number of intermolecular 15N-13C constraints present in the spectra. The increase in the information content is due to the enhanced signal intensities and to the fact that dynamic processes, leading to spectral intensity losses, are quenched at low temperatures. Thus, acquisition of low temperature spectra addresses a problem that is frequently encountered in MAS spectra of proteins. In total the experiments provide 111 intermolecular 13C-13C and 15N-13C constraints that establish that the PI3-SH3 protein strands are aligned in a parallel, in-register arrangement within the amyloid fibril.

Bayro, Marvin J.; Debelouchina, Galia T.; Eddy, Matthew T.; Birkett, Neil R.; MacPhee, Catherine E.; Rosay, Melanie; Maas, Werner E.; Dobson, Christopher M.

2011-01-01

334

Ab initio long-range interaction and adiabatic channel capture model for ultracold reactions between the KRb molecules  

NASA Astrophysics Data System (ADS)

The coefficients at the lowest-order electrostatic, induction, and dispersion terms of the anisotropic long-range potential between the two KRb(1?+) molecules are evaluated through the static and dynamic molecular properties using the ab initio coupled cluster techniques. Adiabatic channel potentials for the ground-state molecules are obtained and used for the numerical quantum capture probability calculations in the spirit of the statistical adiabatic channel models. Capture rate coefficients for indistinguishable (polarized) and distinguishable (unpolarized) molecules at temperatures below 10 ?K agree well with those computed with the simple isotropic dispersion R-6 potential, but underestimate the measured ones [Ospelkaus et al., Science 327, 853 (2010)] up to a factor of 3. Preliminary assessment of the effects of higher-order long-range terms, retardation of dispersion forces, and magnetic dipole-dipole interaction does not offer any clear perspectives for drastic improvement of the capture approximation for the reactions studied.

Buchachenko, A. A.; Stolyarov, A. V.; Szcz??niak, M. M.; Cha?asi?ski, G.

2012-09-01

335

Center motions of nonoverlapping condensates coupled by long-range dipolar interaction in bilayer and multilayer stacks  

SciTech Connect

We investigate the effect of anisotropic and long-range dipole-dipole interaction (DDI) on the center motions of nonoverlapping Bose-Einstein condensates in bilayer and multilayer stacks. In the bilayer, it is shown analytically that while DDI plays no role in the in-phase modes of center motions of condensates, out-of-phase mode frequency ({omega}{sub o}) depends crucially on the strength of DDI (a{sub d}). At the small-a{sub d} limit, {omega}{sub o}{sup 2}(a{sub d})-{omega}{sub o}{sup 2}(0){proportional_to}a{sub d}. In the multilayer stack, transverse modes associated with center motions of coupled condensates are found to be optical-phonon-like. At the long-wavelength limit, phonon velocity is proportional to {radical}(a){sub d}.

Huang, Chao-Chun; Wu, Wen-Chin [Department of Physics, National Taiwan Normal University, Taipei 11650, Taiwan (China)

2010-11-15

336

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

PubMed

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

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

2011-09-22

337

Electron-density-based calculations of intermolecular energy: case of urea.  

PubMed

The intermolecular interaction energy in crystalline urea has been calculated both from diffraction data and from the Hartree-Fock crystalline electron-density distribution, using a modified atom-atom approximation scheme. The electrostatic part of this energy has been calculated from the atomic multipole moments, obtained by adjustment of the multipole model to experimental X-ray and to theoretical Hartree-Fock structure amplitudes. To obtain the induction energy, multipole moments were calculated from structure amplitudes for the crystalline electron density and from those that refer to the electron density of a superposition of isolated molecules. This worked well for the calculation of the interaction energy from Hartree-Fock data (6% difference from the sublimation-energy value), but not for the interaction energy from experimental data, where the moments of the superposition have to come from Hartree-Fock calculations: the two sets of multipole moments are far too different. The uncertainty of the phases of the structure amplitudes, combined with systematic errors in the theoretical data and noise in the experimental values, may account for the discrepancies. The nature of the different contributions to intermol-ecular interactions for urea is examined. PMID:10927292

Suponitsky; Tsirelson; Feil

1999-09-01

338

The fluorobenzene-argon S(1) excited-state intermolecular potential energy surface.  

PubMed

We evaluate the first excited-state (S1) intermolecular potential energy surface for the fluorobenzene-Ar van der Waals complex using the coupled cluster method and the augmented correlation-consistent polarized valence double-zeta basis set extended with a set of 3s3p2d1f1g midbond functions. To calculate the S(1) interaction energies, we use ground-state interaction energies evaluated with the same basis set and the coupled cluster singles and doubles (CCSD) including connected triple excitations [CCSD(T)] model and interaction and excitation energies evaluated at the CCSD level. The surface minima are characterized by the Ar atom located above and below the fluorobenzene ring at a distance of 3.5060 A with respect to the fluorobenzene center of mass and at an angle of 5.89 degrees with respect to the axis perpendicular to the fluorobenzene plane. The corresponding interaction energy is -425.226 cm(-1). The surface is used in the evaluation of the intermolecular level structure of the complex, and the results are compared to the experimental data available and to those found in previous theoretical papers on ground-state potentials for similar complexes. PMID:17658771

Fajín, José Luis Cagide; Capelo, Silvia Bouzón; Fernandez, Berta; Felker, Peter M

2007-07-21

339

Stress and deformation in soft elastic bodies due to intermolecular forces  

NASA Astrophysics Data System (ADS)

Intermolecular interaction within one and between two incompressible, soft elastic bodies is studied at a continuous level. We show that the macroscopic effect of the interaction can be characterized by a deformation-dependent Maxwell stress. The divergence of the Maxwell stress gives the body force, while the inner product of it with the outward normal of a body generates the surface traction. Accordingly, we can replace the contribution of intermolecular forces to the deformation and stress in the body by that of either the body force or the surface traction. Both approaches are proved to be equivalent, in the sense that the resulting displacements are the same and the stresses are linked by an exact correspondence relation. If the deformation induced by the interaction is small, the equations are simplified up to the first order of the displacement gradient. Two examples are given as well to illustrate some features of local stress distribution in a body caused by self and other-body interactions.

He, L. H.

2013-06-01

340

Chemical Exchange Saturation Transfer by Intermolecular Double Quantum Coherence  

PubMed Central

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

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

2008-01-01

341

Dancing Crystals: A Dramatic Illustration of Intermolecular Forces  

ERIC Educational Resources Information Center

|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…

Mundell, Donald W.

2007-01-01

342

Dancing Crystals: A Dramatic Illustration of Intermolecular Forces  

ERIC Educational Resources Information Center

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…

Mundell, Donald W.

2007-01-01

343

Intermolecular potentials from nuclear spin lattice relaxation in pure gases with octahedral symmetry  

NASA Astrophysics Data System (ADS)

Fluorine spin lattice relaxation times per unit density T1/? in pure SF6, MoF6, WF6 and UF6 gases are experimentally found to be proportional to T-1·5 where T is the temperature. These data can be analysed to obtain information on the anisotropic part of the intermolecular potential in these systems. Hard sphere, Lennard-Jones (6-12) and modified Buckingham (exp-6) potentials were used for the isotropic part of the intermolecular interaction. The analysis is made using the Bloom-Oppenheim theory, assuming that the correlation time of the spin rotation interaction can be approximated by the average lifetime of a molecule in the given J state. We have obtained the strengths of the repulsive and attractive terms in the anisotropic potential. From the strength of the attractive term in the anisotropic potential, the hexadecapole moments of all the four molecules are obtained. The hexadecapole moment of SF6 obtained by us using the Lennard-Jones model is in good agreement with the values reported earlier, based on other techniques, while the values for MoF6, WF6 and UF6 are reported for the first time.

Ursu, I.; Bogdan, M.; Balibanu, F.; Fitori, P.; Mihailescu, G.; Demco, D. E.

344

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

PubMed

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

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

2012-07-31

345

A Model DMMP/TiO2 (110) Intermolecular Potential Energy Function Developed from ab Initio Calculations  

SciTech Connect

A hierarchy of electronic structure calculations, scalings, and fittings were used to develop an analytic intermolecular potential for dimethyl methylphosphonate (DMMP) interacting with the TiO2 rutile (110) surface. The MP2/aug-cc-pVDZ (6-311+G** for Ti) level of theory, with basis set superposition error (BSSE) corrections, was used to calculate multiple intermolecular potential curves between TiO5H6 as a model for the Ti and O atoms of the TiO2 surface, and CH3OH and O=P(CH3)(OH)2 as models for different types of atoms comprising DMMP. Each intermolecular potential energy emphasized a particular atom-atom interaction, and the curves were fit simultaneously by a sum of two-body potentials between the atoms of the two interacting molecules. The resulting analytic intermolecular potential gives DMMP/TiO5H6 potential curves in excellent agreement with those calculated using MP2/aug-cc-pVDZ (6-311+G** for Ti) theory. MP2 theory with the smaller basis set, 6-31++G** (6-31G** for Ti), gives DMMP/TiO5H6 potential energy curves similar to those found using MP2/aug-cc-pVDZ (6-311+G** for Ti), suggesting the smaller basis set may be used to describe DMMP interactions with larger cluster models of the TiO2 surface. The TiO5H6 cluster does not model either the 6-fold coordinated Ti-atoms or the bridging O-atoms of the TiO2 (110) surface and to also model these atoms MP2/6-31++G** (6-31G** for Ti) theory was used to calculate potential energy curves for DMMP interacting with the larger Ti3O13H14 cluster and much large cluster Ti11O40H36 cluster. The two-body potential energy curves for DMMP/TiO5H6 were scaled to fit both the DMMP/Ti3O13H14 and DMMP/Ti11O40H36 potential energy curves. The resulting parameters for the 5- and 6-fold coordinated Ti-atoms and bridging and bulk O-atoms were used to develop an analytic intermolecular potential for DMMP interacting with rutile TiO2 (110).

Yang, Li; Taylor, Ramona; De Jong, Wibe A.; Hase, William L.

2011-06-30

346

p-Difluorobenzene-argon ground state intermolecular potential energy surface.  

PubMed

The ground state intermolecular potential energy surface for the p-difluorobenzene-Ar van der Waals complex is evaluated using the coupled cluster singles and doubles including connected triple excitations [CCSD(T)] model and the augmented correlation consistent polarized valence double-zeta basis set extended with a set of 3s3p2d1f1g midbond functions. The surface minima are characterized by the Ar atom located above and below the difluorobenzene center of mass at a distance of 3.5290 A. The corresponding binding energy is -398.856 cm(-1). The surface is used in the evaluation of the intermolecular level structure of the complex. The results clearly improve previously available data and show the importance of using a good correlation method and basis set when dealing with van der Waals complexes. PMID:16354053

Cagide Fajín, José Luis; Fernández, Berta; Felker, Peter M

2005-12-22

347

Influence of Deoxyribonucleic Acid on the Intermolecular Structure of Water  

Microsoft Academic Search

SEVERAL years ago Jacobson1 directed attention to the fact that the helical structure of deoxyribonucleic acid (DNA) proposed by Watson and Crick2 showed a remarkable relationship to the intermolecular structure of liquid water, which has been postulated to be quasi-crystalline and only slightly different from ice3. Jacobson proposed that when DNA is dissolved in water, an increased ordering of the

Joseph Depireux; Dudley Williams

1962-01-01

348

Gold(I)-Catalyzed Stereoconvergent, Intermolecular Enantioselective Hydroamination of Allenes  

PubMed Central

A 1:2 mixture of [(S)-2](AuCl)2 [(S)-2 = (S)-3,5-t-Bu-4-MeO-MeOBIPHEP] and AgBF4 catalyzes the stereoconvergent, intermolecular enantioselective hydroamination of chiral, racemic 1,3-disubstituted allenes with N-unsubstituted carbamates to form N-allylic carbamates in good yield, with high regio- and diastereoselectivity, and up to 92% ee.

Butler, Kristina L.; Tragni, Michele; Widenhoefer, Ross A.

2012-01-01

349

Generation and intermolecular reactions of 2-indolylacyl radicals.  

PubMed

The generation of 2-indolylacyl radicals from the corresponding phenyl selenoesters, aldehydes, and alpha-keto carboxylic acids and the scope of their participation in intermolecular addition reactions to carbon-carbon double bonds have been studied. Whereas the phenyl selenoester method has provided easy access to a variety of 1,4-dicarbonyl compounds bearing the 2-acylindole moiety, the glyoxylic acid route has been employed for the preparation of 2-indolyl pyridyl ketones. PMID:11405689

Bennasar, M L; Roca, T; Griera, R; Bosch, J

2001-05-31

350

Calculations of helical twisting powers from intermolecular torques  

NASA Astrophysics Data System (ADS)

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.

Earl, David J.; Wilson, Mark R.

2004-05-01

351

Solvation and Intermolecular Exploration of Drug Molecule Fragments  

Microsoft Academic Search

The paramagnetic contributions from dioxygen to solute proton spin-lattice relaxation rate constants are reported for a series\\u000a of aromatic hydrocarbons and drug molecule fragments, in order to examine the energetic factors for intermolecular exploration\\u000a in solution. The measurements provide differences in local oxygen concentration at different sites on the solute molecule.\\u000a The relaxation rate differences caused by steric factors are

K. Fumino; G. Diakova; J. D. Andersen; M. L. Brown; R. G. Bryant

2007-01-01

352

Triethylborane-induced intermolecular radical addition to ketimines.  

PubMed

The intermolecular carbon radical addition to ketimines was investigated by using triethylborane as a radical initiator. The screening of reactive radical acceptors showed that pyruvic hydrazone 3 and isatin hydrazone 7 exhibit good reactivities toward nucleophilic alkyl radicals. The reaction of 3 and 7 proceeded effectively even under aqueous-medium reaction conditions. In the presence of BF(3).OEt(2), the radical addition to chiral ketimine 11 proceeded with good diastereoselectivities. PMID:15823008

Miyabe, Hideto; Yamaoka, Yousuke; Takemoto, Yoshiji

2005-04-15

353

Catalytic intermolecular enal-alkyne [3 + 2] reductive cycloadditions.  

PubMed

A catalytic, intermolecular [3 + 2] reductive cycloaddition of enals and alkynes has been developed. The method provides a nickel-catalyzed strategy for combining two simple acyclic pi-systems into a five-membered ring product by effecting a net two-electron reduction of the starting materials mediated by triethylborane as the reducing agent. The use of a protic solvent is a key feature of the process. PMID:17061877

Herath, Ananda; Montgomery, John

2006-11-01

354

Hyperfine interactions in two-dimensional HgTe topological insulators  

NASA Astrophysics Data System (ADS)

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

Lunde, Anders Mathias; Platero, Gloria

2013-09-01

355

Study of intermolecular contacts in proteins and oligomer interfaces and preliminary investigations into the design and production of nanomaterials from proteins  

Microsoft Academic Search

The first part of this research involved a study of the nature and extent of nonbonded interactions at crystal and oligomer interfaces. A survey was compiled of several characteristics of intersubunit contacts in 58 different oligomeric proteins, and of the intermolecular contacts in 223 protein crystal structures. Routines written in \\

Ganesh Hariharan Iyer

1998-01-01

356

Oriented covalent immobilization of antibodies for measurement of intermolecular binding forces between zipper-like contact surfaces of split inteins.  

PubMed

In order to measure the intermolecular binding forces between two halves (or partners) of naturally split protein splicing elements called inteins, a novel thiol-hydrazide linker was designed and used to orient immobilized antibodies specific for each partner. Activation of the surfaces was achieved in one step, allowing direct intermolecular force measurement of the binding of the two partners of the split intein (called protein trans-splicing). Through this binding process, a whole functional intein is formed resulting in subsequent splicing. Atomic force microscopy (AFM) was used to directly measure the split intein partner binding at 1 ?m/s between native (wild-type) and mixed pairs of C- and N-terminal partners of naturally occurring split inteins from three cyanobacteria. Native and mixed pairs exhibit similar binding forces within the error of the measurement technique (~52 pN). Bioinformatic sequence analysis and computational structural analysis discovered a zipper-like contact between the two partners with electrostatic and nonpolar attraction between multiple aligned ion pairs and hydrophobic residues. Also, we tested the Jarzynski's equality and demonstrated, as expected, that nonequilibrium dissipative measurements obtained here gave larger energies of interaction as compared with those for equilibrium. Hence, AFM coupled with our immobilization strategy and computational studies provides a useful analytical tool for the direct measurement of intermolecular association of split inteins and could be extended to any interacting protein pair. PMID:23679912

Sorci, Mirco; Dassa, Bareket; Liu, Hongwei; Anand, Gaurav; Dutta, Amit K; Pietrokovski, Shmuel; Belfort, Marlene; Belfort, Georges

2013-05-31

357

Unconventional magnetism in imbalanced Fermi systems with magnetic dipolar interactions  

SciTech Connect

We study the magnetic structure of the ground state of an itinerant Fermi system of spin-1/2 particles with magnetic dipole-dipole interactions. We show that, quite generally, the spin state of particles depend on its momentum, i.e., spin and orbital degrees of freedom are entangled and taken separately are not 'good' quantum numbers. Specifically, we consider a uniform system with nonzero magnetization at zero temperature. Assuming the magnetization is along z axis, the quantum spin states are k-dependent linear combinations of eigenstates of the sigma{sub z} Pauli matrix. This leads to spin structures in momentum space and to the fact that the Fermi surfaces for 'up' and 'down' spins are not well defined. The system still has a cylindrical axis of symmetry along the magnetization axis. We also show that the self-energy has a universal structure which we determine based on the symmetries of the dipolar interaction and we explicitly calculated it in the Hartree-Fock approximation. We show that the bare magnetic moment of particles is renormalized due to particle-particle interactions and we give order of magnitude estimates of this renormalization effect. We estimate that the above mentioned dipolar effects are small but we discuss possible scenarios where this physics may be realized in future experiments.

Fregoso, Benjamin M.; Fradkin, Eduardo [Department of Physics, University of Illinois, 1110 West Green Street, Urbana, Illinois 61801-3080 (United States)

2010-06-01

358

Mechanical stability of the LHC dipole-dipole 50-75K thermal shield interconnect:\\  

Microsoft Academic Search

The LHC dipole cryostats are equipped with thermal shields carrying super-insulation. A cold helium transfer line equipped with expansion joints is integrated into the shield carrying trays (aluminium profiles supported on three composite feet). The stainless steel (316 L) expansion joints compensate for thermal contraction\\/expansion of the aluminium panels as well as for their misalignment. Design of the LHC thermal

Blazej Skoczen

1998-01-01

359

Odd-even effects and dipole-dipole correlations in the PCH homologous series  

NASA Astrophysics Data System (ADS)

Static electric permittivities of the homologous series of p-cyano-p'- alkylphenylcyclohexanes (PCH) have been measured as a function of temperature in isotropic and nematic phases. The mean square effective dipole moment components along the principal directions of a liquid crystal have been determined. The Kirkwood correlation factors g(i), obtained from Maier and Meier equations, exhibit the odd-even alteration within the studied series. The g-factors values have been interpreted in terms of an anti-parallel association.

Kedziora, Przemyslaw; Jadzyn, Jan

1993-10-01

360

Dipole-Dipole Broadened Line Shape in a Partially Excited Dense Atomic Gas  

SciTech Connect

We have experimentally investigated the resonance line shape of a partially excited dense atomic rubidium vapor at a density where the binary collision approximation starts to break down. The overall spectral shape is well represented by a simple expression for the dielectric function that includes an excitation-dependent linewidth and shift. The results for the excitation dependence of the linewidth agree with an estimate based on a quasistatic picture of the collisions. {copyright} {ital 1996 The American Physical Society.}

Sautenkov, V.A.; van Kampen, H.; Eliel, E.R.; Woerdman, J.P. [Huygens Laboratory, Leiden University, P.O. Box 9504, 2300 RA Leiden (The Netherlands)

1996-10-01

361

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

SciTech Connect

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

Mackelprang, C.E.

1980-09-01

362

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

Microsoft Academic Search

An electrical resistivity survey in the Colado geothermal area, Pershing County, Nevada has defined areas of low resistivity on each of five lines surveyed. Some of these areas appear to be fault controlled. Thermal fluids encountered in several drill holes support the assumption that the hot fluids may be associated with areas of low resistivity. The evidence of faulting as

C. E. Mackelprang

1980-01-01

363

Two-Dimensional DC Resistivity Inversion for Dipole-Dipole Data  

Microsoft Academic Search

A procedure is described for interpreting the results of direct current resistivity measurements in regions where the underlying structure cannot be assumed to be layered but varies little in the ¿strike¿ direction. Automatic inversion of the data is performed with the subsurface model having an arbitrary 2-D conductivity distribution. Results of such inversion are shown for both simple models and

Nariida C. Smith; Keeva Vozoff

1984-01-01

364

Interaction energies associated with short intermolecular contacts of C-H bonds. 1. Ab initio computational study of C-H hor ellipsis anion interactions, C-H hor ellipsis X sup minus (X sup minus = I sub 3 sup minus , IBr sub 2 sup minus , ICl sub 2 sup minus )  

SciTech Connect

The nature of the C-H{hor ellipsis}anion contact interactions found for organic charge-transfer salts was investigated by performing SCF-MO and MP2 level calculations on the model systems H{sub 3}C-H{hor ellipsis}Y-I-Y{sup {minus}} (Y = I, Br, Cl). The binding energies of the H{sub 3}C-H{hor ellipsis}Y-I-Y{sup {minus}} systems are estimated to be 1.1, 1.3, ad 1.6 kcal/mol for Y = I, Br, and Cl, respectively. The binding energy increase, observed when Y varies from I to Br to Cl, is consistent with the expected hydrogen-bonding abilities of the halogen atoms. The C-H bond prefers to make a short contact with the terminal halogen atoms of Y-I-Y{sup {minus}}; this tendency increases as Y changes from I to Br to Cl, and the C-H{hor ellipsis}Y-I-Y{sup {minus}} interaction energies do not strongly depend upon the C-H{hor ellipsis}Y contact angle. 24 refs., 5 figs., 4 tabs.

Mota, F. (Universidad de Barcelona (Spain)); Whangbo, Myunghwan (North Carolina State Univ., Raleigh (USA)); Williams, J.M. (Argonne National Lab., IL (USA)); Novoa, J.J.

1991-01-01

365

Particle Dynamics Studied by Diffusing Wave Spectroscopy in a Ferrofluid Emulsion  

Microsoft Academic Search

A ferrofluid emulsion is used to study the effect of a dipole-dipole interaction on particle dynamics in high concentrations. The dipole moment in each emulsion particle is induced by an external magnetic field. The magnetic dipole-dipole interaction causes the particles to form chains, columns or labyrinthine structures which changes the particle dynamics. In the concentrated regime, diffusing wave spectroscopy is

Sadayoshi Okumoto

1998-01-01

366

Intermolecular energy transfer between the individual zero-field levels of triplet traps in an orientationally disordered solid  

NASA Astrophysics Data System (ADS)

The zero-field transitions and levels of the phosphorescing triplet state of the traps in the orientationally disordered crystal of 1-bromo-4-chloro-naphthalene (BCN) are assigned by using phosphorescence-microwave double resonance techniques at 1.8 K. The relative population of the different zero-field levels are determined at different delays after singlet-singlet excitation and as a function of the energy of the emitting traps within the inhomogeneously broadened bands. For the same delay, the population of the radiating level is found to have a maximum which is at a lower energy within the inhomogeneous profile than that for the dark level. This observation is contrary to predictions based on one-dimensional exchange mechanisms and might suggest the involvement of dipole-dipole coupling for the triplet-triplet energy migration at the relatively large distances involved in the energy transfer between the traps.

Niederwald, H. S.; El-Sayed, M. A.

1985-02-01

367

Protein-Protein Interactions during Bacterial Chemotaxis using Methyl TROSY Nuclear Magnetic Resonance.  

NASA Astrophysics Data System (ADS)

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.

Hamel, Damon; Dahlquist, Frederick

2006-03-01

368

Solitons in the Tonks-Girardeau gas with dipolar interactions  

NASA Astrophysics Data System (ADS)

The existence of bright solitons in the model of the Tonks-Girardeau (TG) gas with dipole-dipole (DD) interactions is reported. The governing equation is taken as the quintic nonlinear Schrödinger equation (NLSE) with the nonlocal cubic term accounting for the DD attraction. In different regions of the parameter space (the dipole moment and atom number), matter-wave solitons feature flat-top or compacton-like shapes. For the flat-top states, the NLSE with the local cubic-quintic (CQ) nonlinearity is shown to be a good approximation. Specific dynamical effects are studied assuming that the strength of the DD interactions is ramped up or drops to zero. Generation of dark-soliton pairs in the gas shrinking under the action of the intensifying DD attraction is observed. Dark solitons exhibit particle-like collision behaviour. Peculiarities of dipole solitons in the TG gas are highlighted by comparison with the NLSE including the local CQ terms. Collisions between the bright solitons are also studied. In many cases, the collisions result in the merger of the solitons into a breather, due to a strong attraction between them.

Baizakov, B. B.; Abdullaev, F. Kh; Malomed, B. A.; Salerno, M.

2009-09-01

369

Combination Bands of the Nonpolar OCS Dimer Involving Intermolecular Modes  

NASA Astrophysics Data System (ADS)

Spectra of the nonpolar carbonyl sulfide in the region of the OCS ?_1 fundamental band were observed in a supersonic slit-jet apparatus. The expansion gas was probed using radiation from a tunable diode laser employed in a rapid-scan signal averaging mode. Three bands centered at 2085.906, 2103.504, and 2114.979 cm-1 were observed and anlysed. The rotational assignment and fitting of the bands were made by fixing the lower state parameters to those for the ground state of nonpolar (OCS)_2, thus confirming that they were indeed combination bands of the of the most stable isomer of OCS dimer. The band centered at 2085.906 cm-1 is a combination of the forbidden A_g intramolecular mode plus the geared bend intermolecular mode and that centered at 2114.979 cm-1 is a combination of the allowed B_u intramolecular mode plus the intermolecular van der Waals stretch. The combination at 2103.504 cm-1 can be assigned as a band whose upper state involves four quanta of the intramolecular bend or the B_u intramolecular mode plus two quanta of the intermolecular torsional mode. Isotopic work is needed to conclusively identify the vibrational assignment of this band. Our experimental frequencies for the geared bend and van der Waals modes are in good agreement with a recent high level ab initio calculation by Brown et al. J. Brown, Xiao-Gang Wang, T. Carrington Jr. and Richard Dawes, Journal of Chemical Physics, submitted.

Rezaei, M.; Oliaee, J. Norooz; Moazzen-Ahmadi, N.; McKellar, A. R. W.

2012-06-01

370

Intermolecular bonding and vibrations of phenol.oxirane  

NASA Astrophysics Data System (ADS)

The supersonically cooled hydrogen-bonded phenol.oxirane complex was studied using mass- and isomer-selective laser spectroscopic techniques. The S1<--S0 vibronic spectrum was measured by mass-selective two-color resonant two-photon ionization. UV/UV-hole-burning experiments prove that the whole observed spectrum is due to only one isomer. High-resolution fluorescence emission spectra yielded five different intermolecular S0 state vibrational fundamentals as 15, 27, 39, 83, and 177 cm-1, which are assigned as the ?1'', ?1'', ?'', ?2'', and ?'' modes, respectively, based on ab initio calculations. The analogous S1 state intermolecular vibrations were also assigned, based on frequency and Franck-Condon activity. The observation of the ?1 and ? intermolecular vibrational transitions in both excitation and emission implies that phenol.oxirane is asymmetric (chiral), even though the H-donor is Cs and the acceptor C2v symmetric. Four different ab initio structure optimizations and normal-mode calculations were made, to compare the performance of the self-consistent field (SCF) and Becke-Lee-Yang-Parr (B-LYP) density functional methods, using the 6-31G(d,p) and 6-311++G(d,p) basis sets. The SCF/6-31G(d,p) method and the B-LYP method with both basis sets indeed predict chiral minimum-energy structures. The B-LYP/6-311++G(d,p) and SCF/6-31G(d,p) normal mode frequencies agree well with the experimental S0 state frequencies, with rms deviations of 4%. The MP2/6-31G(d,p) hydrogen bond well depth is De=6.9 kcal/mol and the dissociation energy is D0=5.7 kcal/mol.

Inauen, Andreas; Hewel, Johannes; Leutwyler, Samuel

1999-01-01

371

Accurate Temperature Imaging Based on Intermolecular Coherences in Magnetic Resonance  

PubMed Central

Conventional magnetic resonance methods that provide interior temperature profiles, which find use in clinical applications such as hyperthermic therapy, can develop inaccuracies caused by the inherently inhomogeneous magnetic field within tissues or by probe dynamics, and work poorly in important applications such as fatty tissues. We present a magnetic resonance method that is suitable for imaging temperature in a wide range of environments. It uses the inherently sharp resonances of intermolecular zero-quantum coherences, in this case flipping up a water spin while flipping down a nearby fat spin. We show that this method can rapidly and accurately assign temperatures in vivo on an absolute scale.

Galiana, Gigi; Branca, Rosa T.; Jenista, Elizabeth R.; Warren, Warren S.

2010-01-01

372

Intermolecular Raman scattering in A3C60  

NASA Astrophysics Data System (ADS)

Raman scattering from intermolecular A-C60 optic modes in A3C60 thin films (A=Rb, K, and Na) yields a single broad band, whose peak frequency increases with decreasing alkali-metal mass. This very weak scattering is associated with disorder-induced contributions from a weighted phonon density of states. The broad band is assigned to vibrations of alkali-metal ions primarily in tetrahedral interstitial sites of the C60 fcc host lattice. Changes in Raman intensity with alkali-metal and thermally varied lattice constants are attributed to A-C distance dependent modulation of C60 electronic states.

Mitch, Michael G.; Lannin, Jeffrey S.

1993-12-01

373

Spectroscopic determination of intermolecular potentials of gas laser components and of major atmospheric constituents. Final report  

SciTech Connect

A systematic study of the structure of weakly bound complexes of hydrogen fluoride has been accomplished. This research provides a broad account of the interaction of hydrogen fluoride with a variety of laser components and atmospheric constituents. Precision structures are now available for the species ArHF, CO/sub 2/HF, N/sub 2/OHF and SCOHF as a result of the present research program. In addition, precision structures have been obtained for ArCO2 and ArN/sub 2/0. This research provides the basic information necessary for reliable modelling of intermolecular forces between HF and Ar, CO/sub 2/, N/sub 2/0 and OCS as well as between Ar and CO/sub 2/ and N/sub 2/0.

Klemperer, W.

1982-01-01

374

Intra- and intermolecular charge transfer in aggregates of tetrathiafulvalene-triphenylmethyl radical derivatives in solution.  

PubMed

An extensive investigation of aggregation phenomena occurring in solution for a family of electron donor-acceptor derivatives, based on polychlorotriphenylmethyl radicals (PTM) linked via a vinylene-bridge to tetrathiafulvalene (TTF) units, is presented. A large set of temperature and/or concentration dependent optical absorption and electron spin resonance (ESR) spectra in a solution of dyads bearing different number of electrons and/or with a hydrogenated PTM residue offer reliable information on the formation of homo dimers and mixed valence dimers. The results shed light on the reciprocal influence of intramolecular electron transfer (IET) within a dyad and the intermolecular charge transfer (CT) occurring in a dimer between the TTF residues and are rationalized based on a theoretical model that describes both interactions. PMID:23517105

Guasch, Judith; Grisanti, Luca; Souto, Manuel; Lloveras, Vega; Vidal-Gancedo, José; Ratera, Imma; Painelli, Anna; Rovira, Concepció; Veciana, Jaume

2013-04-22

375

Conformational diversity in prion protein variants influences intermolecular ?-sheet formation  

PubMed Central

A conformational transition of normal cellular prion protein (PrPC) to its pathogenic form (PrPSc) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild-type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain-swapped dimers or closed monomers; the four mutant PrPs crystallized as non-swapped dimers. Three of the four mutant PrPs aligned to form intermolecular ?-sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular ?-sheets involving the M/V129 polymorphic residue.

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

2010-01-01

376

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

PubMed

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

Suponitsky, Kyrill Yu; Masunov, Artëm E

2013-09-01

377

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

NASA Astrophysics Data System (ADS)

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.

Suponitsky, Kyrill Yu; Masunov, Artëm E.

2013-09-01

378

Study of mesoscopic clouds of cold atoms in the interacting regime  

NASA Astrophysics Data System (ADS)

We present studies on cold and dense atomic ^87Rb clouds containing N˜2-100 interacting atoms. We produced such mesoscopic ensembles by loading a microscopic optical dipole trap from a MOT. Due to 2-body light-assisted collisions, we have found that in steady state such ensembles exhibit reduced number fluctuations with respect to a Poisson distribution. For N >=2, we measured a reduction Fano factor F=0.72±0.07 consistent with the value F=3/4 predicted at large N by a general stochastic model [1,2]. To enhance interactions between the atoms, we are following two tracks. Firstly we evaporatively cooled a few hundreds of trapped atoms and obtained ˜10 atoms close to quantum degeneracy (n?dB^3˜1) in the microscopic trap. In this regime s-wave interactions dominate (n=2 10^14 at.cm-3). Secondly we sent near resonant light (?p) on the small cloud (size l). When ldipole-dipole interactions should lead to collective behaviour.[4pt] [1] A. Fuhrmanek, Y.R.P. Sortais, P. Grangier, A. Browaeys, Phys. Rev. A 82, 023623 (2010).[0pt] [2] Y.R.P. Sortais, A. Fuhrmanek, R. Bourgain, A. Browaeys, ``Sub-Poissonian atom number fluctuations using light-assisted collisions,'' arXiv:1111.5203 (2011).

Bourgain, Ronan; Fuhrmanek, Andreas; Pellegrino, Joseph; R. P Sortais, Yvan; Browaeys, Antoine

2012-06-01

379

Coulomb-like interaction in nematic emulsions induced by external torques exerted on the colloids  

NASA Astrophysics Data System (ADS)

An external mechanical torque on colloids immersed in a nematic liquid crystal can induce a Coulomb-like 1/r interaction between them [Lev and Tomchuk, Phys. Rev. E 59, 591 (1999); Lev , ibid. 65, 021709 (2002)]. In this paper we show that the director-mediated Coulomb-like interaction of two colloids is determined by the vectors ??(1) and ??(2) of the transverse external torques exerted upon these colloids. We derive the 1/r potential in which the scalar product -(??(1)•??(2)) of the two torques plays the role of the product of two electrostatic charges. The 1/r interaction is attractive for (??(1)•??(2))>0 and repulsive for (??(1)•??(2))<0 (“parallel torques” attract whereas “antiparallel torques” repel each other). The vector of transverse torque determines the two-component “elastic charge” (dyad), which is illustrated by the 1/r2 and 1/r3 terms in the elastic energy (the elastic analogs of the monopole-dipole and dipole-dipole interactions). The general status of the pairwise approach to nematic emulsions is considered in terms of the elastic charge density.

Pergamenshchik, V. M.; Uzunova, V. O.

2007-07-01

380

Coulomb-like interaction in nematic emulsions induced by external torques exerted on the colloids.  

PubMed

An external mechanical torque on colloids immersed in a nematic liquid crystal can induce a Coulomb-like 1/r interaction between them [Lev and Tomchuk, Phys. Rev. E 59, 591 (1999); Lev, ibid. 65, 021709 (2002)]. In this paper we show that the director-mediated Coulomb-like interaction of two colloids is determined by the vectors Gamma perpendicular (1) and Gamma perpendicular (2) of the transverse external torques exerted upon these colloids. We derive the 1/r potential in which the scalar product -(Gamma perpendicular (1) x Gamma perpendicular (2)) of the two torques plays the role of the product of two electrostatic charges. The 1/r interaction is attractive for (Gamma perpendicular (1) x Gamma perpendicular (2))>0 and repulsive for (Gamma perpendicular (1) x Gamma perpendicular (2))<0 ("parallel torques" attract whereas "antiparallel torques" repel each other). The vector of transverse torque determines the two-component "elastic charge" (dyad), which is illustrated by the 1/r2 and 1/r3 terms in the elastic energy (the elastic analogs of the monopole-dipole and dipole-dipole interactions). The general status of the pairwise approach to nematic emulsions is considered in terms of the elastic charge density. PMID:17677471

Pergamenshchik, V M; Uzunova, V O

2007-07-19

381

On the thermodynamic characteristics of the benzene...Ar{sub 2} complex: An application of the ab initio intermolecular potential  

SciTech Connect

The benzene...Ar{sub 2} cluster was studied by constant energy molecular dynamics simulations using the ab initio intermolecular potential for the benzene...Ar interaction. The relative population of the energetically less favorable one-sided structure was found to higher that the population of the global minimum (two-sided structure). The preference of the energetically less stable structure was explained by the entropy effect. The thermodynamic functions (entropy, internal energy, and free energy) were calculated independently by integration of the canonical distribution function. 34 refs, 4 fig., 2 tab.

Vacek, J.; Hobza, P. [Institute of Physical Chemistry (Czechoslovakia)

1996-02-15

382

Application of saturation transfer double difference NMR to elucidate the mechanistic interactions of pesticides with humic acid.  

PubMed

Elucidation of mechanistic interactions of anthropogenic chemicals is critical to understanding and eventually predicting their behavior in the environment Here, a recently developed technique, saturation transfer double difference (STDD) NMR spectroscopy is employed to determine the interactions of pesticides with humic acid (HA) at the molecular level. The degree of interaction at each NMR observable nucleus in the pesticide can be quantified in the form of an epitope map, which depicts the mechanism of the pesticide-HA interaction. Our results indicate that, at pH 7, halogen atoms (F and Cl) in water-soluble pesticides (diflufenzopyr, acifluorfen, and chlorsulfuron) play a dominant role in influencing binding to HA, whereas carboxyl groups likely play a secondary role when halogen atoms are also present in the molecule, as observed with diflufenzopyr and acifluorfen. However, when present on its own, the carboxyl group dominates in binding affinityto HA (e.g., imazapyr). Electronegativity and electron density appear to play a key role in the mechanism of binding and results suggest that polar bonds are the primary points of HA contact in the water soluble pesticides investigated. Likely interactions may include hydrogen bonding and dipole-dipole interactions. PMID:18351076

Shirzadi, Azadeh; Simpson, Myrna J; Xu, Yunping; Simpson, André J

2008-02-15

383

Intermolecular domain swapping induces intein-mediated protein alternative splicing.  

PubMed

Protein sequences are diversified on the DNA level by recombination and mutation and can be further increased on the RNA level by alternative RNA splicing, involving introns that have important roles in many biological processes. The protein version of introns (inteins), which catalyze protein splicing, were first reported in the 1990s. The biological roles of protein splicing still remain elusive because inteins neither provide any clear benefits nor have an essential role in their host organisms. We now report protein alternative splicing, in which new protein sequences can be produced by protein recombination by intermolecular domain swapping of inteins, as elucidated by NMR spectroscopy and crystal structures. We demonstrate that intein-mediated protein alternative splicing could be a new strategy to increase protein diversity (that is, functions) without any modification in genetic backgrounds. We also exploited it as a post-translational protein conformation-driven switch of protein functions (for example, as highly specific protein interference). PMID:23974115

Aranko, A Sesilja; Oeemig, Jesper S; Kajander, Tommi; Iwaï, Hideo

2013-08-25

384

Intermolecular potential energy surface of Ar-NO  

NASA Astrophysics Data System (ADS)

Rotational spectra of an open-shell complex, Ar-NO, in the electronic ground state have been analyzed by employing an analysis using a free-rotor model, where previously observed data by Mills et al. [J. Phys. Chem. 90, 3331 (1986); 90, 4961 (1986)] and additional transitions observed by Fourier-transform microwave spectroscopy in the present study are simultaneously analyzed with a standard deviation of the least-squares fit to be 27.5 kHz. A two-dimensional intermolecular potential energy surface for Ar-NO has been determined from the analysis. The determined potential energy surface is compared with those of Ar-OH and Ar-SH, which are also complexes containing an open-shell species with the 2? ground electronic state.

Sumiyoshi, Yoshihiro; Endo, Yasuki

2007-11-01

385

Intermolecular potential energy surface of Ar-NO.  

PubMed

Rotational spectra of an open-shell complex, Ar-NO, in the electronic ground state have been analyzed by employing an analysis using a free-rotor model, where previously observed data by Mills et al. [J. Phys. Chem. 90, 3331 (1986); 90, 4961 (1986)] and additional transitions observed by Fourier-transform microwave spectroscopy in the present study are simultaneously analyzed with a standard deviation of the least-squares fit to be 27.5 kHz. A two-dimensional intermolecular potential energy surface for Ar-NO has been determined from the analysis. The determined potential energy surface is compared with those of Ar-OH and Ar-SH, which are also complexes containing an open-shell species with the 2Pi ground electronic state. PMID:18020641

Sumiyoshi, Yoshihiro; Endo, Yasuki

2007-11-14

386

Iridium-catalyzed intermolecular asymmetric hydroheteroarylation of bicycloalkenes.  

PubMed

Catalytic hydroarylation of alkenes is a desirable process because it can occur under neutral conditions with regioselectivity complementary to that of acid-catalyzed reactions and stereoselectivity derived from the catalyst. We report an intermolecular asymmetric addition of the C-H bonds of indoles, thiophenes, pyrroles, and furans to bicycloalkenes in high yield with high enantiomeric excess. These heteroarene alkylations occur ortho to the heteroatom. This selectivity is observed even with unprotected indoles, which typically undergo alkylation at the C3 position. Initial mechanistic studies revealed that oxidative addition of a heteroarene C-H bond to a neutral Ir(I) species occurs within minutes at room temperature and occurs in the catalytic cycle prior to the turnover-limiting step. Products from syn addition of the C-H bond across the olefin were observed. PMID:23346874

Sevov, Christo S; Hartwig, John F

2013-01-30

387

Intermolecular vibrations and fast relaxations in supercooled ionic liquids  

NASA Astrophysics Data System (ADS)

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 A?) 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.

Ribeiro, Mauro C. C.

2011-06-01

388

Cooperative TPA enhancement via through-space interactions in organic nanodots built from dipolar chromophores  

NASA Astrophysics Data System (ADS)

Whereas structure-properties relationships have been widely investigated at the molecular level, supramolecular structure-property relationships have been somewhat overlooked. In many cases, interchromophoric interactions are found to be detrimental (in particular in second-order NLO) and a lot of efforts have been devoted to circumvent and control these effects to achieve efficient NLO materials for electrooptics. At opposite, we have implemented a countermainstream route based on the confinement of push-pull chromophores in close proximity within organic nanodots where both their number and relative position/distance are controlled by covalent attachment onto appropriate organic scaffolds. In such multichromophoric organic superstructures (namely covalent nanoclusters), dipole-dipole interactions can be tuned by playing on the internal architecture (topology, number of chromophoric subunits, length of the covalent linkers) and on the nature and properties (polarity, polarizability) of the chromophoric subunits. Following this strategy, we present the investigation of two series of such organic nanoclusters built from push-pull chromophores where through-space interactions are shown to modify both one-photon (OPA) and two-photon absorption (TPA) of each chromophoric subunits leading to cooperative enhancement of TPA properties and improved transparency.

Robin, Anne-Claire; Parthasarathy, Venkatakrishnan; Pla-Quintana, Anna; Mongin, Olivier; Terenziani, Francesca; Caminade, Anne-Marie; Majoral, Jean-Pierre; Blanchard-Desce, Mireille

2010-08-01

389

Experimental and theoretical study on the intermolecular complex formation between trehalose and benzene compounds in aqueous solution.  

PubMed

The uniqueness of trehalose as a stress protectant may exist in its potential amphiphilic character capable of interacting with both hydrophilic and hydrophobic partners in aqueous solution. To address this issue, we here investigated the interaction between trehalose and aromatic compounds. NMR measurements, including (1)H-(1)H NOESY spectra, provide direct evidence for the formation of stable intermolecular complexes of trehalose with benzene (or p-cresol) in aqueous solution. In addition, corresponding theoretical evidence is provided by calculating the potential mean force as a function of the distance between trehalose and benzene. In the energy minimum structure, the benzene molecule is located only around the hydrophobic side of trehalose where the first hydration shell is not formed. Therefore, it can be concluded that benzene binds to trehalose in a fashion in which dehydration penalty is minimized. Finally, we discuss the possible biological roles of the trehalose-benzene interaction discovered here. PMID:21740054

Sakakura, Kota; Okabe, Atsutoshi; Oku, Kazuyuki; Sakurai, Minoru

2011-07-22

390

Intermolecular potentials for simulations of collisions of SiNCS + and (CH 3) 2SiNCS + ions with fluorinated self-assembled monolayers  

Microsoft Academic Search

Analytical potential energy functions were developed for interactions of SiNCS+ and (CH3)2SiNCS+ ions with perfluorinated self-assembled monolayer (F-SAM) surfaces. Two model compounds were used to represent an F-SAM: CF4 and nine chains of perfluorobutane forming a miniSAM structure. Density functional theory plus dispersion (DFT-D) calculations were carried out to compute intermolecular potential energy curves (IPECs) for these systems. The applied

Juan José Nogueira; Antonio Sánchez-Coronilla; Jorge M. C. Marques; William L. Hase; Emilio Martínez-Núñez; Saulo A. Vázquez

391

Ab initio potential energy surface and intermolecular vibrations of the naphthalene-argon van der Waals complex  

NASA Astrophysics Data System (ADS)

The intermolecular potential energy surface (PES) of the naphthalene-argon (NpAr) complex is constructed using an ab initio method. The molecule-argon interaction energy is computed at the level of the second-order Møller-Plesset (MP2) theory combined with the augmented correlation consistent polarized valence double-? basis set. The analytical PES fitted to a large set of single energy values is further improved with the help of correction functions determined by calculations of the interaction energy at the coupled cluster level including single and double excitations supplemented by triple excitations performed for a limited set of intermolecular configurations. The PES determined is very flat near its four equivalent global minima of -493 cm-1 located from both sides of the Np plane at a distance of 3.435 A? and shifted from the center of Np by +/-0.43 A? along its long symmetry axis. The large-amplitude motion of Ar in the complex is investigated, and dynamical consequence of a strong intermode coupling is discovered in the excited vibrational states. The theoretical results obtained allow for the reassignment of the spectral bands observed in the electronic transition S1 <-- S0 of the NpAr complex.

Makarewicz, Jan

2011-02-01

392

Intra- and intermolecular charge transfer: twin themes and simultaneous competing transitions involving ferrocenes.  

PubMed

Electronic absorption spectra of ferrocene, ferrocenecarboxylaldehyde, butylferrocene, and 1,1'-diacetylferrocene in pure organic polar and non-polar solvents, pure halocarbon solvents and in several hexane-halocarbon solvent mixtures have been recorded. The investigated ferrocenes have shown several intra-molecular electronic transitions of the types pi-pi*, n-pi*, and d-d*. On using protonic solvents (HA) each of the ferocenes (Fc) acquires a proton exported from the solvent to form a complex with the formula [FcH](+)[A](-). However, on using halocarbon solvents each of the ferrocenes has shown an intermolecular charge-transfer-to-solvent (CTTS) which is characterized by the appearance of new absorption spectral band(s) for each ferrocene-halocarbon solvent interaction. Formation constants (K(CT)) and molar absorption coefficients (epsilon(CT)) of these interactions have been determined and discussed. The study has indicated that the observed different transitions are dependent upon the number and nature of the substituents involved in the ferrocenes. PMID:19733114

Rabie, Usama M

2009-08-12

393

Near-field spatial mapping of strongly interacting multiple plasmonic infrared antennas.  

PubMed

Near-field dipolar plasmon interactions of multiple infrared antenna structures in the strong coupling limit are studied using scattering-type scanning near-field optical microscope (s-SNOM) and theoretical finite-difference time-domain (FDTD) calculations. We monitor in real-space the evolution of plasmon dipolar mode of a stationary antenna structure as multiple resonantly matched dipolar plasmon particles are closely approaching it. Interparticle separation, length and polarization dependent studies show that the cross geometry structure favors strong interparticle charge-charge, dipole-dipole and charge-dipole Coulomb interactions in the nanometer scale gap region, which results in strong field enhancement in cross-bowties and further allows these structures to be used as polarization filters. The nanoscale local field amplitude and phase maps show that due to strong interparticle Coulomb coupling, cross-bowtie structures redistribute and highly enhance the out-of-plane (perpendicular to the plane of the sample) plasmon near-field component at the gap region relative to ordinary bowties. PMID:24097054

Grefe, Sarah E; Leiva, Daan; Mastel, Stefan; Dhuey, Scott D; Cabrini, Stefano; Schuck, P James; Abate, Yohannes

2013-10-16

394

Long-range interactions in ?-helical proteins with interspine coupling: Modulational instability and exact soliton solutions  

NASA Astrophysics Data System (ADS)

The dynamics of ?-helical proteins with interspine coupling by taking into account long-range dipole-dipole interactions and some additional higher order molecular excitations is studied. The model Hamiltonian is transformed into a set of three classical lattice equations, which are further reduced in the multiple scales analysis to a set of three coupled nonlinear Schrödinger (3-CNLS) equations. The linear stability analysis of continuous wave solutions of these 3-CNLS equations is performed and it reveals that the modulational instability (MI) gain is deeply influenced by the long-range interactions (LRI) parameter. Some classes of exact traveling wave solutions are constructed via the solutions of a ?4 model through the F-expansion method and representative wave structures are graphically displayed including localized and periodic solutions. In order to confirm the analytical approach, the numerical experiments show that the solitons are stable at 70 ps. These solitons, exhibited in the model, are a possible carrier of bio-energy transport in the protein molecules.

Mvogo, Alain; Ben-Bolie, Germain Hubert; Crépin Kofané, Timoléon

2013-10-01

395

Impurity modes in Frenkel exciton systems with dipolar interactions and cubic symmetry  

NASA Astrophysics Data System (ADS)

We introduce a continuum model for impurity modes of Frenkel excitons in fully occupied face-centered and body-centered cubic lattices with dipole-dipole interactions and parallel moments. In the absence of impurities, the model reproduces the small-k behavior found in numerical calculations of dipolar lattice sums. The exciton densities of states near the upper and lower band edges are calculated and compared with the corresponding results for a random array of dipoles. The Green function obtained with the continuum model, together with a spherical approximation to the Brillouin zone, is used to determine the conditions for the formation of a localized exciton mode associated with a shift in the transition energy of a single chromophore. The dependence of the local mode energy on the magnitude of the shift is ascertained. The formation of impurity bands at high concentrations of perturbed sites is investigated using the coherent potential approximation. The contribution of the impurity bands to the optical absorption is calculated in the coherent potential approximation. The locations of the optical absorption peaks of the dipolar system are shown to depend on the direction of propagation of the light relative to the dipolar axis, a property that is maintained in the presence of short-range interactions.

Avgin, I.; Huber, D. L.

2013-04-01

396

Multiple-scattering approach to interatomic interactions and superradiance in inhomogeneous dielectrics  

SciTech Connect

The dynamics of a collection of resonant atoms embedded inside an inhomogeneous nondispersive and lossless dielectric is described with a dipole Hamiltonian that is based on a canonical quantization theory. The dielectric is described macroscopically by a position-dependent dielectric function and the atoms as microscopic harmonic oscillators. We identify and discuss the role of several types of Green tensors that describe the spatio-temporal propagation of field operators. After integrating out the atomic degrees of freedom, a multiple-scattering formalism emerges in which an exact Lippmann-Schwinger equation for the electric field operator plays a central role. The equation describes atoms as point sources and point scatterers for light. First, single-atom properties are calculated such as position-dependent spontaneous-emission rates as well as differential cross sections for elastic scattering and for resonance fluorescence. Secondly, multiatom processes are studied. It is shown that the medium modifies both the resonant and the static parts of the dipole-dipole interactions. These interatomic interactions may cause the atoms to scatter and emit light cooperatively. Unlike in free space, differences in position-dependent emission rates and radiative line shifts influence cooperative decay in the dielectric. As a generic example, it is shown that near a partially reflecting plane there is a sharp transition from two-atom superradiance to single-atom emission as the atomic positions are varied.

Wubs, Martijn [Complex Photonic Systems, Faculty of Science and Technology, University of Twente, P.O. Box 217, NL-7500 AE Enschede (Netherlands); Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, NL-1018 XE Amsterdam (Netherlands); Suttorp, L.G. [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, NL-1018 XE Amsterdam (Netherlands); Lagendijk, A. [Complex Photonic Systems, Faculty of Science and Technology, University of Twente, P.O. Box 217, NL-7500 AE Enschede (Netherlands)

2004-11-01

397

Solitons in quasi-one-dimensional Bose-Einstein condensates with competing dipolar and local interactions  

SciTech Connect

We study families of one-dimensional matter-wave bright solitons supported by the competition of contact and dipole-dipole (DD) interactions of opposite signs. Soliton families are found, and their stability is investigated in the free space and in the presence of an optical lattice (OL). Free-space solitons may exist with an arbitrarily weak local attraction if the strength of the DD repulsion is fixed. In the case of the DD attraction, solitons do not exist beyond a maximum value of the local-repulsion strength. In the system which includes the OL, a stability region for subfundamental solitons is found in the second finite band gap. For the existence of gap solitons (GSs) under the attractive DD interaction, the contact repulsion must be strong enough. In the opposite case of the DD repulsion, GSs exist if the contact attraction is not too strong. Collisions between solitons in the free space are studied too. In the case of the local attraction, they merge or pass through each other at small and large velocities, respectively. In the presence of the local repulsion, slowly moving solitons bounce from each other.

Cuevas, J. [Departamento de Fisica Aplicada I, Grupo de Fisica No Lineal, Escuela Universitaria Politecnica, C/Virgen de Africa, 7, 41011 Sevilla (Spain); Malomed, Boris A. [Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978 (Israel); Kevrekidis, P. G. [Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003-4515 (United States); Frantzeskakis, D. J. [Department of Physics, University of Athens, Panepistimiopolis, Zografos, Athens 15784 (Greece)

2009-05-15

398

Enhanced stimulated Raman scattering by intermolecular Fermi resonance  

NASA Astrophysics Data System (ADS)

We demonstrate the stimulated Raman scattering (SRS) of a binary solution of toluene and m-xylene at different volume concentrations in liquid-core optical fiber (LCOF). The results show that SRS of three vibration modes of 1002 cm-1,2920 cm-1 and 3058 cm-1 bands are simultaneously generated at some volume concentrations. The 2920 cm-1 band and the 3058 cm-1 band are generated at one time, the SRS thresholds of the first-order Stokes of the 2920 cm-1 and 3058 cm-1 bands are lower compared with the second-order Stokes threshold of the 1002 cm-1 band and the main peak of the 2920 cm-1 and 3058 cm-1 bands changes from the 2920 cm-1 band to the 3058 cm-1 band as the volume concentrations are changed. We assume that these phenomena are attributed to the intermolecular Fermi resonance. Raman scattering cross section (RSCS) theory is used to explain this assumption.

Fang, W.; Li, Z.; Qu, G.; Cao, A.; Men, Z.; Sun, C.

2012-04-01

399

Determination of stepsize parameters for intermolecular vibrational energy transfer  

SciTech Connect

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.

Tardy, D.C.

1992-03-01

400

Photoinduced intermolecular electron transfer in complex liquids: Experiment and theory  

NASA Astrophysics Data System (ADS)

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

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

2000-12-01

401

Absolute temperature imaging using intermolecular multiple quantum MRI  

PubMed Central

Purpose A review of MRI temperature imaging methods based on intermolecular multiple quantum coherences (iMQCs) is presented. Temperature imaging based on iMQCs can provide absolute temperature maps that circumvent the artefacts that other proton frequency shift techniques suffer from such as distortions to the detected temperature due to susceptibility changes and magnetic field inhomogeneities. Thermometry based on iMQCs is promising in high-fat tissues such as the breast, since it relies on the fat signal as an internal reference. This review covers the theoretical background of iMQCs, and the necessary adaptations for temperature imaging using iMQCs. Materials and methods Data is presented from several papers on iMQC temperature imaging. These studies were done at 7T in both phantoms and in vivo. Results from phantoms of cream (homogeneous mixture of water and fat) are presented as well as in vivo temperature maps in obese mice. Results Thermometry based on iMQCs offers the potential to provide temperature maps which are free of artefacts due to susceptibility and magnetic field inhomogeneities, and detect temperature on an absolute scale. Conclusions The data presented in the papers reviewed highlights the promise of iMQC-based temperature imaging in fatty tissues such as the breast. The change in susceptibility of fat with temperature makes standard proton frequency shift methods (even with fat suppression) challenging and iMQC-based imaging offers an alternative approach.

JENISTA, ELIZABETH R.; BRANCA, ROSA T.; WARREN, WARREN S.

2011-01-01

402

Polyelectrolyte brushes in mixed ionic medium studied via intermolecular forces  

NASA Astrophysics Data System (ADS)

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).

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

2011-03-01

403

Fluorescence studies of furanoxy radicals: Intramolecular and intermolecular processes  

SciTech Connect

Fluorescence properties of furanoxy radicals were used to investigate intramolecular relaxation and intermolecular quenching processes involving these organic doublet species. The emission spectra of several substituted furanoxy radicals are given; maxima lie in the 615-660-nm region. Excited-state lifetimes were measured and lie in the 6-13-ns range. There were solvent effects on the lifetimes as well as on the absorption and emission spectra. The temperature dependence of the fluorescence lifetimes was studied and found to be small, E{sub a} = 0.35 kcal/mol, compared to that in benzyl radical. Rate constants of internal conversion (and fluorescence quantum yields) were estimated and found to follow a previously proposed correlation with Taft polar substituent constants. In addition to the intramolecular photophysics, quenching studies were carried out. In particular, the furanoxy radicals were used to quench the triplet of two polycyclic aromatics where transfer of energy was allowed and where sensitized fluorescence was observed (k{sub q} {approximately} 6 {times} 10{sup 9} M{sup {minus}1} s{sup {minus}1}). Details of an improved method for making measurements of k{sub q} between two transients are given. Recombination kinetics of the radicals were also measured using 5,5{prime}-bis(furanones) as precursors of the radicals.

Bhattacharyya, K.; Das, P.K.; Fessenden, R.W.; Gopidas, K.R.; Hiratsuka, H.; Hug, G.L.; Rajadurai, S.; Samanta, A. (Univ. of Notre Dame, IN (USA)); George, M.V. (Indian Institute of Technology, Kanpur (India))

1989-05-10

404

A STM perspective on covalent intermolecular coupling reactions on surfaces  

NASA Astrophysics Data System (ADS)

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

Lackinger, M.; Heckl, W. M.

2011-11-01

405

Intermolecular vibrational energy exchange directly probed with ultrafast two dimensional infrared spectroscopy  

NASA Astrophysics Data System (ADS)

Ultrafast two dimensional infrared (2D IR) spectroscopy has been applied to probe the intermolecular vibrational energy exchange between two model molecules, benzonitrile and acetonitrile-d3. The vibrational energy exchange between these two molecules is manifested through the growth of cross peaks in their 2D IR spectra. In experiments, their nitrile groups (CN) are not involved in the energy exchange but serve as reporters of the process. Our experiments demonstrate that intermolecular vibrational energy transfer can be directly probed with the 2D IR method. Results also show that the mode specific energy transfer can be important in intermolecular vibrational energy transfers.

Bian, Hongtao; Zhao, Wei; Zheng, Junrong

2009-09-01

406

Intermolecular Potential for the Hexahydro-1,3,5-trinitro- 1,3,5,-s-triazine (RDX) Crystal: A Crystal-Packing, Monte Carlo, and Molecular Dynamics Study.  

National Technical Information Service (NTIS)

We have developed an intermolecular potential that describes the structure of the alpha-form of the hexahydro-1,3,5- trinitro,1,3,5-s-triazine (RDX) crystal. The potential is composed of pairwise atom-atom (6-exp) Buckingham interactions and charge-charge...

D. C. Sorescu D. L. Thompson B. M. Rice

1997-01-01

407

Optimizing Noncovalent Interactions Between Lignin and Synthetic Polymers to Develop Effective Compatibilizers  

SciTech Connect

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.

Henry, Nathan [University of Tennessee, Knoxville (UTK); Harper, David [University of Tennessee, Knoxville (UTK), Center for Renewable Carbon; Dadmun, Mark D [ORNL

2012-01-01

408

Vibrational dependence of an intermolecular potential for H2O-He system  

NASA Astrophysics Data System (ADS)

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.

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

2013-11-01

409

Structure and polarization properties of water: molecular dynamics with a nonadditive intermolecular potential.  

PubMed

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

Shvab, I; Sadus, Richard J

2012-05-30

410

Structure and polarization properties of water: Molecular dynamics with a nonadditive intermolecular potential  

NASA Astrophysics Data System (ADS)

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.

Shvab, I.; Sadus, Richard J.

2012-05-01

411

Frontier orbital symmetry control of intermolecular electron transfer. Progress report, November 1, 1989-October 31, 1990.  

National Technical Information Service (NTIS)

Research continued on the study of intermolecular electron transfer. This report discusses the following topics: fluorescence quenching by electron transfer and the modification of quenching dynamics by solvent properties and net free energy change; trans...

B. Stevens

1990-01-01

412

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

National Technical Information Service (NTIS)

This report discusses the following topics: the recovery of intermolecular transfer parameters from fluorescence quenching in liquids; photoinduced intramolecular electron transfer in flexible donor/space/acceptor systems containing an extended unsaturate...

B. Stevens

1997-01-01

413

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

Microsoft Academic Search

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.

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

1998-01-01

414

The Raman and vibronic activity of intermolecular vibrations in aromatic-containing complexes and clusters  

SciTech Connect

Theoretical and experimental results pertaining to the excitation of intermolecular vibrations in the Raman and vibronic spectra of aromatic-containing, weakly bound complexes and clusters are reported. The theoretical analysis of intermolecular Raman activity is based on the assumption that the polarizability tensor of a weakly bound species is given by the sum of the polarizability tensors of its constituent monomers. The analysis shows that the van der Waals bending fundamentals in aromatic--rare gas complexes may be expected to be strongly Raman active. More generally, it predicts strong Raman activity for intermolecular vibrations that involve the libration or internal rotation of monomer moieties having appreciable permanent polarizability anisotropies. The vibronic activity of intermolecular vibrations in aromatic-rare gas complexes is analyzed under the assumption that every vibronic band gains its strength from an aromatic-localized transition. It is found that intermolecular vibrational excitations can accompany aromatic-localized vibronic excitations by the usual Franck--Condon mechanism or by a mechanism dependent on the librational amplitude of the aromatic moiety during the course of the pertinent intermolecular vibration. The latter mechanism can impart appreciable intensity to bands that are forbidden by rigid-molecule symmetry selection rules. The applicability of such rules is therefore called into question. Finally, experimental spectra of intermolecular transitions, obtained by mass-selective, ionization-detected stimulated Raman spectroscopies, are reported for benzene--X (X=Ar, --Ar[sub 2], N[sub 2], HCl, CO[sub 2], and --fluorene), fluorobenzene--Ar and --Kr, aniline--Ar, and fluorene--Ar and --Ar[sub 2]. The results support the conclusions of the theoretical analyses and provide further evidence for the value of Raman methods in characterizing intermolecular vibrational level structures.

Maxton, P.M.; Schaeffer, M.W.; Ohline, S.M.; Kim, W.; Venturo, V.A.; Felker, P.M. (Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90024-1569 (United States))

1994-11-15

415

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  

Microsoft Academic Search

Two new dual-metal assemblies: 2[Ru(phen)]{sup 2+}.[Fe(SCN)]².2SCN.4HO 1 and [Ru(phen)]{sup 2+}.[Co(SCN)]²2, (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 sequence supported by - 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

Mohamed Ghazzali; Vratislav Langer; Lars Ohrstroem

2008-01-01

416

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

Microsoft Academic Search

Two new dual-metal assemblies: 2[Ru(phen)3]2+·[Fe(SCN)4]2?·2SCN?·4H2O 1 and [Ru(phen)3]2+·[Co(SCN)4]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 ????? sequence supported by ?–? 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

Mohamed Ghazzali; Vratislav Langer; Lars Öhrström

2008-01-01

417

Bright solitons in quasi-one-dimensional dipolar condensates with spatially modulated interactions  

NASA Astrophysics Data System (ADS)

We introduce a model for the condensate of dipolar atoms or molecules, in which the dipole-dipole interaction (DDI) is periodically modulated in space due to a periodic change of the local orientation of the permanent dipoles, imposed by the corresponding structure of an external field (the necessary field can be created, in particular, by means of magnetic lattices, which are available to the experiment). The system represents a realization of a nonlocal nonlinear lattice, which has a potential to support various spatial modes. By means of numerical methods and variational approximation (VA), we construct bright one-dimensional solitons in this system and study their stability. In most cases, the VA provides good accuracy and correctly predicts the stability by means of the Vakhitov-Kolokolov criterion. It is found that the periodic modulation may destroy some solitons, which exist in the usual setting with unmodulated DDI and can create stable solitons in other cases, not verified in the absence of modulations. Unstable solitons typically transform into persistent localized breathers. The solitons are often mobile, with inelastic collisions between them leading to oscillating localized modes.

Abdullaev, F. Kh.; Gammal, A.; Malomed, B. A.; Tomio, Lauro

2013-06-01

418

Interaction  

NSDL National Science Digital Library

Set values for the initial position, velocity, and mass of the two particles, and click on the button "Initialize Animation" to play the animation using your specified values. Note, if m or v are too large, the particles may actually pass through one another which will seem a little strange. Note: the interaction between the particles is a "non-contact" interaction, much like the electrostatic force on two charges. Mathematically, it is actually a Hooke's law interaction.

Christian, Wolfgang; Belloni, Mario

2008-02-19

419

Origin of spontaneous polarization, tilt, and chiral structure of smectic liquid-crystal phases composed of bent-core molecules: a molecular model.  

PubMed

A simple molecular model is proposed for novel bent-core smectic phases that enables one to explain the origin of the experimentally observed chiral structure of the B2 phase composed of nonchiral banana-shaped molecules. It is shown that in the perfectly ordered smectic phase the distributed dispersion interaction between banana-shaped molecules stabilizes the spontaneous polarization and may be responsible for the tilt of the director. The orientation of the spontaneous polarization with respect to the tilt plane is determined by the balance between the dispersion and electrostatic dipole-dipole intermolecular interactions. In particular, sufficiently strong dipole-dipole interaction promotes the B2 phase where the polarization is normal to the tilt plane. The actual chiral structure of each smectic layer in the B2 phase appears as a result of the symmetry breaking. In the case of small molecular dipoles the nonchiral polar smectic phase is formed where the spontaneous polarization is parallel to the tilt plane. The role of the opening angle and of the axial ratio of banana-shaped molecules is also considered and a phase diagram is presented. PMID:15447506

Emelyanenko, A V; Osipov, M A

2004-08-31

420

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations.  

PubMed

The intermolecular interaction energy components for several molecular complexes were calculated using force fields available in the AMBER suite of programs and compared with Density Functional Theory-Symmetry Adapted Perturbation Theory (DFT-SAPT) values. The extent to which such comparison is meaningful is discussed. The comparability is shown to depend strongly on the intermolecular distance, which means that comparisons made at one distance only are of limited value. At large distances the coulombic and van der Waals 1/r(6) empirical terms correspond fairly well with the DFT-SAPT electrostatics and dispersion terms, respectively. At the onset of electronic overlap the empirical values deviate from the reference values considerably. However, the errors in the force fields tend to cancel out in a systematic manner at equilibrium distances. Thus, the overall performance of the force fields displays errors an order of magnitude smaller than those of the individual interaction energy components. The repulsive 1/r(12) component of the van der Waals expression seems to be responsible for a significant part of the deviation of the force field results from the reference values. We suggest that further improvement of the force fields for intermolecular interactions would require replacement of the nonphysical 1/r(12) term by an exponential function. Dispersion anisotropy and its effects are discussed. Our analysis is intended to show that although c